Starting phenix.real_space_refine on Thu Sep 26 04:19:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/09_2024/7a23_11614.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/09_2024/7a23_11614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/09_2024/7a23_11614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/09_2024/7a23_11614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/09_2024/7a23_11614.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a23_11614/09_2024/7a23_11614.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 2 6.06 5 P 13 5.49 5 S 403 5.16 5 C 37423 2.51 5 N 9681 2.21 5 O 10409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 285 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 57959 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3328 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain: "I" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3754 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 16, 'TRANS': 464} Chain: "J" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 800 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain breaks: 1 Chain: "N" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1201 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain breaks: 1 Chain: "H" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2493 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 16, 'TRANS': 301} Chain: "K" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 667 Classifications: {'peptide': 85} Link IDs: {'TRANS': 84} Chain: "Y" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "Z" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1103 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 12, 'TRANS': 127} Chain: "V" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 461 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "W" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "S" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 821 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "i" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 514 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "j" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 582 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "G" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3049 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 18, 'TRANS': 363} Chain: "C" Number of atoms: 5288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5288 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 37, 'TRANS': 655} Chain: "T" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2535 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 21, 'TRANS': 306} Chain: "F" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1518 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1702 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 17, 'TRANS': 201} Chain: "O" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 874 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "P" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Chain: "R" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1039 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 10, 'TRANS': 118} Chain: "U" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1011 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "E" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1215 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 10, 'TRANS': 142} Chain: "D" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1438 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain: "X" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 843 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 1 Chain: "c" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 744 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "Q" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 722 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 6, 'TRANS': 85} Chain: "k" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 614 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "r" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "n" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 205 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "o" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1568 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain: "q" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1736 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "p" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1705 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "M" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3825 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "f" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 640 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "g" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 386 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "d" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 329 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'TRANS': 65} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 168 Chain: "a" Number of atoms: 4677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4677 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 20, 'TRANS': 579} Chain breaks: 3 Chain: "b" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 519 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "h" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 232 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "e" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 417 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "l" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 112 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 21} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "s" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "m" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 605 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 64} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "t" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 232 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 252 Unusual residues: {'CDL': 2, 'T7X': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "J" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 87 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "H" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'PEV': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' ZN': 1, 'BCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2707 SG CYS A 405 45.079 97.093 240.749 1.00 18.90 S ATOM 2727 SG CYS A 408 42.608 101.026 243.200 1.00 17.31 S ATOM 2688 SG CYS A 402 48.320 98.123 247.044 1.00 21.30 S ATOM 3052 SG CYS A 448 42.364 95.010 246.590 1.00 20.05 S ATOM 20796 SG CYS C 179 57.081 103.179 225.404 1.00 15.05 S ATOM 20735 SG CYS C 170 54.532 109.490 223.855 1.00 22.03 S ATOM 20756 SG CYS C 173 60.676 107.948 226.496 1.00 22.61 S ATOM 21124 SG CYS C 221 56.904 98.536 235.001 1.00 19.30 S ATOM 21101 SG CYS C 218 57.727 104.690 237.124 1.00 13.72 S ATOM 21148 SG CYS C 224 62.406 100.396 238.076 1.00 14.17 S ATOM 21469 SG CYS C 268 61.798 101.834 232.693 1.00 19.62 S ATOM 20251 SG CYS C 106 53.322 93.992 235.260 1.00 16.72 S ATOM 20335 SG CYS C 117 50.387 95.350 233.794 1.00 18.39 S ATOM 20462 SG CYS C 134 51.121 89.114 235.186 1.00 21.47 S ATOM 29959 SG CYS B 130 37.106 110.377 259.265 1.00 36.50 S ATOM 29990 SG CYS B 135 34.466 111.783 261.022 1.00 40.45 S ATOM 30263 SG CYS B 171 36.572 104.382 258.800 1.00 39.22 S ATOM 30287 SG CYS B 175 33.510 105.250 260.474 1.00 41.46 S ATOM 32009 SG CYS P 72 56.166 125.098 229.527 1.00 28.54 S ATOM 32195 SG CYS P 97 58.359 122.238 229.043 1.00 25.54 S ATOM 35074 SG CYS E 158 62.501 114.846 191.300 1.00 22.55 S ATOM 34574 SG CYS E 94 59.303 121.008 189.343 1.00 17.23 S ATOM 34568 SG CYS E 93 57.003 116.664 187.958 1.00 18.81 S ATOM 35304 SG CYS E 188 58.741 118.270 194.603 1.00 26.47 S ATOM 36539 SG CYS D 165 56.736 115.922 202.178 1.00 19.17 S ATOM 36513 SG CYS D 162 62.502 119.464 201.359 1.00 11.81 S ATOM 36560 SG CYS D 168 59.292 119.439 206.811 1.00 21.11 S ATOM 36281 SG CYS D 133 62.639 114.173 204.136 1.00 27.13 S ATOM 36589 SG CYS D 172 57.719 120.105 215.427 1.00 21.71 S ATOM 36254 SG CYS D 129 62.245 116.588 211.673 1.00 38.74 S ATOM 36212 SG CYS D 123 64.681 120.078 216.118 1.00 25.74 S ATOM 36231 SG CYS D 126 60.390 114.809 217.361 1.00 18.74 S Time building chain proxies: 25.88, per 1000 atoms: 0.45 Number of scatterers: 57959 At special positions: 0 Unit cell: (129.87, 197.58, 297.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 28 26.01 S 403 16.00 P 13 15.00 O 10409 8.00 N 9681 7.00 C 37423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS I 336 " - pdb=" SG CYS I 420 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 29 " - pdb=" SG CYS Y 59 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 39 " - pdb=" SG CYS Y 49 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 81 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS j 14 " - pdb=" SG CYS j 44 " distance=2.03 Simple disulfide: pdb=" SG CYS j 24 " - pdb=" SG CYS j 34 " distance=2.03 Simple disulfide: pdb=" SG CYS j 28 " - pdb=" SG CYS j 34 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 53 " distance=2.05 Simple disulfide: pdb=" SG CYS f 58 " - pdb=" SG CYS f 70 " distance=2.04 Simple disulfide: pdb=" SG CYS b 40 " - pdb=" SG CYS b 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.30 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 135 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 175 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 130 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 171 " pdb=" FES C 803 " pdb="FE2 FES C 803 " - pdb=" SG CYS C 134 " pdb="FE1 FES C 803 " - pdb=" SG CYS C 117 " pdb="FE1 FES C 803 " - pdb=" SG CYS C 106 " pdb="FE2 FES C 803 " - pdb=" SG CYS C 120 " pdb=" SF4 A 501 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 405 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 402 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 448 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 408 " pdb=" SF4 C 801 " pdb="FE3 SF4 C 801 " - pdb=" NE2 HIS C 166 " pdb="FE1 SF4 C 801 " - pdb=" SG CYS C 179 " pdb="FE2 SF4 C 801 " - pdb=" SG CYS C 170 " pdb="FE4 SF4 C 801 " - pdb=" SG CYS C 173 " pdb=" SF4 C 802 " pdb="FE3 SF4 C 802 " - pdb=" SG CYS C 224 " pdb="FE4 SF4 C 802 " - pdb=" SG CYS C 268 " pdb="FE1 SF4 C 802 " - pdb=" SG CYS C 221 " pdb="FE2 SF4 C 802 " - pdb=" SG CYS C 218 " pdb=" SF4 D 301 " pdb="FE4 SF4 D 301 " - pdb=" SG CYS D 133 " pdb="FE3 SF4 D 301 " - pdb=" SG CYS D 168 " pdb="FE2 SF4 D 301 " - pdb=" SG CYS D 162 " pdb="FE1 SF4 D 301 " - pdb=" SG CYS D 165 " pdb=" SF4 D 302 " pdb="FE4 SF4 D 302 " - pdb=" SG CYS D 126 " pdb="FE2 SF4 D 302 " - pdb=" SG CYS D 129 " pdb="FE3 SF4 D 302 " - pdb=" SG CYS D 123 " pdb="FE1 SF4 D 302 " - pdb=" SG CYS D 172 " pdb=" SF4 E 301 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 158 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS E 188 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS E 93 " pdb="FE2 SF4 E 301 " - pdb=" SG CYS E 94 " pdb="FE3 SF4 E 301 " - pdb=" NE2 HIS G 154 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN P 201 " pdb="ZN ZN P 201 " - pdb=" NE2 HIS P 82 " pdb="ZN ZN P 201 " - pdb=" SG CYS P 72 " pdb="ZN ZN P 201 " - pdb=" SG CYS P 97 " pdb=" ZN q 801 " pdb="ZN ZN q 801 " - pdb=" NE2 HIS q 107 " pdb="ZN ZN q 801 " - pdb=" NE2 HIS p 130 " 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13646 Finding SS restraints... Secondary structure from input PDB file: 293 helices and 47 sheets defined 52.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.690A pdb=" N ILE A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.609A pdb=" N MET A 125 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.836A pdb=" N ARG A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 185 through 202 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.673A pdb=" N GLY A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 231 through 241 removed outlier: 3.838A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 268 through 280 Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 405 through 423 removed outlier: 4.269A pdb=" N GLY A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 444 removed outlier: 4.473A pdb=" N GLY A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 480 Proline residue: A 457 - end of helix Proline residue: A 467 - end of helix Processing helix chain 'I' and resid 19 through 41 Processing helix chain 'I' and resid 59 through 72 removed outlier: 3.734A pdb=" N GLY I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 78 removed outlier: 3.738A pdb=" N THR I 77 " --> pdb=" O PRO I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 117 removed outlier: 3.518A pdb=" N CYS I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASP I 113 " --> pdb=" O SER I 109 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE I 114 " --> pdb=" O MET I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 141 removed outlier: 3.608A pdb=" N VAL I 127 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 164 Processing helix chain 'I' and resid 169 through 202 removed outlier: 3.840A pdb=" N THR I 173 " --> pdb=" O SER I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 213 removed outlier: 3.969A pdb=" N LYS I 211 " --> pdb=" O ASP I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 241 Processing helix chain 'I' and resid 243 through 247 Processing helix chain 'I' and resid 249 through 257 Processing helix chain 'I' and resid 258 through 283 removed outlier: 3.722A pdb=" N ILE I 267 " --> pdb=" O ALA I 263 " (cutoff:3.500A) Proline residue: I 269 - end of helix Processing helix chain 'I' and resid 290 through 312 removed outlier: 4.008A pdb=" N PHE I 294 " --> pdb=" O LEU I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 335 removed outlier: 4.568A pdb=" N GLY I 333 " --> pdb=" O TYR I 329 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE I 334 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 366 removed outlier: 3.642A pdb=" N MET I 355 " --> pdb=" O ILE I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 378 Processing helix chain 'I' and resid 384 through 400 Processing helix chain 'I' and resid 404 through 420 removed outlier: 3.757A pdb=" N CYS I 408 " --> pdb=" O LEU I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 422 through 449 Processing helix chain 'I' and resid 462 through 478 Processing helix chain 'I' and resid 483 through 497 Processing helix chain 'J' and resid 4 through 29 removed outlier: 4.512A pdb=" N ILE J 8 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL J 13 " --> pdb=" O PHE J 9 " (cutoff:3.500A) Proline residue: J 26 - end of helix removed outlier: 3.604A pdb=" N PHE J 29 " --> pdb=" O VAL J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 84 removed outlier: 3.645A pdb=" N SER J 65 " --> pdb=" O PHE J 61 " (cutoff:3.500A) Proline residue: J 80 - end of helix Processing helix chain 'J' and resid 91 through 114 Processing helix chain 'N' and resid 4 through 6 No H-bonds generated for 'chain 'N' and resid 4 through 6' Processing helix chain 'N' and resid 7 through 18 removed outlier: 3.843A pdb=" N VAL N 18 " --> pdb=" O GLY N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 44 Processing helix chain 'N' and resid 46 through 59 Processing helix chain 'N' and resid 60 through 71 Processing helix chain 'N' and resid 135 through 145 removed outlier: 4.828A pdb=" N LEU N 143 " --> pdb=" O THR N 139 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR N 145 " --> pdb=" O GLY N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 171 Proline residue: N 155 - end of helix Processing helix chain 'H' and resid 9 through 35 Proline residue: H 15 - end of helix removed outlier: 3.840A pdb=" N LEU H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN H 35 " --> pdb=" O MET H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 76 through 88 Processing helix chain 'H' and resid 105 through 127 removed outlier: 4.079A pdb=" N TYR H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 162 removed outlier: 3.765A pdb=" N GLU H 148 " --> pdb=" O MET H 144 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER H 150 " --> pdb=" O SER H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 173 Processing helix chain 'H' and resid 183 through 198 removed outlier: 3.654A pdb=" N ALA H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 214 removed outlier: 4.236A pdb=" N VAL H 213 " --> pdb=" O GLU H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 241 Processing helix chain 'H' and resid 264 through 286 removed outlier: 3.525A pdb=" N TRP H 268 " --> pdb=" O PRO H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 300 removed outlier: 3.557A pdb=" N TRP H 300 " --> pdb=" O MET H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 321 removed outlier: 3.833A pdb=" N TRP H 310 " --> pdb=" O LEU H 306 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 318 " --> pdb=" O VAL H 314 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE H 321 " --> pdb=" O LEU H 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 24 removed outlier: 4.097A pdb=" N SER K 10 " --> pdb=" O TYR K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 42 removed outlier: 3.579A pdb=" N MET K 31 " --> pdb=" O ASN K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 54 Processing helix chain 'K' and resid 56 through 84 removed outlier: 4.347A pdb=" N ALA K 71 " --> pdb=" O THR K 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 21 Processing helix chain 'Y' and resid 21 through 28 Processing helix chain 'Y' and resid 29 through 43 Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing helix chain 'Y' and resid 49 through 68 Processing helix chain 'Y' and resid 73 through 85 removed outlier: 3.935A pdb=" N VAL Y 79 " --> pdb=" O MET Y 75 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Y' and resid 92 through 103 removed outlier: 3.649A pdb=" N GLN Y 96 " --> pdb=" O CYS Y 92 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N CYS Y 103 " --> pdb=" O PHE Y 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 112 removed outlier: 3.660A pdb=" N TYR Z 62 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) Proline residue: Z 87 - end of helix removed outlier: 3.557A pdb=" N ASP Z 110 " --> pdb=" O GLU Z 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 29 Proline residue: V 11 - end of helix removed outlier: 4.190A pdb=" N MET V 18 " --> pdb=" O ILE V 14 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU V 19 " --> pdb=" O ILE V 15 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE V 21 " --> pdb=" O GLY V 17 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN V 26 " --> pdb=" O MET V 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR V 27 " --> pdb=" O GLY V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 34 Processing helix chain 'V' and resid 43 through 57 Processing helix chain 'W' and resid 5 through 14 Processing helix chain 'W' and resid 14 through 19 Processing helix chain 'W' and resid 24 through 29 Processing helix chain 'W' and resid 29 through 38 removed outlier: 4.426A pdb=" N ARG W 35 " --> pdb=" O PRO W 31 " (cutoff:3.500A) Proline residue: W 36 - end of helix Processing helix chain 'S' and resid 63 through 67 removed outlier: 3.591A pdb=" N VAL S 67 " --> pdb=" O PRO S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 101 Processing helix chain 'i' and resid 8 through 25 Processing helix chain 'i' and resid 31 through 35 Processing helix chain 'i' and resid 36 through 67 Processing helix chain 'i' and resid 68 through 72 removed outlier: 4.117A pdb=" N ASN i 71 " --> pdb=" O ARG i 68 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 28 Processing helix chain 'j' and resid 34 through 47 removed outlier: 3.526A pdb=" N ARG j 38 " --> pdb=" O CYS j 34 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 70 Processing helix chain 'G' and resid 50 through 55 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'G' and resid 63 through 69 removed outlier: 4.087A pdb=" N PHE G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 84 removed outlier: 4.368A pdb=" N GLN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 120 removed outlier: 3.509A pdb=" N LEU G 116 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 126 Processing helix chain 'G' and resid 127 through 149 removed outlier: 4.484A pdb=" N PHE G 131 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU G 132 " --> pdb=" O LEU G 128 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 147 " --> pdb=" O GLU G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 180 removed outlier: 3.504A pdb=" N ASP G 174 " --> pdb=" O GLY G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 192 removed outlier: 3.897A pdb=" N ARG G 185 " --> pdb=" O GLN G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 204 Processing helix chain 'G' and resid 210 through 217 Processing helix chain 'G' and resid 240 through 244 Processing helix chain 'G' and resid 256 through 281 removed outlier: 4.115A pdb=" N ARG G 269 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU G 272 " --> pdb=" O MET G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 305 Processing helix chain 'G' and resid 305 through 317 Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.523A pdb=" N GLY G 365 " --> pdb=" O ALA G 361 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP G 367 " --> pdb=" O LEU G 363 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE G 368 " --> pdb=" O GLN G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 376 No H-bonds generated for 'chain 'G' and resid 374 through 376' Processing helix chain 'G' and resid 377 through 385 removed outlier: 3.520A pdb=" N ILE G 382 " --> pdb=" O VAL G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 392 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 148 through 163 Processing helix chain 'C' and resid 179 through 186 Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.614A pdb=" N SER C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.589A pdb=" N GLY C 245 " --> pdb=" O ARG C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 329 through 334 removed outlier: 3.708A pdb=" N PHE C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 360 through 374 Processing helix chain 'C' and resid 376 through 378 No H-bonds generated for 'chain 'C' and resid 376 through 378' Processing helix chain 'C' and resid 389 through 403 Processing helix chain 'C' and resid 421 through 426 removed outlier: 3.526A pdb=" N TYR C 425 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 426 " --> pdb=" O TYR C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 437 Processing helix chain 'C' and resid 451 through 464 Processing helix chain 'C' and resid 489 through 497 Processing helix chain 'C' and resid 502 through 509 Processing helix chain 'C' and resid 517 through 522 removed outlier: 3.878A pdb=" N ASN C 522 " --> pdb=" O GLY C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 541 Processing helix chain 'C' and resid 556 through 565 removed outlier: 4.020A pdb=" N ALA C 560 " --> pdb=" O TYR C 556 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 614 removed outlier: 3.669A pdb=" N ARG C 613 " --> pdb=" O LYS C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 664 Processing helix chain 'C' and resid 672 through 684 Processing helix chain 'C' and resid 685 through 688 Processing helix chain 'C' and resid 699 through 703 removed outlier: 3.995A pdb=" N LEU C 702 " --> pdb=" O GLY C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 731 Processing helix chain 'T' and resid 78 through 91 removed outlier: 4.166A pdb=" N TYR T 83 " --> pdb=" O PHE T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 110 removed outlier: 4.300A pdb=" N HIS T 108 " --> pdb=" O SER T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 130 through 135 Processing helix chain 'T' and resid 156 through 161 Processing helix chain 'T' and resid 163 through 174 removed outlier: 3.506A pdb=" N HIS T 174 " --> pdb=" O VAL T 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 194 through 211 Processing helix chain 'T' and resid 248 through 250 No H-bonds generated for 'chain 'T' and resid 248 through 250' Processing helix chain 'T' and resid 258 through 271 removed outlier: 3.774A pdb=" N LEU T 269 " --> pdb=" O ILE T 265 " (cutoff:3.500A) Processing helix chain 'T' and resid 290 through 301 removed outlier: 3.579A pdb=" N ASP T 299 " --> pdb=" O GLU T 295 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 319 Processing helix chain 'T' and resid 340 through 349 removed outlier: 4.243A pdb=" N THR T 349 " --> pdb=" O ASN T 345 " (cutoff:3.500A) Processing helix chain 'T' and resid 359 through 364 Processing helix chain 'T' and resid 372 through 382 removed outlier: 5.758A pdb=" N PHE T 377 " --> pdb=" O PRO T 374 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN T 380 " --> pdb=" O PHE T 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 8 No H-bonds generated for 'chain 'F' and resid 8 through 8' Processing helix chain 'F' and resid 9 through 14 Processing helix chain 'F' and resid 37 through 44 Processing helix chain 'F' and resid 107 through 119 removed outlier: 3.881A pdb=" N TRP F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 64 removed outlier: 3.890A pdb=" N TYR B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 72 through 84 Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.843A pdb=" N VAL B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'O' and resid 46 through 50 Processing helix chain 'O' and resid 110 through 121 Processing helix chain 'O' and resid 139 through 143 removed outlier: 3.581A pdb=" N ASP O 142 " --> pdb=" O SER O 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 45 removed outlier: 4.163A pdb=" N TRP P 44 " --> pdb=" O HIS P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 59 Processing helix chain 'R' and resid 28 through 44 Processing helix chain 'R' and resid 45 through 47 No H-bonds generated for 'chain 'R' and resid 45 through 47' Processing helix chain 'R' and resid 51 through 71 Processing helix chain 'R' and resid 73 through 81 Processing helix chain 'R' and resid 85 through 104 Processing helix chain 'U' and resid 38 through 45 Processing helix chain 'U' and resid 104 through 109 Processing helix chain 'E' and resid 66 through 83 Processing helix chain 'E' and resid 93 through 102 Processing helix chain 'E' and resid 135 through 144 Processing helix chain 'E' and resid 156 through 161 Processing helix chain 'E' and resid 162 through 166 removed outlier: 3.688A pdb=" N TYR E 165 " --> pdb=" O GLY E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 191 through 208 removed outlier: 3.595A pdb=" N LYS E 204 " --> pdb=" O LEU E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 216 Processing helix chain 'D' and resid 46 through 56 Processing helix chain 'D' and resid 62 through 72 Processing helix chain 'D' and resid 74 through 89 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 127 through 133 Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 189 through 193 removed outlier: 3.586A pdb=" N LEU D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 189 through 193' Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 203 through 219 removed outlier: 3.750A pdb=" N TRP D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR D 209 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU D 210 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU D 213 " --> pdb=" O THR D 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 44 removed outlier: 3.568A pdb=" N ALA X 22 " --> pdb=" O ASN X 18 " (cutoff:3.500A) Proline residue: X 38 - end of helix Processing helix chain 'X' and resid 51 through 66 Processing helix chain 'X' and resid 71 through 91 Processing helix chain 'X' and resid 98 through 103 Processing helix chain 'X' and resid 123 through 128 Processing helix chain 'c' and resid 32 through 50 removed outlier: 3.597A pdb=" N THR c 41 " --> pdb=" O PHE c 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL c 47 " --> pdb=" O ILE c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 51 through 54 removed outlier: 3.941A pdb=" N LYS c 54 " --> pdb=" O SER c 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 51 through 54' Processing helix chain 'c' and resid 58 through 86 Processing helix chain 'c' and resid 94 through 100 Processing helix chain 'Q' and resid 25 through 43 removed outlier: 5.354A pdb=" N LYS Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP Q 38 " --> pdb=" O LYS Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 92 Processing helix chain 'k' and resid 46 through 56 Processing helix chain 'k' and resid 78 through 93 Processing helix chain 'k' and resid 98 through 103 Processing helix chain 'k' and resid 107 through 117 removed outlier: 3.975A pdb=" N ASN k 117 " --> pdb=" O GLU k 113 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 101 Processing helix chain 'o' and resid 206 through 229 Proline residue: o 214 - end of helix Processing helix chain 'o' and resid 236 through 247 removed outlier: 3.681A pdb=" N GLU o 240 " --> pdb=" O THR o 236 " (cutoff:3.500A) Processing helix chain 'q' and resid 11 through 23 Processing helix chain 'q' and resid 24 through 28 Processing helix chain 'q' and resid 193 through 212 removed outlier: 4.075A pdb=" N ILE q 197 " --> pdb=" O THR q 193 " (cutoff:3.500A) Processing helix chain 'q' and resid 213 through 214 No H-bonds generated for 'chain 'q' and resid 213 through 214' Processing helix chain 'q' and resid 215 through 219 Processing helix chain 'q' and resid 220 through 228 Processing helix chain 'q' and resid 229 through 232 Processing helix chain 'p' and resid 7 through 27 Processing helix chain 'p' and resid 193 through 213 removed outlier: 3.594A pdb=" N ALA p 204 " --> pdb=" O ILE p 200 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR p 205 " --> pdb=" O SER p 201 " (cutoff:3.500A) Processing helix chain 'p' and resid 220 through 229 Processing helix chain 'M' and resid 17 through 27 Processing helix chain 'M' and resid 34 through 58 Processing helix chain 'M' and resid 76 through 80 removed outlier: 4.485A pdb=" N ILE M 80 " --> pdb=" O TYR M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 107 removed outlier: 3.966A pdb=" N PHE M 92 " --> pdb=" O GLY M 88 " (cutoff:3.500A) Proline residue: M 102 - end of helix Processing helix chain 'M' and resid 117 through 124 Processing helix chain 'M' and resid 128 through 136 Processing helix chain 'M' and resid 138 through 149 Proline residue: M 146 - end of helix Processing helix chain 'M' and resid 149 through 160 removed outlier: 4.184A pdb=" N TRP M 160 " --> pdb=" O ILE M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 195 removed outlier: 3.742A pdb=" N THR M 195 " --> pdb=" O ILE M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 206 Processing helix chain 'M' and resid 209 through 228 removed outlier: 3.564A pdb=" N ILE M 214 " --> pdb=" O GLU M 210 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE M 215 " --> pdb=" O ARG M 211 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER M 223 " --> pdb=" O ALA M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 243 removed outlier: 3.712A pdb=" N GLU M 239 " --> pdb=" O ILE M 235 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU M 243 " --> pdb=" O GLU M 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 245 through 268 removed outlier: 3.617A pdb=" N VAL M 250 " --> pdb=" O THR M 246 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU M 257 " --> pdb=" O ALA M 253 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYS M 258 " --> pdb=" O GLY M 254 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY M 260 " --> pdb=" O LEU M 256 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR M 261 " --> pdb=" O LEU M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 298 Proline residue: M 281 - end of helix removed outlier: 4.456A pdb=" N THR M 298 " --> pdb=" O THR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 303 through 324 removed outlier: 3.579A pdb=" N PHE M 324 " --> pdb=" O THR M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 327 through 360 removed outlier: 4.116A pdb=" N SER M 346 " --> pdb=" O GLY M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 369 through 374 Processing helix chain 'M' and resid 374 through 389 removed outlier: 4.429A pdb=" N ALA M 387 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 394 through 406 removed outlier: 3.550A pdb=" N ILE M 398 " --> pdb=" O THR M 394 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 438 removed outlier: 4.381A pdb=" N LEU M 420 " --> pdb=" O THR M 416 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY M 425 " --> pdb=" O GLY M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 473 Proline residue: M 462 - end of helix Processing helix chain 'M' and resid 474 through 479 Processing helix chain 'M' and resid 481 through 492 Processing helix chain 'f' and resid 26 through 63 removed outlier: 3.772A pdb=" N ARG f 39 " --> pdb=" O GLU f 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 79 Processing helix chain 'g' and resid 67 through 79 Processing helix chain 'g' and resid 88 through 103 removed outlier: 3.775A pdb=" N GLN g 95 " --> pdb=" O THR g 91 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU g 98 " --> pdb=" O HIS g 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 21 Processing helix chain 'd' and resid 23 through 33 Processing helix chain 'd' and resid 38 through 55 Processing helix chain 'd' and resid 60 through 77 removed outlier: 3.585A pdb=" N LYS d 77 " --> pdb=" O ALA d 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 23 removed outlier: 4.112A pdb=" N PHE a 18 " --> pdb=" O SER a 14 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY a 20 " --> pdb=" O ALA a 16 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG a 21 " --> pdb=" O GLY a 17 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE a 22 " --> pdb=" O PHE a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 49 Processing helix chain 'a' and resid 50 through 54 Processing helix chain 'a' and resid 81 through 104 Processing helix chain 'a' and resid 109 through 129 Processing helix chain 'a' and resid 132 through 152 removed outlier: 3.603A pdb=" N HIS a 152 " --> pdb=" O TYR a 148 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 189 removed outlier: 4.803A pdb=" N LYS a 166 " --> pdb=" O LYS a 162 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL a 170 " --> pdb=" O LYS a 166 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN a 171 " --> pdb=" O ALA a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 196 through 203 removed outlier: 4.032A pdb=" N VAL a 203 " --> pdb=" O ALA a 199 " (cutoff:3.500A) Processing helix chain 'a' and resid 216 through 232 removed outlier: 3.627A pdb=" N LEU a 220 " --> pdb=" O ASN a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 249 through 259 Processing helix chain 'a' and resid 262 through 272 removed outlier: 3.554A pdb=" N MET a 268 " --> pdb=" O ALA a 264 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE a 269 " --> pdb=" O GLY a 265 " (cutoff:3.500A) Processing helix chain 'a' and resid 272 through 278 Processing helix chain 'a' and resid 279 through 301 Processing helix chain 'a' and resid 309 through 328 removed outlier: 5.092A pdb=" N SER a 317 " --> pdb=" O TYR a 313 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET a 322 " --> pdb=" O GLN a 318 " (cutoff:3.500A) Processing helix chain 'a' and resid 330 through 362 Processing helix chain 'a' and resid 381 through 390 Processing helix chain 'a' and resid 401 through 416 removed outlier: 3.688A pdb=" N THR a 410 " --> pdb=" O GLU a 406 " (cutoff:3.500A) Processing helix chain 'a' and resid 426 through 439 Processing helix chain 'a' and resid 460 through 474 Proline residue: a 466 - end of helix Processing helix chain 'a' and resid 495 through 500 removed outlier: 4.155A pdb=" N VAL a 499 " --> pdb=" O ASN a 495 " (cutoff:3.500A) Processing helix chain 'a' and resid 515 through 518 Processing helix chain 'a' and resid 519 through 531 removed outlier: 4.063A pdb=" N LEU a 523 " --> pdb=" O LEU a 519 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE a 524 " --> pdb=" O ILE a 520 " (cutoff:3.500A) Processing helix chain 'a' and resid 532 through 534 No H-bonds generated for 'chain 'a' and resid 532 through 534' Processing helix chain 'a' and resid 555 through 560 removed outlier: 3.893A pdb=" N ASN a 560 " --> pdb=" O TYR a 556 " (cutoff:3.500A) Processing helix chain 'a' and resid 567 through 615 Proline residue: a 599 - end of helix Processing helix chain 'a' and resid 616 through 618 No H-bonds generated for 'chain 'a' and resid 616 through 618' Processing helix chain 'a' and resid 619 through 637 removed outlier: 5.247A pdb=" N ALA a 625 " --> pdb=" O VAL a 621 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE a 626 " --> pdb=" O TYR a 622 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA a 627 " --> pdb=" O HIS a 623 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 25 removed outlier: 4.196A pdb=" N LEU b 24 " --> pdb=" O LYS b 21 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 44 removed outlier: 4.238A pdb=" N LEU b 37 " --> pdb=" O LEU b 33 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN b 38 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU b 44 " --> pdb=" O CYS b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 52 through 74 Processing helix chain 'h' and resid 21 through 29 removed outlier: 3.757A pdb=" N THR h 27 " --> pdb=" O TRP h 23 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS h 29 " --> pdb=" O THR h 25 " (cutoff:3.500A) Processing helix chain 'h' and resid 32 through 46 Processing helix chain 'e' and resid 46 through 59 Processing helix chain 'e' and resid 82 through 97 removed outlier: 4.703A pdb=" N GLU e 95 " --> pdb=" O MET e 91 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU e 96 " --> pdb=" O ALA e 92 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 109 removed outlier: 3.814A pdb=" N ILE e 109 " --> pdb=" O ALA e 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 122 Processing helix chain 'l' and resid 39 through 60 Proline residue: l 45 - end of helix removed outlier: 3.748A pdb=" N ASP l 60 " --> pdb=" O PHE l 56 " (cutoff:3.500A) Processing helix chain 's' and resid 7 through 25 Processing helix chain 'm' and resid 20 through 36 removed outlier: 3.602A pdb=" N LYS m 25 " --> pdb=" O GLU m 21 " (cutoff:3.500A) Processing helix chain 'm' and resid 53 through 61 removed outlier: 4.059A pdb=" N HIS m 59 " --> pdb=" O THR m 55 " (cutoff:3.500A) Processing helix chain 't' and resid 21 through 26 Processing helix chain 't' and resid 26 through 32 removed outlier: 4.492A pdb=" N LEU t 32 " --> pdb=" O MET t 28 " (cutoff:3.500A) Processing helix chain 't' and resid 34 through 50 Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 222 removed outlier: 5.862A pdb=" N ALA A 177 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N HIS A 221 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE A 179 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 136 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR A 180 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 138 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 341 removed outlier: 6.870A pdb=" N MET A 380 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 340 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 378 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 85 through 89 removed outlier: 5.822A pdb=" N GLU F 23 " --> pdb=" O ILE R 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 117 through 119 Processing sheet with id=AA5, first strand: chain 'G' and resid 12 through 13 removed outlier: 5.886A pdb=" N ASN G 33 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 325 through 332 removed outlier: 3.570A pdb=" N THR G 327 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR G 329 " --> pdb=" O VAL G 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 65 removed outlier: 7.416A pdb=" N ARG C 64 " --> pdb=" O LEU O 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 81 through 85 removed outlier: 8.598A pdb=" N ILE C 144 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE C 77 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 211 through 213 Processing sheet with id=AB1, first strand: chain 'C' and resid 238 through 240 Processing sheet with id=AB2, first strand: chain 'C' and resid 288 through 290 removed outlier: 3.600A pdb=" N THR C 290 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG C 308 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 341 through 343 removed outlier: 6.117A pdb=" N GLN U 151 " --> pdb=" O ARG C 341 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AB5, first strand: chain 'C' and resid 380 through 381 removed outlier: 3.648A pdb=" N VAL C 381 " --> pdb=" O PHE C 580 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 484 through 486 removed outlier: 6.944A pdb=" N LEU C 485 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR C 471 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE C 440 " --> pdb=" O GLY C 470 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL C 472 " --> pdb=" O PHE C 440 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU C 442 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU C 439 " --> pdb=" O ALA C 513 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE C 515 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU C 441 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN C 551 " --> pdb=" O PRO C 512 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE C 514 " --> pdb=" O ASN C 551 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 601 through 602 Processing sheet with id=AB8, first strand: chain 'T' and resid 98 through 99 Processing sheet with id=AB9, first strand: chain 'T' and resid 140 through 143 removed outlier: 6.286A pdb=" N VAL T 141 " --> pdb=" O ILE T 181 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL T 183 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN T 143 " --> pdb=" O VAL T 183 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N MET T 217 " --> pdb=" O TYR T 180 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN T 182 " --> pdb=" O MET T 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'T' and resid 222 through 223 Processing sheet with id=AC2, first strand: chain 'T' and resid 242 through 246 removed outlier: 6.402A pdb=" N LEU T 243 " --> pdb=" O VAL T 308 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU T 310 " --> pdb=" O LEU T 243 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU T 245 " --> pdb=" O LEU T 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'T' and resid 252 through 253 Processing sheet with id=AC4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.799A pdb=" N ASN F 29 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN F 89 " --> pdb=" O ASN F 29 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE F 31 " --> pdb=" O GLN F 89 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL F 55 " --> pdb=" O LEU F 78 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.799A pdb=" N ASN F 29 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN F 89 " --> pdb=" O ASN F 29 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE F 31 " --> pdb=" O GLN F 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.987A pdb=" N ILE F 98 " --> pdb=" O ILE F 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 166 through 169 removed outlier: 6.437A pdb=" N LEU B 127 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET B 169 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL B 129 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS B 130 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N MET B 180 " --> pdb=" O CYS B 130 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR B 197 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 54 through 57 Processing sheet with id=AC9, first strand: chain 'O' and resid 83 through 85 removed outlier: 3.524A pdb=" N TRP O 84 " --> pdb=" O SER O 93 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 63 through 64 Processing sheet with id=AD2, first strand: chain 'P' and resid 69 through 70 Processing sheet with id=AD3, first strand: chain 'U' and resid 50 through 54 removed outlier: 4.328A pdb=" N TYR U 61 " --> pdb=" O VAL U 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 126 through 128 removed outlier: 6.443A pdb=" N VAL E 127 " --> pdb=" O MET E 155 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER E 154 " --> pdb=" O VAL E 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 110 through 113 Processing sheet with id=AD6, first strand: chain 'D' and resid 138 through 144 removed outlier: 6.251A pdb=" N THR D 139 " --> pdb=" O TYR D 155 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR D 155 " --> pdb=" O THR D 139 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU D 141 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG D 151 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 48 through 50 Processing sheet with id=AD8, first strand: chain 'o' and resid 58 through 59 removed outlier: 6.187A pdb=" N VAL o 79 " --> pdb=" O LEU o 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'o' and resid 73 through 74 Processing sheet with id=AE1, first strand: chain 'o' and resid 84 through 86 removed outlier: 6.491A pdb=" N THR o 106 " --> pdb=" O ILE o 135 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'o' and resid 118 through 120 Processing sheet with id=AE3, first strand: chain 'o' and resid 140 through 141 removed outlier: 6.413A pdb=" N THR o 140 " --> pdb=" O ILE o 158 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE o 157 " --> pdb=" O LEU o 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'o' and resid 192 through 193 Processing sheet with id=AE5, first strand: chain 'q' and resid 92 through 94 removed outlier: 6.389A pdb=" N SER q 93 " --> pdb=" O ILE q 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'q' and resid 133 through 134 removed outlier: 6.372A pdb=" N VAL q 133 " --> pdb=" O LEU q 151 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR q 150 " --> pdb=" O VAL q 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'q' and resid 179 through 182 removed outlier: 6.705A pdb=" N VAL q 180 " --> pdb=" O LEU q 189 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG q 187 " --> pdb=" O GLY q 182 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'p' and resid 53 through 55 removed outlier: 7.118A pdb=" N ASP p 70 " --> pdb=" O VAL p 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'p' and resid 127 through 128 removed outlier: 6.689A pdb=" N THR p 127 " --> pdb=" O ILE p 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'p' and resid 156 through 157 Processing sheet with id=AF2, first strand: chain 'p' and resid 179 through 181 removed outlier: 6.907A pdb=" N VAL p 180 " --> pdb=" O LEU p 189 " (cutoff:3.500A) 2635 hydrogen bonds defined for protein. 7659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.48 Time building geometry restraints manager: 14.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 23475 1.39 - 1.61: 35157 1.61 - 1.84: 601 1.84 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 59313 Sorted by residual: bond pdb=" C8 U10 H 501 " pdb=" C9 U10 H 501 " ideal model delta sigma weight residual 1.470 1.316 0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" C13 U10 H 501 " pdb=" C14 U10 H 501 " ideal model delta sigma weight residual 1.470 1.327 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" C23 U10 H 501 " pdb=" C24 U10 H 501 " ideal model delta sigma weight residual 1.470 1.328 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C18 U10 H 501 " pdb=" C19 U10 H 501 " ideal model delta sigma weight residual 1.470 1.329 0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C33 U10 H 501 " pdb=" C34 U10 H 501 " ideal model delta sigma weight residual 1.470 1.331 0.139 2.00e-02 2.50e+03 4.86e+01 ... (remaining 59308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 79925 4.85 - 9.70: 388 9.70 - 14.55: 29 14.55 - 19.39: 5 19.39 - 24.24: 1 Bond angle restraints: 80348 Sorted by residual: angle pdb=" S1 FES C 803 " pdb="FE2 FES C 803 " pdb=" S2 FES C 803 " ideal model delta sigma weight residual 104.33 89.56 14.77 1.14e+00 7.69e-01 1.68e+02 angle pdb=" S1 FES B 301 " pdb="FE2 FES B 301 " pdb=" S2 FES B 301 " ideal model delta sigma weight residual 104.33 89.97 14.36 1.14e+00 7.69e-01 1.59e+02 angle pdb=" PA NDP T 501 " pdb=" O3 NDP T 501 " pdb=" PN NDP T 501 " ideal model delta sigma weight residual 107.74 131.98 -24.24 1.95e+00 2.62e-01 1.54e+02 angle pdb=" S1 FES C 803 " pdb="FE1 FES C 803 " pdb=" S2 FES C 803 " ideal model delta sigma weight residual 104.33 89.45 14.88 1.20e+00 6.94e-01 1.54e+02 angle pdb=" S1 FES B 301 " pdb="FE1 FES B 301 " pdb=" S2 FES B 301 " ideal model delta sigma weight residual 104.33 90.08 14.25 1.20e+00 6.94e-01 1.41e+02 ... (remaining 80343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 34520 35.49 - 70.98: 780 70.98 - 106.46: 49 106.46 - 141.95: 10 141.95 - 177.44: 6 Dihedral angle restraints: 35365 sinusoidal: 14157 harmonic: 21208 Sorted by residual: dihedral pdb=" C THR I 356 " pdb=" N THR I 356 " pdb=" CA THR I 356 " pdb=" CB THR I 356 " ideal model delta harmonic sigma weight residual -122.00 -146.04 24.04 0 2.50e+00 1.60e-01 9.25e+01 dihedral pdb=" C PHE H 229 " pdb=" N PHE H 229 " pdb=" CA PHE H 229 " pdb=" CB PHE H 229 " ideal model delta harmonic sigma weight residual -122.60 -145.38 22.78 0 2.50e+00 1.60e-01 8.31e+01 dihedral pdb=" N THR I 356 " pdb=" C THR I 356 " pdb=" CA THR I 356 " pdb=" CB THR I 356 " ideal model delta harmonic sigma weight residual 123.40 144.62 -21.22 0 2.50e+00 1.60e-01 7.20e+01 ... (remaining 35362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.238: 8949 4.238 - 8.475: 0 8.475 - 12.713: 0 12.713 - 16.951: 0 16.951 - 21.189: 20 Chirality restraints: 8969 Sorted by residual: chirality pdb="FE4 SF4 E 301 " pdb=" S1 SF4 E 301 " pdb=" S2 SF4 E 301 " pdb=" S3 SF4 E 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE2 SF4 E 301 " pdb=" S1 SF4 E 301 " pdb=" S3 SF4 E 301 " pdb=" S4 SF4 E 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.45 21.00 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE1 SF4 E 301 " pdb=" S2 SF4 E 301 " pdb=" S3 SF4 E 301 " pdb=" S4 SF4 E 301 " both_signs ideal model delta sigma weight residual False -10.55 10.44 -20.99 2.00e-01 2.50e+01 1.10e+04 ... (remaining 8966 not shown) Planarity restraints: 10136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 H 501 " 0.004 2.00e-02 2.50e+03 1.01e-01 1.80e+02 pdb=" C1M U10 H 501 " -0.008 2.00e-02 2.50e+03 pdb=" C2 U10 H 501 " -0.119 2.00e-02 2.50e+03 pdb=" C3 U10 H 501 " 0.112 2.00e-02 2.50e+03 pdb=" C4 U10 H 501 " 0.019 2.00e-02 2.50e+03 pdb=" C5 U10 H 501 " -0.154 2.00e-02 2.50e+03 pdb=" C6 U10 H 501 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP T 501 " 0.180 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" C3N NDP T 501 " 0.041 2.00e-02 2.50e+03 pdb=" C4N NDP T 501 " 0.021 2.00e-02 2.50e+03 pdb=" C7N NDP T 501 " -0.100 2.00e-02 2.50e+03 pdb=" N1N NDP T 501 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 T7X I 501 " -0.064 2.00e-02 2.50e+03 6.39e-02 4.08e+01 pdb=" C21 T7X I 501 " 0.063 2.00e-02 2.50e+03 pdb=" C22 T7X I 501 " 0.065 2.00e-02 2.50e+03 pdb=" C23 T7X I 501 " -0.064 2.00e-02 2.50e+03 ... (remaining 10133 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 60 2.26 - 2.92: 26175 2.92 - 3.58: 90158 3.58 - 4.24: 147030 4.24 - 4.90: 245386 Nonbonded interactions: 508809 Sorted by model distance: nonbonded pdb=" OE2 GLU I 340 " pdb=" CD LYS m 38 " model vdw 1.596 3.440 nonbonded pdb=" CG1 ILE S 84 " pdb=" OD1 ASN R 122 " model vdw 1.707 3.440 nonbonded pdb=" CG GLU q 17 " pdb=" O GLY p 19 " model vdw 2.026 3.440 nonbonded pdb=" NH2 ARG A 182 " pdb=" O CYS B 171 " model vdw 2.052 3.120 nonbonded pdb=" O LYS C 205 " pdb=" OG1 THR C 213 " model vdw 2.055 3.040 ... (remaining 508804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'p' and resid 6 through 229) selection = (chain 'q' and resid 6 through 229) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 1.960 Check model and map are aligned: 0.360 Set scattering table: 0.430 Process input model: 125.450 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.218 59313 Z= 0.503 Angle : 1.036 24.242 80348 Z= 0.668 Chirality : 0.992 21.189 8969 Planarity : 0.006 0.114 10136 Dihedral : 15.860 177.440 21689 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.54 % Favored : 89.27 % Rotamer: Outliers : 1.07 % Allowed : 9.16 % Favored : 89.76 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.08), residues: 7252 helix: -2.03 (0.07), residues: 3636 sheet: -3.81 (0.26), residues: 279 loop : -3.39 (0.09), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP m 65 HIS 0.012 0.002 HIS q 107 PHE 0.032 0.002 PHE D 185 TYR 0.036 0.002 TYR R 115 ARG 0.009 0.001 ARG S 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2527 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 2462 time to evaluate : 5.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.6685 (m-30) cc_final: 0.5406 (m-30) REVERT: I 144 ASP cc_start: 0.6096 (t0) cc_final: 0.5794 (t0) REVERT: I 264 PHE cc_start: 0.7394 (m-80) cc_final: 0.7118 (m-80) REVERT: I 299 ILE cc_start: 0.8126 (mt) cc_final: 0.6944 (mt) REVERT: I 369 THR cc_start: 0.5258 (p) cc_final: 0.5026 (t) REVERT: J 60 ARG cc_start: 0.7030 (mtm-85) cc_final: 0.6757 (ptm160) REVERT: J 100 LEU cc_start: 0.8847 (tp) cc_final: 0.8637 (tt) REVERT: J 111 TRP cc_start: 0.8069 (t60) cc_final: 0.7628 (t60) REVERT: N 29 PHE cc_start: 0.8177 (m-80) cc_final: 0.7907 (m-10) REVERT: N 56 VAL cc_start: 0.8536 (m) cc_final: 0.8117 (m) REVERT: N 148 TYR cc_start: 0.8415 (m-80) cc_final: 0.7500 (m-80) REVERT: N 174 THR cc_start: 0.6830 (p) cc_final: 0.6407 (p) REVERT: H 41 ASP cc_start: 0.8154 (t0) cc_final: 0.7782 (t0) REVERT: H 50 GLN cc_start: 0.8393 (tp40) cc_final: 0.7621 (tm-30) REVERT: H 126 TRP cc_start: 0.7807 (t60) cc_final: 0.7237 (t-100) REVERT: H 199 ASN cc_start: 0.7753 (m-40) cc_final: 0.7549 (m-40) REVERT: K 5 LYS cc_start: 0.7024 (tttt) cc_final: 0.6792 (mmtt) REVERT: K 18 ILE cc_start: 0.8199 (tt) cc_final: 0.7989 (tt) REVERT: K 29 LEU cc_start: 0.8736 (tp) cc_final: 0.8430 (tt) REVERT: V 22 MET cc_start: 0.5366 (mtp) cc_final: 0.5095 (mtm) REVERT: S 97 MET cc_start: 0.7562 (mtt) cc_final: 0.7132 (ttm) REVERT: i 29 MET cc_start: 0.2208 (ptt) cc_final: 0.1810 (ptp) REVERT: i 31 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6902 (p-80) REVERT: j 10 ASN cc_start: 0.8540 (m-40) cc_final: 0.8043 (m-40) REVERT: j 59 LYS cc_start: 0.8322 (ttpt) cc_final: 0.8105 (tptt) REVERT: j 62 GLN cc_start: 0.6267 (tp40) cc_final: 0.5882 (tt0) REVERT: G 94 VAL cc_start: 0.9190 (m) cc_final: 0.8966 (m) REVERT: G 174 ASP cc_start: 0.7053 (m-30) cc_final: 0.6838 (m-30) REVERT: G 302 MET cc_start: 0.7855 (ppp) cc_final: 0.6649 (ppp) REVERT: G 384 THR cc_start: 0.8034 (p) cc_final: 0.7229 (p) REVERT: C 218 CYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7939 (t) REVERT: C 500 HIS cc_start: 0.7104 (t70) cc_final: 0.6443 (t70) REVERT: C 633 THR cc_start: 0.8135 (p) cc_final: 0.7858 (p) REVERT: T 222 MET cc_start: 0.7207 (mtm) cc_final: 0.6759 (mtm) REVERT: T 356 ASN cc_start: 0.5463 (p0) cc_final: 0.4208 (t0) REVERT: T 368 HIS cc_start: 0.7180 (m170) cc_final: 0.6966 (m90) REVERT: T 381 TYR cc_start: 0.7869 (m-80) cc_final: 0.7376 (m-80) REVERT: F 155 VAL cc_start: 0.7795 (m) cc_final: 0.7556 (m) REVERT: O 65 GLN cc_start: 0.7856 (pt0) cc_final: 0.7532 (pt0) REVERT: O 68 SER cc_start: 0.8141 (m) cc_final: 0.7843 (t) REVERT: O 142 ASP cc_start: 0.7342 (m-30) cc_final: 0.7129 (m-30) REVERT: P 57 ILE cc_start: 0.8948 (tp) cc_final: 0.8623 (tp) REVERT: P 88 CYS cc_start: 0.6898 (t) cc_final: 0.6615 (t) REVERT: U 35 PRO cc_start: 0.8149 (Cg_endo) cc_final: 0.7824 (Cg_exo) REVERT: U 50 THR cc_start: 0.7470 (p) cc_final: 0.7138 (m) REVERT: U 75 TRP cc_start: 0.8017 (p90) cc_final: 0.7783 (p90) REVERT: E 141 LYS cc_start: 0.7553 (ttpt) cc_final: 0.7068 (ttmt) REVERT: E 164 TYR cc_start: 0.8908 (t80) cc_final: 0.8420 (t80) REVERT: E 188 CYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7326 (t) REVERT: E 205 LYS cc_start: 0.8445 (tttp) cc_final: 0.8049 (ttmm) REVERT: D 54 LYS cc_start: 0.5027 (mmtt) cc_final: 0.3836 (mmtt) REVERT: X 73 LYS cc_start: 0.8459 (mttt) cc_final: 0.8164 (mttm) REVERT: X 125 LYS cc_start: 0.5669 (mppt) cc_final: 0.5254 (mptt) REVERT: c 20 PRO cc_start: 0.8829 (Cg_exo) cc_final: 0.8545 (Cg_endo) REVERT: c 38 SER cc_start: 0.8489 (m) cc_final: 0.8268 (t) REVERT: c 86 MET cc_start: 0.7480 (mtm) cc_final: 0.7269 (mtm) REVERT: Q 21 SER cc_start: 0.7351 (m) cc_final: 0.6622 (p) REVERT: Q 63 ARG cc_start: 0.7496 (mtp-110) cc_final: 0.6417 (mtp-110) REVERT: k 80 LEU cc_start: 0.8270 (tp) cc_final: 0.7967 (tp) REVERT: k 105 ILE cc_start: 0.4398 (mp) cc_final: 0.3788 (mt) REVERT: o 123 TRP cc_start: 0.5668 (t-100) cc_final: 0.5420 (m-90) REVERT: o 156 CYS cc_start: 0.5402 (m) cc_final: 0.5181 (m) REVERT: q 108 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7891 (m) REVERT: q 147 MET cc_start: 0.6373 (ptp) cc_final: 0.6136 (ptp) REVERT: q 157 VAL cc_start: 0.7977 (t) cc_final: 0.7667 (t) REVERT: p 29 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7749 (tt) REVERT: p 34 TYR cc_start: 0.6586 (m-80) cc_final: 0.6132 (m-80) REVERT: p 49 PHE cc_start: 0.4456 (m-80) cc_final: 0.3544 (m-80) REVERT: M 86 ILE cc_start: 0.7767 (pt) cc_final: 0.7149 (mt) REVERT: M 261 THR cc_start: 0.8935 (p) cc_final: 0.8634 (p) REVERT: M 316 MET cc_start: 0.7220 (mmm) cc_final: 0.6992 (mmm) REVERT: M 338 MET cc_start: 0.7280 (mtm) cc_final: 0.6997 (mtm) REVERT: M 362 ARG cc_start: 0.6264 (mmp-170) cc_final: 0.5920 (mtm180) REVERT: M 367 TYR cc_start: 0.6042 (m-80) cc_final: 0.5802 (m-80) REVERT: M 397 PHE cc_start: 0.7738 (t80) cc_final: 0.7139 (t80) REVERT: M 458 PHE cc_start: 0.7422 (t80) cc_final: 0.7093 (t80) REVERT: f 39 ARG cc_start: 0.6647 (tpt170) cc_final: 0.6411 (mmm160) REVERT: f 54 LYS cc_start: 0.6281 (mttt) cc_final: 0.5951 (tmtt) REVERT: g 70 SER cc_start: 0.8316 (m) cc_final: 0.8013 (p) REVERT: a 45 ILE cc_start: 0.6979 (mm) cc_final: 0.6643 (mm) REVERT: a 137 PHE cc_start: 0.8245 (t80) cc_final: 0.7789 (t80) REVERT: a 341 HIS cc_start: 0.5105 (t70) cc_final: 0.4861 (t-90) REVERT: a 349 PHE cc_start: 0.5619 (m-80) cc_final: 0.5144 (m-80) REVERT: a 615 GLN cc_start: 0.2407 (tt0) cc_final: 0.1516 (mm-40) REVERT: b 70 MET cc_start: 0.7576 (tpt) cc_final: 0.7022 (tpt) REVERT: m 15 LEU cc_start: 0.5699 (pt) cc_final: 0.4678 (tp) REVERT: t 21 HIS cc_start: 0.3708 (p-80) cc_final: 0.2753 (m170) outliers start: 65 outliers final: 21 residues processed: 2498 average time/residue: 0.5881 time to fit residues: 2411.6026 Evaluate side-chains 1485 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1459 time to evaluate : 5.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 107 HIS Chi-restraints excluded: chain q residue 108 VAL Chi-restraints excluded: chain p residue 29 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 391 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 602 optimal weight: 0.0370 chunk 540 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 364 optimal weight: 4.9990 chunk 288 optimal weight: 7.9990 chunk 558 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 339 optimal weight: 9.9990 chunk 415 optimal weight: 6.9990 chunk 647 optimal weight: 7.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN A 436 GLN A 441 GLN I 53 ASN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN I 326 HIS ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 33 ASN Y 87 ASN Z 8 ASN Z 126 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS V 42 HIS W 13 GLN ** i 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN G 312 HIS C 66 HIS C 165 ASN C 284 ASN ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 ASN C 569 GLN ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 GLN T 94 GLN T 117 GLN T 143 ASN T 209 ASN T 291 HIS T 340 ASN F 54 GLN F 125 ASN ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 81 GLN B 84 ASN O 49 HIS O 77 ASN ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 149 ASN ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 141 ASN E 121 GLN D 111 HIS D 190 HIS X 15 ASN X 68 HIS ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 ASN Q 35 ASN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 57 GLN ** o 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 160 GLN o 197 ASN q 33 ASN ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 218 ASN q 223 ASN ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 135 HIS p 206 ASN M 67 GLN ** M 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 66 HIS a 417 ASN a 495 ASN a 541 GLN a 567 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.249 59313 Z= 0.566 Angle : 1.673 51.852 80348 Z= 1.055 Chirality : 0.308 6.647 8969 Planarity : 0.006 0.085 10136 Dihedral : 10.647 173.358 8479 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.51 % Favored : 91.44 % Rotamer: Outliers : 4.91 % Allowed : 19.38 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.09), residues: 7252 helix: -1.03 (0.08), residues: 3667 sheet: -3.13 (0.27), residues: 290 loop : -2.88 (0.10), residues: 3295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP U 93 HIS 0.019 0.002 HIS C 166 PHE 0.052 0.003 PHE H 229 TYR 0.039 0.003 TYR I 373 ARG 0.010 0.001 ARG G 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1867 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1569 time to evaluate : 5.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.7964 (m100) cc_final: 0.7467 (m100) REVERT: A 150 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.5952 (m-30) REVERT: A 154 MET cc_start: 0.7432 (mpp) cc_final: 0.7019 (mpp) REVERT: I 113 ASP cc_start: 0.7228 (t70) cc_final: 0.6895 (t0) REVERT: I 162 ILE cc_start: 0.8981 (pt) cc_final: 0.8649 (pt) REVERT: I 297 CYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6961 (t) REVERT: I 445 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6426 (tttm) REVERT: I 492 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8007 (tm-30) REVERT: J 100 LEU cc_start: 0.8965 (tp) cc_final: 0.8608 (tt) REVERT: J 111 TRP cc_start: 0.8167 (t60) cc_final: 0.7634 (t60) REVERT: N 32 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7919 (mm) REVERT: N 42 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8491 (mm) REVERT: N 57 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6514 (m-80) REVERT: N 148 TYR cc_start: 0.8575 (m-80) cc_final: 0.7750 (m-80) REVERT: N 186 ASN cc_start: 0.6034 (p0) cc_final: 0.5743 (p0) REVERT: H 41 ASP cc_start: 0.7734 (t0) cc_final: 0.7489 (t0) REVERT: H 126 TRP cc_start: 0.7902 (t60) cc_final: 0.7457 (t-100) REVERT: H 188 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8435 (t) REVERT: H 236 MET cc_start: 0.7833 (ttp) cc_final: 0.7472 (ttp) REVERT: H 281 ILE cc_start: 0.8931 (mm) cc_final: 0.8599 (mt) REVERT: H 290 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: K 5 LYS cc_start: 0.7518 (tttt) cc_final: 0.7229 (mmtt) REVERT: K 54 ASP cc_start: 0.7438 (t0) cc_final: 0.7173 (t0) REVERT: Y 14 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7627 (p) REVERT: Y 95 GLU cc_start: 0.6716 (mp0) cc_final: 0.6446 (mt-10) REVERT: i 30 ARG cc_start: 0.6194 (mtt-85) cc_final: 0.5549 (mtm-85) REVERT: i 31 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.6682 (p-80) REVERT: i 33 TRP cc_start: 0.7255 (m-90) cc_final: 0.6701 (m-90) REVERT: j 19 MET cc_start: 0.7166 (tmm) cc_final: 0.6852 (tmm) REVERT: j 23 GLU cc_start: 0.7542 (tp30) cc_final: 0.7331 (mm-30) REVERT: j 42 LEU cc_start: 0.8780 (mp) cc_final: 0.8391 (mm) REVERT: j 59 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7993 (tptt) REVERT: j 62 GLN cc_start: 0.6306 (tp40) cc_final: 0.5724 (tt0) REVERT: G 153 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7356 (mtm) REVERT: G 174 ASP cc_start: 0.7273 (m-30) cc_final: 0.6807 (m-30) REVERT: G 259 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7656 (t0) REVERT: C 119 MET cc_start: 0.8378 (tpp) cc_final: 0.8026 (tmm) REVERT: C 718 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8455 (p) REVERT: C 735 MET cc_start: 0.8249 (mmt) cc_final: 0.8029 (mmt) REVERT: T 356 ASN cc_start: 0.6092 (p0) cc_final: 0.4561 (t0) REVERT: F 37 TYR cc_start: 0.6996 (m-80) cc_final: 0.6662 (m-10) REVERT: F 49 THR cc_start: 0.6647 (m) cc_final: 0.6063 (m) REVERT: O 124 ASP cc_start: 0.6775 (t70) cc_final: 0.6544 (t70) REVERT: O 142 ASP cc_start: 0.7326 (m-30) cc_final: 0.7113 (m-30) REVERT: P 57 ILE cc_start: 0.8867 (tp) cc_final: 0.8594 (tp) REVERT: P 99 TYR cc_start: 0.7744 (m-80) cc_final: 0.7381 (m-80) REVERT: R 64 ARG cc_start: 0.7412 (mtt180) cc_final: 0.6971 (mtt90) REVERT: U 35 PRO cc_start: 0.8254 (Cg_endo) cc_final: 0.7876 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8425 (p90) cc_final: 0.7914 (p90) REVERT: U 129 ASP cc_start: 0.7627 (m-30) cc_final: 0.7349 (m-30) REVERT: E 139 LEU cc_start: 0.8925 (tp) cc_final: 0.8497 (tt) REVERT: E 164 TYR cc_start: 0.9199 (t80) cc_final: 0.8798 (t80) REVERT: D 54 LYS cc_start: 0.5110 (mmtt) cc_final: 0.4092 (mmtt) REVERT: X 18 ASN cc_start: 0.7179 (p0) cc_final: 0.6762 (p0) REVERT: X 63 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8539 (tp) REVERT: X 98 HIS cc_start: 0.6599 (m-70) cc_final: 0.6272 (m90) REVERT: c 38 SER cc_start: 0.8880 (m) cc_final: 0.8299 (t) REVERT: c 58 LYS cc_start: 0.7809 (ptmt) cc_final: 0.7546 (ptmm) REVERT: o 61 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8468 (pp) REVERT: o 223 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7880 (mt) REVERT: q 108 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7876 (m) REVERT: p 24 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.5452 (ttp-170) REVERT: M 65 LYS cc_start: 0.6303 (ptmt) cc_final: 0.5398 (pttp) REVERT: M 80 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8777 (mm) REVERT: M 86 ILE cc_start: 0.7800 (pt) cc_final: 0.7159 (mt) REVERT: M 106 LEU cc_start: 0.9150 (tp) cc_final: 0.8908 (mt) REVERT: M 136 MET cc_start: 0.8008 (tpp) cc_final: 0.6977 (tpp) REVERT: M 153 MET cc_start: 0.8252 (tpp) cc_final: 0.7718 (tpp) REVERT: M 261 THR cc_start: 0.8994 (p) cc_final: 0.8716 (p) REVERT: M 316 MET cc_start: 0.7364 (mmm) cc_final: 0.7057 (mmm) REVERT: M 356 TYR cc_start: 0.7565 (t80) cc_final: 0.7310 (t80) REVERT: M 367 TYR cc_start: 0.6428 (m-80) cc_final: 0.5887 (m-80) REVERT: M 389 MET cc_start: 0.8385 (ptm) cc_final: 0.8025 (ptp) REVERT: f 22 ASN cc_start: 0.6658 (p0) cc_final: 0.5544 (p0) REVERT: f 54 LYS cc_start: 0.6131 (mttt) cc_final: 0.5804 (tmtt) REVERT: g 67 TYR cc_start: 0.4065 (p90) cc_final: 0.3805 (p90) REVERT: g 70 SER cc_start: 0.8095 (m) cc_final: 0.7809 (p) REVERT: g 72 LEU cc_start: 0.8078 (mt) cc_final: 0.7780 (mt) REVERT: a 45 ILE cc_start: 0.7088 (mm) cc_final: 0.6815 (mm) REVERT: a 78 PHE cc_start: 0.1210 (m-80) cc_final: 0.0993 (t80) REVERT: a 117 LEU cc_start: 0.7975 (tp) cc_final: 0.7664 (mt) REVERT: a 137 PHE cc_start: 0.8391 (t80) cc_final: 0.7575 (t80) REVERT: a 182 ILE cc_start: 0.8160 (pt) cc_final: 0.7885 (pt) REVERT: a 278 TYR cc_start: 0.3557 (p90) cc_final: 0.2983 (p90) REVERT: a 382 MET cc_start: 0.5643 (ppp) cc_final: 0.5256 (ppp) REVERT: a 404 ILE cc_start: 0.6608 (mp) cc_final: 0.6240 (mm) REVERT: t 21 HIS cc_start: 0.4085 (OUTLIER) cc_final: 0.2605 (m170) outliers start: 298 outliers final: 178 residues processed: 1734 average time/residue: 0.5553 time to fit residues: 1640.0499 Evaluate side-chains 1521 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1323 time to evaluate : 5.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 445 LYS Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 476 ILE Chi-restraints excluded: chain I residue 495 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain W residue 16 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 45 PHE Chi-restraints excluded: chain i residue 50 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 163 ILE Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 213 GLU Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 141 ASN Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain c residue 3 THR Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 62 MET Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 57 GLN Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 113 VAL Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain o residue 223 LEU Chi-restraints excluded: chain o residue 238 TYR Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 107 HIS Chi-restraints excluded: chain q residue 108 VAL Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain p residue 15 ILE Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 130 HIS Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 312 SER Chi-restraints excluded: chain M residue 396 SER Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 77 TYR Chi-restraints excluded: chain a residue 35 CYS Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 493 TRP Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 359 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 538 optimal weight: 4.9990 chunk 440 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 648 optimal weight: 9.9990 chunk 700 optimal weight: 5.9990 chunk 577 optimal weight: 3.9990 chunk 643 optimal weight: 20.0000 chunk 221 optimal weight: 1.9990 chunk 520 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 ASN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 HIS ** H 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 87 ASN ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 284 ASN ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 209 ASN T 368 HIS ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 84 ASN ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 HIS U 134 HIS U 141 ASN E 100 HIS ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN X 54 GLN ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 161 HIS q 72 HIS ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 218 ASN ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 359 HIS ** M 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.257 59313 Z= 0.541 Angle : 1.628 51.135 80348 Z= 1.035 Chirality : 0.302 6.393 8969 Planarity : 0.006 0.103 10136 Dihedral : 10.070 171.246 8461 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.26 % Favored : 91.70 % Rotamer: Outliers : 5.39 % Allowed : 22.53 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.09), residues: 7252 helix: -0.49 (0.08), residues: 3664 sheet: -3.06 (0.27), residues: 309 loop : -2.60 (0.10), residues: 3279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP g 92 HIS 0.013 0.002 HIS C 166 PHE 0.036 0.002 PHE q 49 TYR 0.035 0.002 TYR M 119 ARG 0.007 0.001 ARG b 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1806 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 1479 time to evaluate : 5.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.7928 (m100) cc_final: 0.7052 (m100) REVERT: A 154 MET cc_start: 0.7501 (mpp) cc_final: 0.7077 (mpp) REVERT: A 439 THR cc_start: 0.8640 (p) cc_final: 0.8429 (p) REVERT: I 113 ASP cc_start: 0.7284 (t70) cc_final: 0.6370 (t0) REVERT: I 117 GLN cc_start: 0.7221 (tt0) cc_final: 0.6885 (pt0) REVERT: I 139 MET cc_start: 0.7787 (ttm) cc_final: 0.7484 (ttm) REVERT: I 162 ILE cc_start: 0.9026 (pt) cc_final: 0.8693 (pt) REVERT: I 178 LYS cc_start: 0.8493 (ptpt) cc_final: 0.7819 (pttm) REVERT: I 297 CYS cc_start: 0.7407 (t) cc_final: 0.7027 (t) REVERT: I 450 ASP cc_start: 0.7016 (p0) cc_final: 0.4596 (m-30) REVERT: J 111 TRP cc_start: 0.8170 (t60) cc_final: 0.7482 (t60) REVERT: N 29 PHE cc_start: 0.7827 (m-10) cc_final: 0.7615 (m-10) REVERT: N 42 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8479 (mm) REVERT: N 148 TYR cc_start: 0.8554 (m-80) cc_final: 0.7678 (m-10) REVERT: H 41 ASP cc_start: 0.7653 (t0) cc_final: 0.7336 (t0) REVERT: H 126 TRP cc_start: 0.7851 (t60) cc_final: 0.7504 (t-100) REVERT: H 236 MET cc_start: 0.7795 (ttp) cc_final: 0.7499 (ttp) REVERT: K 5 LYS cc_start: 0.7671 (tttt) cc_final: 0.7360 (mmtt) REVERT: K 54 ASP cc_start: 0.7282 (t0) cc_final: 0.6909 (t0) REVERT: Y 82 MET cc_start: 0.7950 (mmp) cc_final: 0.7660 (mmp) REVERT: i 31 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.6881 (p-80) REVERT: j 16 ASP cc_start: 0.7709 (m-30) cc_final: 0.7398 (m-30) REVERT: j 59 LYS cc_start: 0.8378 (ttpt) cc_final: 0.8062 (tptt) REVERT: j 62 GLN cc_start: 0.6273 (tp40) cc_final: 0.5678 (tt0) REVERT: G 47 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8011 (tt) REVERT: G 153 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7312 (mtm) REVERT: G 173 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6263 (mtm-85) REVERT: G 174 ASP cc_start: 0.6975 (m-30) cc_final: 0.6552 (m-30) REVERT: G 188 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6278 (pt0) REVERT: G 257 CYS cc_start: 0.7254 (t) cc_final: 0.7046 (t) REVERT: G 259 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7827 (t0) REVERT: C 718 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8232 (p) REVERT: T 91 MET cc_start: 0.7803 (ppp) cc_final: 0.7282 (tmm) REVERT: T 119 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8730 (p) REVERT: T 368 HIS cc_start: 0.7027 (m90) cc_final: 0.6762 (m90) REVERT: F 37 TYR cc_start: 0.7017 (m-80) cc_final: 0.6814 (m-10) REVERT: F 84 SER cc_start: 0.8863 (p) cc_final: 0.8572 (t) REVERT: O 65 GLN cc_start: 0.7997 (pt0) cc_final: 0.7577 (pt0) REVERT: O 142 ASP cc_start: 0.7380 (m-30) cc_final: 0.7134 (m-30) REVERT: P 57 ILE cc_start: 0.8956 (tp) cc_final: 0.8549 (tp) REVERT: P 99 TYR cc_start: 0.8038 (m-80) cc_final: 0.7759 (m-80) REVERT: R 53 TYR cc_start: 0.7312 (t80) cc_final: 0.7097 (t80) REVERT: R 64 ARG cc_start: 0.7093 (mtt180) cc_final: 0.6797 (mtt90) REVERT: U 35 PRO cc_start: 0.8285 (Cg_endo) cc_final: 0.7955 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8352 (p90) cc_final: 0.7808 (p90) REVERT: U 129 ASP cc_start: 0.7542 (m-30) cc_final: 0.7211 (m-30) REVERT: E 139 LEU cc_start: 0.8827 (tp) cc_final: 0.8520 (tt) REVERT: E 164 TYR cc_start: 0.9165 (t80) cc_final: 0.8713 (t80) REVERT: E 205 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8509 (ttmm) REVERT: D 54 LYS cc_start: 0.5106 (mmtt) cc_final: 0.3800 (mmtt) REVERT: D 111 HIS cc_start: 0.8297 (m-70) cc_final: 0.7885 (m170) REVERT: D 197 LYS cc_start: 0.5383 (OUTLIER) cc_final: 0.4924 (mtpt) REVERT: X 18 ASN cc_start: 0.7262 (p0) cc_final: 0.6791 (p0) REVERT: X 63 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8559 (tp) REVERT: X 95 GLN cc_start: 0.4964 (OUTLIER) cc_final: 0.4331 (mt0) REVERT: c 38 SER cc_start: 0.8901 (m) cc_final: 0.8313 (t) REVERT: Q 21 SER cc_start: 0.7404 (m) cc_final: 0.6636 (p) REVERT: o 61 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8452 (pp) REVERT: o 212 GLU cc_start: 0.6961 (pt0) cc_final: 0.6760 (mp0) REVERT: o 223 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8103 (mt) REVERT: q 86 ARG cc_start: 0.3209 (OUTLIER) cc_final: 0.2808 (ttm170) REVERT: q 105 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5687 (mm) REVERT: q 128 ILE cc_start: 0.6327 (mt) cc_final: 0.5754 (mt) REVERT: M 51 TYR cc_start: 0.5526 (m-80) cc_final: 0.5273 (m-10) REVERT: M 65 LYS cc_start: 0.6231 (ptmt) cc_final: 0.5415 (pttp) REVERT: M 80 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8753 (mm) REVERT: M 86 ILE cc_start: 0.7696 (pt) cc_final: 0.7162 (mt) REVERT: M 106 LEU cc_start: 0.9132 (tp) cc_final: 0.8894 (mt) REVERT: M 136 MET cc_start: 0.7807 (tpp) cc_final: 0.7084 (tpp) REVERT: M 153 MET cc_start: 0.8063 (tpp) cc_final: 0.7601 (tpp) REVERT: M 316 MET cc_start: 0.7373 (mmm) cc_final: 0.6942 (mmm) REVERT: M 336 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8441 (mm) REVERT: M 367 TYR cc_start: 0.6184 (m-80) cc_final: 0.5704 (m-80) REVERT: M 389 MET cc_start: 0.8359 (ptm) cc_final: 0.8113 (ptm) REVERT: M 458 PHE cc_start: 0.7300 (t80) cc_final: 0.7012 (t80) REVERT: f 34 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8249 (mtp85) REVERT: f 54 LYS cc_start: 0.6267 (mttt) cc_final: 0.5896 (tmtt) REVERT: f 69 LYS cc_start: 0.7308 (mptt) cc_final: 0.5755 (tttm) REVERT: f 79 ASP cc_start: 0.6151 (OUTLIER) cc_final: 0.5764 (m-30) REVERT: g 70 SER cc_start: 0.8158 (m) cc_final: 0.7744 (p) REVERT: a 78 PHE cc_start: 0.1357 (m-80) cc_final: 0.1107 (t80) REVERT: a 137 PHE cc_start: 0.8445 (t80) cc_final: 0.7658 (t80) REVERT: a 141 GLU cc_start: 0.5912 (tp30) cc_final: 0.5528 (tp30) REVERT: a 278 TYR cc_start: 0.3594 (p90) cc_final: 0.3063 (p90) REVERT: a 365 MET cc_start: -0.0759 (mmt) cc_final: -0.1242 (mmm) REVERT: a 467 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6886 (mt) REVERT: a 518 LYS cc_start: 0.2385 (tptt) cc_final: 0.1397 (mmtp) REVERT: b 44 GLU cc_start: 0.3087 (pm20) cc_final: 0.2652 (pt0) REVERT: m 7 PHE cc_start: 0.6021 (p90) cc_final: 0.5549 (p90) REVERT: m 15 LEU cc_start: 0.5937 (pt) cc_final: 0.5030 (tp) REVERT: t 21 HIS cc_start: 0.4025 (OUTLIER) cc_final: 0.2471 (m170) outliers start: 327 outliers final: 198 residues processed: 1667 average time/residue: 0.5417 time to fit residues: 1549.0032 Evaluate side-chains 1516 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1298 time to evaluate : 5.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 373 TYR Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 495 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 267 ILE Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain Y residue 49 CYS Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 45 PHE Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 268 MET Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 358 LEU Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain O residue 147 LYS Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 104 ILE Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 141 ASN Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 62 MET Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 113 VAL Chi-restraints excluded: chain o residue 161 HIS Chi-restraints excluded: chain o residue 223 LEU Chi-restraints excluded: chain o residue 238 TYR Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 105 LEU Chi-restraints excluded: chain q residue 107 HIS Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 68 ILE Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 104 SER Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 130 HIS Chi-restraints excluded: chain p residue 163 VAL Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 193 PHE Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 396 SER Chi-restraints excluded: chain M residue 398 ILE Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain g residue 92 TRP Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 333 VAL Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 493 TRP Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 640 optimal weight: 5.9990 chunk 487 optimal weight: 1.9990 chunk 336 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 chunk 435 optimal weight: 2.9990 chunk 650 optimal weight: 10.0000 chunk 689 optimal weight: 5.9990 chunk 340 optimal weight: 0.0040 chunk 616 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 GLN H 322 GLN ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 HIS ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 94 GLN ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 141 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 161 HIS q 20 GLN ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 206 ASN ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 HIS ** a 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.256 59313 Z= 0.537 Angle : 1.620 50.929 80348 Z= 1.032 Chirality : 0.302 6.381 8969 Planarity : 0.005 0.075 10136 Dihedral : 9.601 172.617 8454 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.40 % Favored : 91.57 % Rotamer: Outliers : 6.20 % Allowed : 23.01 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.10), residues: 7252 helix: -0.24 (0.08), residues: 3654 sheet: -2.87 (0.27), residues: 327 loop : -2.44 (0.10), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP g 92 HIS 0.024 0.002 HIS o 161 PHE 0.031 0.002 PHE R 60 TYR 0.035 0.002 TYR M 119 ARG 0.012 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1807 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 376 poor density : 1431 time to evaluate : 5.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 86 LEU cc_start: 0.9018 (mt) cc_final: 0.8782 (mt) REVERT: I 139 MET cc_start: 0.7900 (ttm) cc_final: 0.7576 (ttm) REVERT: I 162 ILE cc_start: 0.9074 (pt) cc_final: 0.8787 (pt) REVERT: I 297 CYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6739 (t) REVERT: I 395 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7610 (mmt) REVERT: I 450 ASP cc_start: 0.6860 (p0) cc_final: 0.4400 (m-30) REVERT: J 111 TRP cc_start: 0.8148 (t60) cc_final: 0.7373 (t60) REVERT: N 42 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8431 (mm) REVERT: N 148 TYR cc_start: 0.8504 (m-80) cc_final: 0.7412 (m-80) REVERT: H 41 ASP cc_start: 0.7930 (t0) cc_final: 0.7621 (t0) REVERT: H 126 TRP cc_start: 0.7863 (t60) cc_final: 0.7389 (t-100) REVERT: H 236 MET cc_start: 0.7847 (ttp) cc_final: 0.7484 (ttp) REVERT: K 5 LYS cc_start: 0.7712 (tttt) cc_final: 0.7322 (mmtt) REVERT: Z 47 MET cc_start: 0.7125 (mmt) cc_final: 0.6878 (mtm) REVERT: V 26 GLN cc_start: 0.7413 (pt0) cc_final: 0.6792 (pt0) REVERT: V 56 VAL cc_start: 0.7854 (OUTLIER) cc_final: 0.7592 (t) REVERT: i 31 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.6864 (p-80) REVERT: i 34 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7070 (tp30) REVERT: j 16 ASP cc_start: 0.7708 (m-30) cc_final: 0.7493 (m-30) REVERT: j 59 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8026 (tptt) REVERT: G 47 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8064 (tt) REVERT: G 153 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7164 (mtm) REVERT: G 188 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6316 (pt0) REVERT: G 197 ARG cc_start: 0.8205 (ptp-110) cc_final: 0.7612 (ptp-170) REVERT: C 311 GLU cc_start: 0.7764 (pt0) cc_final: 0.7548 (pt0) REVERT: C 421 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6320 (mm) REVERT: C 453 MET cc_start: 0.7692 (mmm) cc_final: 0.7476 (mmm) REVERT: C 632 ASN cc_start: 0.8717 (p0) cc_final: 0.8424 (p0) REVERT: C 654 TRP cc_start: 0.8302 (p-90) cc_final: 0.8065 (p-90) REVERT: T 91 MET cc_start: 0.7774 (ppp) cc_final: 0.7349 (tmm) REVERT: T 119 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8793 (p) REVERT: T 217 MET cc_start: 0.7159 (mmp) cc_final: 0.6927 (mmm) REVERT: T 325 MET cc_start: 0.6949 (pmm) cc_final: 0.6738 (pmm) REVERT: T 368 HIS cc_start: 0.6710 (m90) cc_final: 0.6509 (m-70) REVERT: F 84 SER cc_start: 0.8865 (p) cc_final: 0.8593 (t) REVERT: O 65 GLN cc_start: 0.8072 (pt0) cc_final: 0.7620 (pt0) REVERT: P 57 ILE cc_start: 0.8894 (tp) cc_final: 0.8510 (tp) REVERT: P 99 TYR cc_start: 0.8089 (m-80) cc_final: 0.7666 (m-80) REVERT: R 53 TYR cc_start: 0.7256 (t80) cc_final: 0.6755 (t80) REVERT: U 35 PRO cc_start: 0.8271 (Cg_endo) cc_final: 0.7912 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8318 (p90) cc_final: 0.7808 (p90) REVERT: U 129 ASP cc_start: 0.7322 (m-30) cc_final: 0.6924 (m-30) REVERT: U 149 ARG cc_start: 0.7798 (mmt90) cc_final: 0.6935 (mmt180) REVERT: E 139 LEU cc_start: 0.8846 (tp) cc_final: 0.8585 (tt) REVERT: E 164 TYR cc_start: 0.9166 (t80) cc_final: 0.8746 (t80) REVERT: E 205 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8518 (ttmm) REVERT: D 54 LYS cc_start: 0.5109 (mmtt) cc_final: 0.3859 (mmtt) REVERT: D 210 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7552 (tm-30) REVERT: X 18 ASN cc_start: 0.6980 (p0) cc_final: 0.6503 (p0) REVERT: X 63 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8578 (tp) REVERT: X 95 GLN cc_start: 0.4711 (OUTLIER) cc_final: 0.4387 (mt0) REVERT: Q 21 SER cc_start: 0.7402 (m) cc_final: 0.6613 (p) REVERT: Q 36 TYR cc_start: 0.7535 (t80) cc_final: 0.7296 (t80) REVERT: o 61 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8422 (pp) REVERT: o 160 GLN cc_start: 0.7838 (mm110) cc_final: 0.7481 (mm110) REVERT: o 244 PHE cc_start: 0.8377 (t80) cc_final: 0.8173 (t80) REVERT: p 24 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.5518 (ptt90) REVERT: p 50 ASP cc_start: 0.5263 (m-30) cc_final: 0.5049 (m-30) REVERT: M 65 LYS cc_start: 0.6331 (ptmt) cc_final: 0.5681 (pttm) REVERT: M 80 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8808 (mm) REVERT: M 86 ILE cc_start: 0.7755 (pt) cc_final: 0.7552 (pt) REVERT: M 106 LEU cc_start: 0.9104 (tp) cc_final: 0.8879 (mt) REVERT: M 136 MET cc_start: 0.7790 (tpp) cc_final: 0.7152 (tpp) REVERT: M 237 LEU cc_start: 0.8051 (mt) cc_final: 0.7846 (mt) REVERT: M 261 THR cc_start: 0.8852 (p) cc_final: 0.8641 (p) REVERT: M 316 MET cc_start: 0.7552 (mmm) cc_final: 0.7254 (mmm) REVERT: M 458 PHE cc_start: 0.7200 (t80) cc_final: 0.6908 (t80) REVERT: f 34 ARG cc_start: 0.8409 (ttp80) cc_final: 0.8150 (mtp85) REVERT: f 40 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: f 54 LYS cc_start: 0.6169 (mttt) cc_final: 0.5756 (tmtt) REVERT: f 69 LYS cc_start: 0.7361 (mptt) cc_final: 0.6785 (mtpp) REVERT: f 75 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7879 (tm-30) REVERT: f 79 ASP cc_start: 0.6159 (OUTLIER) cc_final: 0.5647 (m-30) REVERT: g 70 SER cc_start: 0.8127 (m) cc_final: 0.7802 (p) REVERT: a 126 MET cc_start: 0.7841 (mtp) cc_final: 0.7620 (ttp) REVERT: a 137 PHE cc_start: 0.8427 (t80) cc_final: 0.7584 (t80) REVERT: a 168 MET cc_start: 0.7590 (tpt) cc_final: 0.7349 (tpp) REVERT: a 186 PHE cc_start: 0.5906 (OUTLIER) cc_final: 0.4457 (t80) REVERT: a 247 GLU cc_start: 0.1520 (OUTLIER) cc_final: 0.1121 (tm-30) REVERT: a 278 TYR cc_start: 0.3617 (p90) cc_final: 0.3111 (p90) REVERT: a 322 MET cc_start: 0.5283 (mmm) cc_final: 0.4810 (mmm) REVERT: a 365 MET cc_start: -0.0541 (mmt) cc_final: -0.1086 (mmm) REVERT: a 406 GLU cc_start: 0.4937 (mm-30) cc_final: 0.4710 (mm-30) REVERT: a 467 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7104 (mt) REVERT: a 518 LYS cc_start: 0.2534 (tptt) cc_final: 0.1557 (mmtp) REVERT: m 7 PHE cc_start: 0.5939 (p90) cc_final: 0.5418 (p90) REVERT: m 15 LEU cc_start: 0.6019 (pt) cc_final: 0.5007 (tp) REVERT: m 51 TYR cc_start: 0.6777 (p90) cc_final: 0.6550 (p90) REVERT: t 21 HIS cc_start: 0.4002 (OUTLIER) cc_final: 0.2674 (m170) outliers start: 376 outliers final: 217 residues processed: 1640 average time/residue: 0.5679 time to fit residues: 1597.6150 Evaluate side-chains 1522 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1284 time to evaluate : 5.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 373 TYR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 495 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain Y residue 12 ILE Chi-restraints excluded: chain Y residue 49 CYS Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 34 GLU Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 41 LEU Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 268 MET Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 358 LEU Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 48 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 141 ASN Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain c residue 3 THR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain o residue 238 TYR Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 218 ASN Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain p residue 68 ILE Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 104 SER Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 130 HIS Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 139 VAL Chi-restraints excluded: chain p residue 163 VAL Chi-restraints excluded: chain p residue 222 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 104 CYS Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 312 SER Chi-restraints excluded: chain M residue 396 SER Chi-restraints excluded: chain M residue 398 ILE Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 247 GLU Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 333 VAL Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 493 TRP Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain b residue 45 PHE Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 573 optimal weight: 0.9980 chunk 391 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 513 optimal weight: 7.9990 chunk 284 optimal weight: 8.9990 chunk 588 optimal weight: 0.8980 chunk 476 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 351 optimal weight: 0.8980 chunk 618 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 GLN ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 131 ASN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 55 GLN o 57 GLN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 160 HIS ** p 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 318 GLN ** a 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 357 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.255 59313 Z= 0.545 Angle : 1.626 51.006 80348 Z= 1.033 Chirality : 0.301 6.395 8969 Planarity : 0.005 0.096 10136 Dihedral : 9.352 174.048 8451 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.47 % Favored : 91.51 % Rotamer: Outliers : 5.70 % Allowed : 24.86 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.10), residues: 7252 helix: -0.13 (0.08), residues: 3642 sheet: -2.81 (0.27), residues: 325 loop : -2.34 (0.10), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP g 92 HIS 0.017 0.001 HIS C 166 PHE 0.049 0.002 PHE M 142 TYR 0.038 0.002 TYR H 147 ARG 0.013 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1716 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 1370 time to evaluate : 5.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7306 (mmt) cc_final: 0.6808 (mmt) REVERT: A 439 THR cc_start: 0.8709 (p) cc_final: 0.8459 (p) REVERT: I 139 MET cc_start: 0.7934 (ttm) cc_final: 0.7631 (ttm) REVERT: I 162 ILE cc_start: 0.9143 (pt) cc_final: 0.8904 (pt) REVERT: I 174 GLU cc_start: 0.6891 (tm-30) cc_final: 0.5962 (tp30) REVERT: I 395 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7616 (mmt) REVERT: I 471 MET cc_start: 0.6842 (mtm) cc_final: 0.6486 (mtp) REVERT: N 148 TYR cc_start: 0.8543 (m-80) cc_final: 0.7384 (m-80) REVERT: H 62 GLU cc_start: 0.8251 (mp0) cc_final: 0.7725 (mp0) REVERT: H 82 PHE cc_start: 0.7656 (t80) cc_final: 0.7400 (t80) REVERT: H 220 TYR cc_start: 0.5995 (m-80) cc_final: 0.5595 (m-80) REVERT: K 5 LYS cc_start: 0.7686 (tttt) cc_final: 0.7263 (mmtt) REVERT: K 35 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8694 (mm) REVERT: K 54 ASP cc_start: 0.7367 (t0) cc_final: 0.6984 (t0) REVERT: V 26 GLN cc_start: 0.7765 (pt0) cc_final: 0.6895 (pt0) REVERT: i 31 HIS cc_start: 0.7578 (OUTLIER) cc_final: 0.6848 (p-80) REVERT: i 52 TRP cc_start: 0.6544 (t60) cc_final: 0.6341 (t60) REVERT: i 63 MET cc_start: 0.7478 (mtt) cc_final: 0.7145 (mpp) REVERT: j 16 ASP cc_start: 0.7722 (m-30) cc_final: 0.7493 (m-30) REVERT: j 59 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8048 (tptt) REVERT: G 47 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8181 (tt) REVERT: G 153 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7264 (mtm) REVERT: G 188 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6314 (pt0) REVERT: G 197 ARG cc_start: 0.8258 (ptp-110) cc_final: 0.7873 (ptp-170) REVERT: G 223 MET cc_start: 0.7950 (mmm) cc_final: 0.7646 (tpp) REVERT: C 119 MET cc_start: 0.8191 (tpp) cc_final: 0.7939 (mmm) REVERT: C 421 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6344 (mm) REVERT: C 654 TRP cc_start: 0.8359 (p-90) cc_final: 0.8098 (p-90) REVERT: C 705 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6680 (pp20) REVERT: T 91 MET cc_start: 0.7851 (ppp) cc_final: 0.7422 (tmm) REVERT: T 119 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8779 (p) REVERT: T 358 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6392 (mp) REVERT: T 369 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7113 (mtpp) REVERT: F 84 SER cc_start: 0.8936 (p) cc_final: 0.8634 (t) REVERT: O 65 GLN cc_start: 0.8113 (pt0) cc_final: 0.7659 (pt0) REVERT: P 57 ILE cc_start: 0.8930 (tp) cc_final: 0.8530 (tp) REVERT: P 99 TYR cc_start: 0.8177 (m-80) cc_final: 0.7737 (m-80) REVERT: R 53 TYR cc_start: 0.7057 (t80) cc_final: 0.6723 (t80) REVERT: U 35 PRO cc_start: 0.8220 (Cg_endo) cc_final: 0.7822 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8281 (p90) cc_final: 0.7808 (p90) REVERT: U 129 ASP cc_start: 0.7357 (m-30) cc_final: 0.6857 (m-30) REVERT: E 97 GLU cc_start: 0.8295 (tp30) cc_final: 0.7439 (tp30) REVERT: E 139 LEU cc_start: 0.8873 (tp) cc_final: 0.8645 (tt) REVERT: E 164 TYR cc_start: 0.9152 (t80) cc_final: 0.8727 (t80) REVERT: E 205 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8577 (ttmm) REVERT: D 54 LYS cc_start: 0.5078 (mmtt) cc_final: 0.3664 (mmtt) REVERT: X 18 ASN cc_start: 0.6998 (p0) cc_final: 0.6522 (p0) REVERT: X 63 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8532 (tp) REVERT: X 95 GLN cc_start: 0.4525 (OUTLIER) cc_final: 0.4096 (tt0) REVERT: c 36 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6924 (mtt90) REVERT: c 71 MET cc_start: 0.7547 (tpp) cc_final: 0.6988 (ttp) REVERT: c 75 MET cc_start: 0.7463 (mtp) cc_final: 0.7141 (mtp) REVERT: o 61 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8461 (pp) REVERT: o 123 TRP cc_start: 0.6183 (m100) cc_final: 0.5753 (m100) REVERT: p 24 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.5523 (ptt90) REVERT: M 80 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8833 (mm) REVERT: M 83 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.6098 (t80) REVERT: M 106 LEU cc_start: 0.9038 (tp) cc_final: 0.8829 (mt) REVERT: M 136 MET cc_start: 0.7741 (tpp) cc_final: 0.7222 (tpp) REVERT: M 261 THR cc_start: 0.8818 (p) cc_final: 0.8505 (p) REVERT: M 316 MET cc_start: 0.7539 (mmm) cc_final: 0.7183 (mmm) REVERT: M 458 PHE cc_start: 0.7246 (t80) cc_final: 0.6968 (t80) REVERT: f 34 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8283 (mtp85) REVERT: f 40 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: f 54 LYS cc_start: 0.6102 (mttt) cc_final: 0.5541 (tmtt) REVERT: f 69 LYS cc_start: 0.7223 (mptt) cc_final: 0.6727 (mtpp) REVERT: g 70 SER cc_start: 0.8053 (m) cc_final: 0.7691 (p) REVERT: a 134 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7824 (mm) REVERT: a 137 PHE cc_start: 0.8378 (t80) cc_final: 0.7591 (t80) REVERT: a 154 TRP cc_start: 0.6655 (m-10) cc_final: 0.6386 (m100) REVERT: a 155 PHE cc_start: 0.3997 (OUTLIER) cc_final: 0.3631 (t80) REVERT: a 186 PHE cc_start: 0.5928 (OUTLIER) cc_final: 0.4538 (t80) REVERT: a 278 TYR cc_start: 0.3543 (p90) cc_final: 0.2968 (p90) REVERT: a 365 MET cc_start: -0.0374 (mmt) cc_final: -0.1014 (mmm) REVERT: a 467 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7091 (mt) REVERT: a 518 LYS cc_start: 0.2529 (tptt) cc_final: 0.1552 (mmtp) REVERT: m 7 PHE cc_start: 0.6116 (p90) cc_final: 0.5480 (p90) REVERT: m 15 LEU cc_start: 0.5919 (pt) cc_final: 0.4858 (tp) REVERT: t 21 HIS cc_start: 0.4375 (OUTLIER) cc_final: 0.2990 (m-70) outliers start: 346 outliers final: 238 residues processed: 1569 average time/residue: 0.5658 time to fit residues: 1524.5386 Evaluate side-chains 1518 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1258 time to evaluate : 5.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 310 MET Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 373 TYR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain Y residue 12 ILE Chi-restraints excluded: chain Y residue 49 CYS Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 268 MET Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 301 ILE Chi-restraints excluded: chain T residue 358 LEU Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 48 GLU Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 108 HIS Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 141 ASN Chi-restraints excluded: chain U residue 148 THR Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 36 ARG Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain k residue 53 VAL Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 145 SER Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 161 HIS Chi-restraints excluded: chain o residue 168 SER Chi-restraints excluded: chain o residue 238 TYR Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 218 ASN Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 104 SER Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 139 VAL Chi-restraints excluded: chain p residue 163 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 83 TYR Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 396 SER Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain g residue 66 CYS Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain a residue 155 PHE Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 333 VAL Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 231 optimal weight: 0.8980 chunk 620 optimal weight: 50.0000 chunk 136 optimal weight: 0.7980 chunk 404 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 689 optimal weight: 20.0000 chunk 572 optimal weight: 0.7980 chunk 319 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 228 optimal weight: 0.3980 chunk 362 optimal weight: 0.0030 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN A 436 GLN A 459 GLN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 GLN Y 42 ASN ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 GLN ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 368 HIS ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 ASN U 141 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 47 ASN q 72 HIS ** q 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 184 ASN ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 214 HIS ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 59313 Z= 0.510 Angle : 1.615 50.800 80348 Z= 1.027 Chirality : 0.301 6.362 8969 Planarity : 0.005 0.073 10136 Dihedral : 9.035 167.995 8451 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.94 % Favored : 92.03 % Rotamer: Outliers : 4.90 % Allowed : 26.59 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.10), residues: 7252 helix: 0.03 (0.08), residues: 3668 sheet: -2.73 (0.28), residues: 320 loop : -2.30 (0.10), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP M 236 HIS 0.014 0.001 HIS R 129 PHE 0.055 0.002 PHE M 142 TYR 0.042 0.002 TYR H 147 ARG 0.012 0.001 ARG C 318 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1739 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1442 time to evaluate : 5.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.7893 (m100) cc_final: 0.7114 (m100) REVERT: A 154 MET cc_start: 0.7242 (mmt) cc_final: 0.6871 (mmt) REVERT: I 136 MET cc_start: 0.7078 (mtp) cc_final: 0.6839 (mtp) REVERT: I 162 ILE cc_start: 0.9102 (pt) cc_final: 0.8860 (pt) REVERT: I 174 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6121 (tp30) REVERT: I 226 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8127 (mt) REVERT: I 297 CYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6899 (t) REVERT: I 395 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7665 (mmt) REVERT: I 471 MET cc_start: 0.6808 (mtm) cc_final: 0.6410 (mtp) REVERT: N 28 LEU cc_start: 0.8316 (tp) cc_final: 0.7495 (mt) REVERT: N 64 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8456 (mp) REVERT: N 148 TYR cc_start: 0.8542 (m-80) cc_final: 0.7572 (m-10) REVERT: N 157 LEU cc_start: 0.8754 (mt) cc_final: 0.8437 (mt) REVERT: H 13 ILE cc_start: 0.8446 (mm) cc_final: 0.8105 (mt) REVERT: H 62 GLU cc_start: 0.8154 (mp0) cc_final: 0.7689 (mp0) REVERT: H 220 TYR cc_start: 0.5901 (m-80) cc_final: 0.5524 (m-80) REVERT: K 5 LYS cc_start: 0.7682 (tttt) cc_final: 0.7258 (mmtt) REVERT: K 31 MET cc_start: 0.7899 (mmp) cc_final: 0.7484 (mmm) REVERT: V 26 GLN cc_start: 0.7606 (pt0) cc_final: 0.6934 (pt0) REVERT: S 99 ASN cc_start: 0.7871 (p0) cc_final: 0.7554 (m-40) REVERT: i 31 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6512 (p-80) REVERT: i 63 MET cc_start: 0.7448 (mtt) cc_final: 0.7067 (mpp) REVERT: j 59 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8057 (tptt) REVERT: G 44 ILE cc_start: 0.8974 (mm) cc_final: 0.8737 (mm) REVERT: G 47 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8246 (tt) REVERT: G 153 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6833 (mtm) REVERT: G 223 MET cc_start: 0.7907 (mmm) cc_final: 0.7661 (tpp) REVERT: C 178 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6141 (pt0) REVERT: C 394 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7406 (tpp) REVERT: C 427 MET cc_start: 0.7371 (mmm) cc_final: 0.6114 (mtp) REVERT: C 654 TRP cc_start: 0.8302 (p-90) cc_final: 0.8003 (p-90) REVERT: C 705 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6545 (pp20) REVERT: T 91 MET cc_start: 0.7777 (ppp) cc_final: 0.7409 (tmm) REVERT: T 119 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8765 (p) REVERT: T 163 ILE cc_start: 0.7893 (mm) cc_final: 0.7661 (mt) REVERT: T 300 MET cc_start: 0.7167 (tpp) cc_final: 0.6950 (mpp) REVERT: T 369 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6987 (mtpp) REVERT: F 84 SER cc_start: 0.8819 (p) cc_final: 0.8575 (t) REVERT: O 65 GLN cc_start: 0.7955 (pt0) cc_final: 0.7597 (pt0) REVERT: O 86 ASN cc_start: 0.7743 (t0) cc_final: 0.7312 (t0) REVERT: P 57 ILE cc_start: 0.8846 (tp) cc_final: 0.8491 (tp) REVERT: P 99 TYR cc_start: 0.8027 (m-80) cc_final: 0.7518 (m-80) REVERT: U 35 PRO cc_start: 0.8193 (Cg_endo) cc_final: 0.7873 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8261 (p90) cc_final: 0.7790 (p90) REVERT: U 129 ASP cc_start: 0.7106 (m-30) cc_final: 0.6649 (m-30) REVERT: E 97 GLU cc_start: 0.8056 (tp30) cc_final: 0.7674 (tp30) REVERT: E 139 LEU cc_start: 0.8779 (tp) cc_final: 0.8552 (tt) REVERT: E 164 TYR cc_start: 0.9125 (t80) cc_final: 0.8646 (t80) REVERT: D 54 LYS cc_start: 0.5101 (mmtt) cc_final: 0.3694 (mmtt) REVERT: X 18 ASN cc_start: 0.6747 (p0) cc_final: 0.6545 (p0) REVERT: X 63 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8442 (tp) REVERT: X 95 GLN cc_start: 0.4962 (OUTLIER) cc_final: 0.4562 (tt0) REVERT: X 130 SER cc_start: 0.8210 (p) cc_final: 0.7597 (m) REVERT: c 26 VAL cc_start: 0.8534 (p) cc_final: 0.8279 (p) REVERT: Q 63 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6950 (mtp180) REVERT: o 61 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8433 (pp) REVERT: o 116 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7589 (mtp85) REVERT: o 212 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6991 (mp0) REVERT: q 162 MET cc_start: 0.5584 (tpt) cc_final: 0.5151 (tpt) REVERT: p 20 GLN cc_start: 0.7928 (mt0) cc_final: 0.7689 (mt0) REVERT: p 24 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.5491 (ptt90) REVERT: p 49 PHE cc_start: 0.5353 (m-80) cc_final: 0.5118 (m-80) REVERT: p 144 PHE cc_start: 0.5744 (t80) cc_final: 0.4694 (t80) REVERT: M 86 ILE cc_start: 0.7599 (pt) cc_final: 0.7275 (mm) REVERT: M 136 MET cc_start: 0.7695 (tpp) cc_final: 0.7182 (tpp) REVERT: M 261 THR cc_start: 0.8880 (p) cc_final: 0.8523 (p) REVERT: M 316 MET cc_start: 0.7456 (mmm) cc_final: 0.7202 (mmm) REVERT: f 40 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: f 54 LYS cc_start: 0.5996 (mttt) cc_final: 0.5222 (tmtt) REVERT: f 69 LYS cc_start: 0.7163 (mptt) cc_final: 0.6738 (mtpp) REVERT: g 70 SER cc_start: 0.8107 (m) cc_final: 0.7812 (p) REVERT: g 72 LEU cc_start: 0.8108 (mt) cc_final: 0.7859 (mt) REVERT: a 45 ILE cc_start: 0.6774 (mm) cc_final: 0.6554 (mm) REVERT: a 89 VAL cc_start: 0.6627 (p) cc_final: 0.6403 (p) REVERT: a 124 MET cc_start: 0.8096 (tpt) cc_final: 0.7462 (tpt) REVERT: a 137 PHE cc_start: 0.8342 (t80) cc_final: 0.7693 (t80) REVERT: a 186 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5148 (t80) REVERT: a 278 TYR cc_start: 0.3237 (p90) cc_final: 0.2785 (p90) REVERT: a 365 MET cc_start: -0.0661 (mmt) cc_final: -0.1219 (mmm) REVERT: a 518 LYS cc_start: 0.2660 (tptt) cc_final: 0.1733 (mmtp) REVERT: m 7 PHE cc_start: 0.5856 (p90) cc_final: 0.5164 (p90) REVERT: m 15 LEU cc_start: 0.5973 (pt) cc_final: 0.4993 (tt) REVERT: m 16 MET cc_start: 0.5412 (mmp) cc_final: 0.5195 (mmm) REVERT: t 21 HIS cc_start: 0.4422 (OUTLIER) cc_final: 0.3024 (m-70) outliers start: 297 outliers final: 184 residues processed: 1607 average time/residue: 0.5481 time to fit residues: 1501.7626 Evaluate side-chains 1485 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1282 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 310 MET Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain Y residue 12 ILE Chi-restraints excluded: chain Y residue 49 CYS Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 71 ASN Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 268 MET Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 301 ILE Chi-restraints excluded: chain T residue 368 HIS Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 48 GLU Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 147 LYS Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 108 HIS Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 141 ASN Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 169 VAL Chi-restraints excluded: chain q residue 218 ASN Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 13 PHE Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 139 VAL Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 398 ILE Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 296 LEU Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 333 VAL Chi-restraints excluded: chain a residue 338 LEU Chi-restraints excluded: chain a residue 407 LEU Chi-restraints excluded: chain a residue 542 PHE Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain b residue 45 PHE Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 665 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 393 optimal weight: 3.9990 chunk 503 optimal weight: 7.9990 chunk 390 optimal weight: 0.7980 chunk 580 optimal weight: 4.9990 chunk 385 optimal weight: 7.9990 chunk 687 optimal weight: 0.1980 chunk 430 optimal weight: 1.9990 chunk 418 optimal weight: 6.9990 chunk 317 optimal weight: 0.0370 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN I 53 ASN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 126 ASN ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 368 HIS ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN U 141 ASN E 121 GLN X 68 HIS ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 42 HIS q 72 HIS q 90 ASN ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 HIS a 171 ASN ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 59 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.254 59313 Z= 0.517 Angle : 1.621 50.810 80348 Z= 1.029 Chirality : 0.301 6.362 8969 Planarity : 0.005 0.073 10136 Dihedral : 8.838 168.082 8449 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.97 % Favored : 92.00 % Rotamer: Outliers : 4.94 % Allowed : 27.18 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.10), residues: 7252 helix: 0.10 (0.09), residues: 3670 sheet: -2.57 (0.28), residues: 333 loop : -2.24 (0.10), residues: 3249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP M 236 HIS 0.014 0.001 HIS a 152 PHE 0.064 0.002 PHE K 61 TYR 0.044 0.002 TYR H 147 ARG 0.013 0.001 ARG C 318 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1646 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1346 time to evaluate : 5.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7170 (mmt) cc_final: 0.6840 (mmt) REVERT: I 139 MET cc_start: 0.7724 (ttm) cc_final: 0.7408 (ttm) REVERT: I 162 ILE cc_start: 0.9159 (pt) cc_final: 0.8936 (pt) REVERT: I 174 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6457 (tp30) REVERT: I 226 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8192 (mt) REVERT: I 345 LEU cc_start: 0.9146 (tt) cc_final: 0.8921 (tp) REVERT: I 395 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7718 (mmt) REVERT: I 471 MET cc_start: 0.6833 (mtm) cc_final: 0.6509 (mtp) REVERT: N 64 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8404 (mp) REVERT: N 148 TYR cc_start: 0.8654 (m-80) cc_final: 0.7834 (m-10) REVERT: H 13 ILE cc_start: 0.8462 (mm) cc_final: 0.7943 (mt) REVERT: H 62 GLU cc_start: 0.8212 (mp0) cc_final: 0.7799 (mp0) REVERT: H 220 TYR cc_start: 0.5960 (m-80) cc_final: 0.5576 (m-80) REVERT: K 5 LYS cc_start: 0.7608 (tttt) cc_final: 0.7167 (mmtt) REVERT: K 33 MET cc_start: 0.7907 (mmt) cc_final: 0.7638 (mmm) REVERT: Z 84 THR cc_start: 0.8366 (t) cc_final: 0.7951 (t) REVERT: V 26 GLN cc_start: 0.7836 (pt0) cc_final: 0.7031 (pt0) REVERT: S 99 ASN cc_start: 0.8040 (p0) cc_final: 0.7529 (m-40) REVERT: i 63 MET cc_start: 0.7606 (mtt) cc_final: 0.7217 (mpp) REVERT: j 59 LYS cc_start: 0.8488 (ttpt) cc_final: 0.7998 (tptt) REVERT: G 44 ILE cc_start: 0.8992 (mm) cc_final: 0.8740 (mm) REVERT: G 47 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8299 (tt) REVERT: G 115 LEU cc_start: 0.8206 (mt) cc_final: 0.8003 (mm) REVERT: G 153 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7109 (mtm) REVERT: G 223 MET cc_start: 0.8005 (mmm) cc_final: 0.7740 (tpp) REVERT: C 178 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6455 (pt0) REVERT: C 284 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8486 (t0) REVERT: C 427 MET cc_start: 0.7354 (mmm) cc_final: 0.6276 (mtp) REVERT: C 705 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6555 (pp20) REVERT: T 91 MET cc_start: 0.7791 (ppp) cc_final: 0.7380 (tmm) REVERT: T 119 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8754 (p) REVERT: T 163 ILE cc_start: 0.7849 (mm) cc_final: 0.7632 (mt) REVERT: F 17 LYS cc_start: 0.7246 (ttpt) cc_final: 0.6084 (tttt) REVERT: F 84 SER cc_start: 0.8858 (p) cc_final: 0.8592 (t) REVERT: O 65 GLN cc_start: 0.8137 (pt0) cc_final: 0.7617 (pt0) REVERT: O 86 ASN cc_start: 0.7686 (t0) cc_final: 0.7282 (t0) REVERT: P 57 ILE cc_start: 0.8891 (tp) cc_final: 0.8530 (tp) REVERT: P 99 TYR cc_start: 0.7971 (m-80) cc_final: 0.7602 (m-80) REVERT: R 73 ASP cc_start: 0.4853 (t70) cc_final: 0.4585 (t0) REVERT: U 35 PRO cc_start: 0.8181 (Cg_endo) cc_final: 0.7852 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8201 (p90) cc_final: 0.7792 (p90) REVERT: U 129 ASP cc_start: 0.7054 (m-30) cc_final: 0.6613 (m-30) REVERT: U 149 ARG cc_start: 0.7328 (mmt180) cc_final: 0.6403 (mmt180) REVERT: E 164 TYR cc_start: 0.9153 (t80) cc_final: 0.8811 (t80) REVERT: E 184 TYR cc_start: 0.8652 (m-80) cc_final: 0.8448 (m-80) REVERT: D 54 LYS cc_start: 0.5200 (mmtt) cc_final: 0.3886 (mmtt) REVERT: X 18 ASN cc_start: 0.6610 (p0) cc_final: 0.6394 (p0) REVERT: X 63 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8359 (tp) REVERT: X 95 GLN cc_start: 0.4869 (OUTLIER) cc_final: 0.4435 (tt0) REVERT: X 132 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6684 (m-80) REVERT: c 36 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.7032 (mtm-85) REVERT: o 61 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8413 (pp) REVERT: o 212 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7000 (mp0) REVERT: o 216 LEU cc_start: 0.8349 (tt) cc_final: 0.8131 (tp) REVERT: p 20 GLN cc_start: 0.7936 (mt0) cc_final: 0.7641 (mt0) REVERT: p 24 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.5621 (ptt90) REVERT: p 107 HIS cc_start: 0.4360 (m170) cc_final: 0.3951 (m170) REVERT: M 86 ILE cc_start: 0.7493 (pt) cc_final: 0.7138 (mm) REVERT: M 136 MET cc_start: 0.7728 (tpp) cc_final: 0.7190 (tpp) REVERT: M 261 THR cc_start: 0.8850 (p) cc_final: 0.8513 (p) REVERT: M 316 MET cc_start: 0.7484 (mmm) cc_final: 0.7092 (mmm) REVERT: M 323 MET cc_start: 0.6982 (ttp) cc_final: 0.6228 (tmm) REVERT: M 432 LEU cc_start: 0.7200 (mp) cc_final: 0.6959 (mt) REVERT: f 40 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6632 (mp0) REVERT: f 54 LYS cc_start: 0.5972 (mttt) cc_final: 0.5332 (tmtt) REVERT: f 69 LYS cc_start: 0.7283 (mptt) cc_final: 0.6711 (mtpp) REVERT: g 72 LEU cc_start: 0.8114 (mt) cc_final: 0.7843 (mt) REVERT: g 87 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6147 (mp) REVERT: g 99 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7357 (mm-30) REVERT: a 31 MET cc_start: 0.2280 (ttp) cc_final: 0.2068 (ttp) REVERT: a 45 ILE cc_start: 0.6786 (mm) cc_final: 0.6559 (mm) REVERT: a 89 VAL cc_start: 0.6798 (p) cc_final: 0.6583 (p) REVERT: a 124 MET cc_start: 0.8215 (tpt) cc_final: 0.7741 (tpt) REVERT: a 126 MET cc_start: 0.7718 (tmm) cc_final: 0.7358 (tmm) REVERT: a 137 PHE cc_start: 0.8325 (t80) cc_final: 0.7674 (t80) REVERT: a 186 PHE cc_start: 0.6038 (OUTLIER) cc_final: 0.5127 (t80) REVERT: a 278 TYR cc_start: 0.3188 (p90) cc_final: 0.2720 (p90) REVERT: a 365 MET cc_start: -0.0500 (mmt) cc_final: -0.0927 (mmm) REVERT: a 392 PHE cc_start: 0.4067 (t80) cc_final: 0.3669 (t80) REVERT: a 518 LYS cc_start: 0.2809 (tptt) cc_final: 0.1872 (mmtp) REVERT: m 15 LEU cc_start: 0.5923 (pt) cc_final: 0.4769 (tp) REVERT: m 16 MET cc_start: 0.5254 (mmp) cc_final: 0.4951 (mmm) REVERT: t 21 HIS cc_start: 0.4524 (OUTLIER) cc_final: 0.3176 (m-70) outliers start: 300 outliers final: 211 residues processed: 1516 average time/residue: 0.5826 time to fit residues: 1522.0723 Evaluate side-chains 1475 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1246 time to evaluate : 5.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 310 MET Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 466 SER Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 236 MET Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 61 PHE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 41 LEU Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 71 ASN Chi-restraints excluded: chain j residue 14 CYS Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain C residue 284 ASN Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 301 ILE Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 48 GLU Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 147 LYS Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 108 HIS Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 57 TYR Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 36 ARG Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain q residue 42 HIS Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 210 LEU Chi-restraints excluded: chain q residue 218 ASN Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 13 PHE Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 46 MET Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 139 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 328 ILE Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 33 MET Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain a residue 170 VAL Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 203 VAL Chi-restraints excluded: chain a residue 296 LEU Chi-restraints excluded: chain a residue 338 LEU Chi-restraints excluded: chain a residue 542 PHE Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain b residue 45 PHE Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 425 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 410 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 436 optimal weight: 0.9980 chunk 468 optimal weight: 8.9990 chunk 339 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 540 optimal weight: 8.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 HIS ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 ASN T 182 GLN ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 GLN ** U 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 20 GLN q 42 HIS q 72 HIS ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 30 GLN ** p 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 453 ASN ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 337 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.253 59313 Z= 0.543 Angle : 1.635 50.941 80348 Z= 1.036 Chirality : 0.301 6.376 8969 Planarity : 0.006 0.078 10136 Dihedral : 8.744 170.251 8447 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.67 % Favored : 91.29 % Rotamer: Outliers : 5.13 % Allowed : 27.67 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 7252 helix: 0.08 (0.09), residues: 3652 sheet: -2.48 (0.28), residues: 336 loop : -2.18 (0.11), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP M 236 HIS 0.040 0.002 HIS q 42 PHE 0.061 0.002 PHE K 61 TYR 0.046 0.002 TYR o 144 ARG 0.012 0.001 ARG Q 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1585 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1274 time to evaluate : 6.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7389 (mpp) cc_final: 0.6461 (mtm) REVERT: A 154 MET cc_start: 0.7208 (mmt) cc_final: 0.6823 (mmt) REVERT: I 139 MET cc_start: 0.7750 (ttm) cc_final: 0.7061 (ttm) REVERT: I 174 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6266 (tp30) REVERT: I 226 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8236 (mt) REVERT: I 272 SER cc_start: 0.9024 (t) cc_final: 0.7454 (t) REVERT: I 302 MET cc_start: 0.7324 (mpp) cc_final: 0.6252 (mpp) REVERT: I 345 LEU cc_start: 0.9121 (tt) cc_final: 0.8892 (tp) REVERT: I 395 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7768 (mmt) REVERT: I 461 MET cc_start: 0.7821 (ppp) cc_final: 0.7554 (ppp) REVERT: I 471 MET cc_start: 0.6864 (mtm) cc_final: 0.6658 (mtp) REVERT: J 96 MET cc_start: 0.7929 (tpp) cc_final: 0.7659 (tpp) REVERT: N 148 TYR cc_start: 0.8688 (m-80) cc_final: 0.8020 (m-10) REVERT: H 13 ILE cc_start: 0.8464 (mm) cc_final: 0.8075 (mt) REVERT: H 27 GLU cc_start: 0.6146 (tt0) cc_final: 0.5871 (tt0) REVERT: H 62 GLU cc_start: 0.8261 (mp0) cc_final: 0.7832 (mp0) REVERT: H 220 TYR cc_start: 0.5777 (m-80) cc_final: 0.5416 (m-80) REVERT: K 5 LYS cc_start: 0.7679 (tttt) cc_final: 0.7139 (mmtt) REVERT: Z 84 THR cc_start: 0.8548 (t) cc_final: 0.8179 (t) REVERT: Z 113 LYS cc_start: 0.7220 (mptt) cc_final: 0.6459 (mttt) REVERT: V 14 ILE cc_start: 0.7572 (tt) cc_final: 0.7347 (tt) REVERT: V 26 GLN cc_start: 0.8035 (pt0) cc_final: 0.7088 (pt0) REVERT: W 20 SER cc_start: 0.9100 (m) cc_final: 0.8867 (m) REVERT: S 99 ASN cc_start: 0.8138 (p0) cc_final: 0.7667 (m-40) REVERT: i 63 MET cc_start: 0.7608 (mtt) cc_final: 0.7244 (mpp) REVERT: j 59 LYS cc_start: 0.8501 (ttpt) cc_final: 0.7954 (tptt) REVERT: G 47 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8408 (tt) REVERT: G 223 MET cc_start: 0.8182 (mmm) cc_final: 0.7920 (tpp) REVERT: C 427 MET cc_start: 0.7399 (mmm) cc_final: 0.6425 (mtp) REVERT: C 705 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6518 (pp20) REVERT: T 91 MET cc_start: 0.7729 (ppp) cc_final: 0.7429 (tmm) REVERT: T 119 VAL cc_start: 0.9013 (OUTLIER) cc_final: 0.8730 (p) REVERT: T 163 ILE cc_start: 0.7984 (mm) cc_final: 0.7762 (mt) REVERT: T 369 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7102 (mtpp) REVERT: F 84 SER cc_start: 0.8933 (p) cc_final: 0.8689 (t) REVERT: O 65 GLN cc_start: 0.8241 (pt0) cc_final: 0.7722 (pt0) REVERT: O 86 ASN cc_start: 0.7767 (t0) cc_final: 0.7325 (t0) REVERT: P 57 ILE cc_start: 0.8967 (tp) cc_final: 0.8555 (tp) REVERT: P 99 TYR cc_start: 0.8137 (m-80) cc_final: 0.7699 (m-80) REVERT: U 35 PRO cc_start: 0.8122 (Cg_endo) cc_final: 0.7830 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8257 (p90) cc_final: 0.7898 (p90) REVERT: U 129 ASP cc_start: 0.7240 (m-30) cc_final: 0.6742 (m-30) REVERT: E 164 TYR cc_start: 0.9162 (t80) cc_final: 0.8849 (t80) REVERT: D 54 LYS cc_start: 0.5230 (mmtt) cc_final: 0.3836 (mmtt) REVERT: X 63 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8284 (tp) REVERT: X 95 GLN cc_start: 0.5061 (OUTLIER) cc_final: 0.4696 (tt0) REVERT: X 132 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: c 71 MET cc_start: 0.7657 (tpp) cc_final: 0.7198 (ttp) REVERT: o 61 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8451 (pp) REVERT: o 212 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7053 (mp0) REVERT: o 216 LEU cc_start: 0.8396 (tt) cc_final: 0.8183 (tp) REVERT: p 24 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.5734 (ptt180) REVERT: p 107 HIS cc_start: 0.4359 (m170) cc_final: 0.4120 (m170) REVERT: M 86 ILE cc_start: 0.7624 (pt) cc_final: 0.7188 (mt) REVERT: M 136 MET cc_start: 0.7713 (tpp) cc_final: 0.7353 (tpp) REVERT: M 261 THR cc_start: 0.8827 (p) cc_final: 0.8476 (p) REVERT: M 316 MET cc_start: 0.7575 (mmm) cc_final: 0.7136 (mmm) REVERT: M 328 ILE cc_start: 0.8388 (pt) cc_final: 0.7979 (mp) REVERT: M 432 LEU cc_start: 0.7210 (mp) cc_final: 0.6978 (mt) REVERT: f 40 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: f 54 LYS cc_start: 0.6032 (mttt) cc_final: 0.5375 (tmtt) REVERT: g 72 LEU cc_start: 0.8054 (mt) cc_final: 0.7803 (mt) REVERT: a 45 ILE cc_start: 0.6916 (mm) cc_final: 0.6673 (mm) REVERT: a 69 MET cc_start: 0.3851 (mmp) cc_final: 0.3517 (mmp) REVERT: a 89 VAL cc_start: 0.6772 (p) cc_final: 0.6535 (p) REVERT: a 124 MET cc_start: 0.8172 (tpt) cc_final: 0.7734 (tpt) REVERT: a 126 MET cc_start: 0.7781 (tmm) cc_final: 0.7383 (tmm) REVERT: a 137 PHE cc_start: 0.8206 (t80) cc_final: 0.7548 (t80) REVERT: a 186 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.5326 (t80) REVERT: a 278 TYR cc_start: 0.3173 (p90) cc_final: 0.2685 (p90) REVERT: a 349 PHE cc_start: 0.5940 (OUTLIER) cc_final: 0.4504 (m-80) REVERT: a 365 MET cc_start: -0.0641 (mmt) cc_final: -0.1115 (mmm) REVERT: a 392 PHE cc_start: 0.4321 (t80) cc_final: 0.3942 (t80) REVERT: a 518 LYS cc_start: 0.2800 (tptt) cc_final: 0.1815 (mmtp) REVERT: m 15 LEU cc_start: 0.6177 (pt) cc_final: 0.4995 (tp) REVERT: m 16 MET cc_start: 0.5508 (mmp) cc_final: 0.5250 (mmm) REVERT: t 21 HIS cc_start: 0.4644 (OUTLIER) cc_final: 0.3267 (m-70) outliers start: 311 outliers final: 234 residues processed: 1461 average time/residue: 0.5431 time to fit residues: 1372.0179 Evaluate side-chains 1460 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1212 time to evaluate : 5.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 310 MET Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain H residue 31 MET Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 236 MET Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 61 PHE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain i residue 34 GLU Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 41 LEU Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 71 ASN Chi-restraints excluded: chain j residue 14 CYS Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 235 MET Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain P residue 108 HIS Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 88 GLN Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 76 ASP Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 11 MET Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 145 SER Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 210 LEU Chi-restraints excluded: chain q residue 218 ASN Chi-restraints excluded: chain q residue 222 LEU Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 13 PHE Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 46 MET Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 139 VAL Chi-restraints excluded: chain p residue 222 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 170 VAL Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 296 LEU Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 338 LEU Chi-restraints excluded: chain a residue 349 PHE Chi-restraints excluded: chain a residue 542 PHE Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain b residue 45 PHE Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain m residue 54 TRP Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain t residue 21 HIS Chi-restraints excluded: chain t residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 625 optimal weight: 7.9990 chunk 658 optimal weight: 9.9990 chunk 600 optimal weight: 9.9990 chunk 640 optimal weight: 6.9990 chunk 385 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 502 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 578 optimal weight: 3.9990 chunk 605 optimal weight: 1.9990 chunk 638 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN K 45 ASN ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 ASN ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 337 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.252 59313 Z= 0.548 Angle : 1.646 50.934 80348 Z= 1.041 Chirality : 0.302 6.378 8969 Planarity : 0.005 0.074 10136 Dihedral : 8.723 170.921 8447 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.55 % Favored : 91.42 % Rotamer: Outliers : 4.78 % Allowed : 28.17 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.10), residues: 7252 helix: 0.09 (0.09), residues: 3655 sheet: -2.47 (0.28), residues: 326 loop : -2.16 (0.11), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP M 236 HIS 0.016 0.001 HIS R 129 PHE 0.060 0.002 PHE K 61 TYR 0.037 0.002 TYR H 147 ARG 0.014 0.001 ARG c 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1259 time to evaluate : 5.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7608 (mpp) cc_final: 0.6648 (mtm) REVERT: A 154 MET cc_start: 0.7191 (mmt) cc_final: 0.6841 (mmt) REVERT: I 139 MET cc_start: 0.7734 (ttm) cc_final: 0.7124 (ttm) REVERT: I 174 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6272 (tp30) REVERT: I 226 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8364 (mt) REVERT: I 272 SER cc_start: 0.8933 (t) cc_final: 0.7235 (t) REVERT: I 302 MET cc_start: 0.7358 (mpp) cc_final: 0.6251 (mpp) REVERT: I 345 LEU cc_start: 0.9136 (tt) cc_final: 0.8917 (tp) REVERT: I 395 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7856 (mmt) REVERT: I 461 MET cc_start: 0.7865 (ppp) cc_final: 0.7579 (ppp) REVERT: N 148 TYR cc_start: 0.8673 (m-80) cc_final: 0.8033 (m-10) REVERT: N 163 MET cc_start: 0.7879 (mtt) cc_final: 0.7577 (mmm) REVERT: H 13 ILE cc_start: 0.8461 (mm) cc_final: 0.8112 (mt) REVERT: H 62 GLU cc_start: 0.8312 (mp0) cc_final: 0.7853 (mp0) REVERT: H 220 TYR cc_start: 0.5773 (m-80) cc_final: 0.5442 (m-80) REVERT: K 5 LYS cc_start: 0.7711 (tttt) cc_final: 0.7133 (mmtt) REVERT: Z 84 THR cc_start: 0.8561 (t) cc_final: 0.8346 (t) REVERT: Z 113 LYS cc_start: 0.7279 (mptt) cc_final: 0.6549 (mttt) REVERT: V 14 ILE cc_start: 0.7682 (tt) cc_final: 0.7452 (tt) REVERT: V 26 GLN cc_start: 0.7964 (pt0) cc_final: 0.6939 (pt0) REVERT: W 20 SER cc_start: 0.9180 (m) cc_final: 0.8941 (m) REVERT: S 99 ASN cc_start: 0.8017 (p0) cc_final: 0.7720 (m-40) REVERT: j 59 LYS cc_start: 0.8507 (ttpt) cc_final: 0.7915 (tptt) REVERT: G 72 TYR cc_start: 0.7373 (p90) cc_final: 0.7160 (p90) REVERT: G 197 ARG cc_start: 0.7899 (ptp-110) cc_final: 0.7593 (ptp-170) REVERT: G 223 MET cc_start: 0.8178 (mmm) cc_final: 0.7960 (tpp) REVERT: G 294 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8295 (tt) REVERT: C 427 MET cc_start: 0.7314 (mmm) cc_final: 0.6418 (mtp) REVERT: C 705 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6624 (pp20) REVERT: T 91 MET cc_start: 0.7791 (ppp) cc_final: 0.7538 (tmm) REVERT: T 119 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8701 (p) REVERT: T 163 ILE cc_start: 0.8073 (mm) cc_final: 0.7834 (mt) REVERT: T 369 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7090 (mtpp) REVERT: F 84 SER cc_start: 0.8960 (p) cc_final: 0.8704 (t) REVERT: B 234 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5928 (tp30) REVERT: O 65 GLN cc_start: 0.8335 (pt0) cc_final: 0.7777 (pt0) REVERT: O 86 ASN cc_start: 0.7792 (t0) cc_final: 0.7286 (t0) REVERT: P 57 ILE cc_start: 0.8977 (tp) cc_final: 0.8577 (tp) REVERT: P 99 TYR cc_start: 0.8172 (m-80) cc_final: 0.7732 (m-80) REVERT: U 35 PRO cc_start: 0.8193 (Cg_endo) cc_final: 0.7872 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8242 (p90) cc_final: 0.7907 (p90) REVERT: U 129 ASP cc_start: 0.7269 (m-30) cc_final: 0.6747 (m-30) REVERT: E 164 TYR cc_start: 0.9117 (t80) cc_final: 0.8734 (t80) REVERT: D 54 LYS cc_start: 0.5137 (mmtt) cc_final: 0.3707 (mmtt) REVERT: X 18 ASN cc_start: 0.6195 (p0) cc_final: 0.5936 (p0) REVERT: X 63 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8118 (tp) REVERT: X 75 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8783 (tt) REVERT: X 95 GLN cc_start: 0.5178 (OUTLIER) cc_final: 0.4734 (tt0) REVERT: X 132 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6626 (m-80) REVERT: c 36 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6944 (mtt90) REVERT: c 71 MET cc_start: 0.7661 (tpp) cc_final: 0.6959 (ttm) REVERT: o 61 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8469 (pp) REVERT: o 212 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7138 (mp0) REVERT: o 216 LEU cc_start: 0.8457 (tt) cc_final: 0.8176 (tp) REVERT: q 14 TRP cc_start: 0.4983 (OUTLIER) cc_final: 0.4018 (m-90) REVERT: p 20 GLN cc_start: 0.7699 (mt0) cc_final: 0.7494 (mt0) REVERT: p 24 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.5701 (ptt90) REVERT: p 107 HIS cc_start: 0.3989 (m170) cc_final: 0.3785 (m170) REVERT: M 86 ILE cc_start: 0.7612 (pt) cc_final: 0.7192 (mt) REVERT: M 136 MET cc_start: 0.7675 (tpp) cc_final: 0.7404 (tpp) REVERT: M 184 MET cc_start: 0.8755 (tmm) cc_final: 0.8437 (tmm) REVERT: M 197 THR cc_start: 0.5024 (p) cc_final: 0.4808 (p) REVERT: M 328 ILE cc_start: 0.8396 (pt) cc_final: 0.7966 (mp) REVERT: M 432 LEU cc_start: 0.7236 (mp) cc_final: 0.7016 (mt) REVERT: f 40 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6515 (mp0) REVERT: f 54 LYS cc_start: 0.5939 (mttt) cc_final: 0.5284 (tmtt) REVERT: g 72 LEU cc_start: 0.8043 (mt) cc_final: 0.7795 (mt) REVERT: g 99 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7418 (mm-30) REVERT: a 69 MET cc_start: 0.3839 (mmp) cc_final: 0.3576 (mmp) REVERT: a 126 MET cc_start: 0.7743 (tmm) cc_final: 0.7378 (tmm) REVERT: a 137 PHE cc_start: 0.8155 (t80) cc_final: 0.7608 (t80) REVERT: a 145 LEU cc_start: 0.8697 (tp) cc_final: 0.8486 (tp) REVERT: a 186 PHE cc_start: 0.6331 (OUTLIER) cc_final: 0.5400 (t80) REVERT: a 278 TYR cc_start: 0.3151 (p90) cc_final: 0.2679 (p90) REVERT: a 318 GLN cc_start: 0.6709 (pm20) cc_final: 0.6377 (pm20) REVERT: a 349 PHE cc_start: 0.6004 (OUTLIER) cc_final: 0.4511 (m-80) REVERT: a 365 MET cc_start: -0.0547 (mmt) cc_final: -0.1044 (mmm) REVERT: a 392 PHE cc_start: 0.4329 (t80) cc_final: 0.3933 (t80) REVERT: a 463 MET cc_start: 0.7444 (mtm) cc_final: 0.7070 (mtp) REVERT: a 518 LYS cc_start: 0.2911 (tptt) cc_final: 0.1888 (mmtp) REVERT: m 15 LEU cc_start: 0.6193 (pt) cc_final: 0.4971 (tt) REVERT: m 16 MET cc_start: 0.5433 (mmp) cc_final: 0.5194 (mmm) REVERT: m 27 ARG cc_start: 0.6421 (mmp80) cc_final: 0.6142 (mmp80) REVERT: t 21 HIS cc_start: 0.4592 (OUTLIER) cc_final: 0.3293 (m-70) REVERT: t 23 MET cc_start: 0.1506 (tmm) cc_final: 0.1222 (ptm) outliers start: 290 outliers final: 229 residues processed: 1435 average time/residue: 0.5368 time to fit residues: 1325.5816 Evaluate side-chains 1455 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1208 time to evaluate : 5.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 310 MET Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain i residue 34 GLU Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 41 LEU Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 71 ASN Chi-restraints excluded: chain j residue 14 CYS Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain P residue 108 HIS Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 88 GLN Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 ASP Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 36 ARG Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 141 VAL Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain o residue 238 TYR Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain q residue 67 VAL Chi-restraints excluded: chain q residue 88 ASP Chi-restraints excluded: chain q residue 92 VAL Chi-restraints excluded: chain q residue 96 SER Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 210 LEU Chi-restraints excluded: chain q residue 218 ASN Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 46 MET Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 139 VAL Chi-restraints excluded: chain p residue 157 VAL Chi-restraints excluded: chain p residue 222 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 147 SER Chi-restraints excluded: chain a residue 165 ILE Chi-restraints excluded: chain a residue 170 VAL Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 296 LEU Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 338 LEU Chi-restraints excluded: chain a residue 349 PHE Chi-restraints excluded: chain a residue 542 PHE Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain m residue 54 TRP Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain t residue 21 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 420 optimal weight: 4.9990 chunk 677 optimal weight: 5.9990 chunk 413 optimal weight: 7.9990 chunk 321 optimal weight: 6.9990 chunk 470 optimal weight: 3.9990 chunk 710 optimal weight: 5.9990 chunk 653 optimal weight: 7.9990 chunk 565 optimal weight: 0.0980 chunk 58 optimal weight: 7.9990 chunk 436 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 ASN ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN U 88 GLN X 68 HIS ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 257 HIS a 337 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.246 59313 Z= 0.561 Angle : 1.657 50.933 80348 Z= 1.046 Chirality : 0.302 6.383 8969 Planarity : 0.006 0.104 10136 Dihedral : 8.747 171.491 8447 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.95 % Favored : 91.02 % Rotamer: Outliers : 4.43 % Allowed : 28.93 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.10), residues: 7252 helix: -0.00 (0.08), residues: 3662 sheet: -2.43 (0.28), residues: 331 loop : -2.15 (0.11), residues: 3259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP M 236 HIS 0.015 0.001 HIS p 130 PHE 0.065 0.003 PHE K 61 TYR 0.050 0.002 TYR H 147 ARG 0.014 0.001 ARG p 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14504 Ramachandran restraints generated. 7252 Oldfield, 0 Emsley, 7252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1246 time to evaluate : 5.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7170 (mmt) cc_final: 0.6838 (mmt) REVERT: I 139 MET cc_start: 0.7757 (ttm) cc_final: 0.7107 (ttm) REVERT: I 166 LYS cc_start: 0.6209 (tmtt) cc_final: 0.5612 (tmtt) REVERT: I 174 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6272 (tp30) REVERT: I 226 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8417 (mt) REVERT: I 264 PHE cc_start: 0.7634 (m-80) cc_final: 0.7412 (m-10) REVERT: I 272 SER cc_start: 0.8955 (t) cc_final: 0.7201 (t) REVERT: I 302 MET cc_start: 0.7318 (mpp) cc_final: 0.6241 (mpp) REVERT: I 345 LEU cc_start: 0.9149 (tt) cc_final: 0.8942 (tp) REVERT: I 395 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7802 (mmt) REVERT: N 148 TYR cc_start: 0.8684 (m-80) cc_final: 0.8119 (m-10) REVERT: N 163 MET cc_start: 0.7858 (mtt) cc_final: 0.7560 (mmm) REVERT: H 13 ILE cc_start: 0.8426 (mm) cc_final: 0.8077 (mt) REVERT: H 62 GLU cc_start: 0.8396 (mp0) cc_final: 0.7916 (mp0) REVERT: H 103 LEU cc_start: 0.8247 (tp) cc_final: 0.7885 (mm) REVERT: H 220 TYR cc_start: 0.5883 (m-80) cc_final: 0.5467 (m-80) REVERT: H 293 ASP cc_start: 0.7561 (m-30) cc_final: 0.7300 (m-30) REVERT: K 5 LYS cc_start: 0.7735 (tttt) cc_final: 0.7132 (mmtt) REVERT: Z 84 THR cc_start: 0.8693 (t) cc_final: 0.8398 (t) REVERT: Z 113 LYS cc_start: 0.7154 (mptt) cc_final: 0.6498 (mttt) REVERT: V 26 GLN cc_start: 0.8152 (pt0) cc_final: 0.7062 (pt0) REVERT: W 14 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6597 (mt-10) REVERT: W 20 SER cc_start: 0.9183 (m) cc_final: 0.8983 (m) REVERT: i 31 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6561 (p-80) REVERT: i 63 MET cc_start: 0.7583 (mtt) cc_final: 0.7354 (mpp) REVERT: j 59 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8033 (tptt) REVERT: j 71 LYS cc_start: 0.2849 (mttt) cc_final: 0.1895 (tppt) REVERT: G 72 TYR cc_start: 0.7405 (p90) cc_final: 0.7176 (p90) REVERT: G 223 MET cc_start: 0.8248 (mmm) cc_final: 0.7958 (tpp) REVERT: C 427 MET cc_start: 0.7273 (mmm) cc_final: 0.6360 (mtp) REVERT: C 705 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6565 (pp20) REVERT: T 87 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7994 (mm-40) REVERT: T 91 MET cc_start: 0.7873 (ppp) cc_final: 0.7649 (tmm) REVERT: T 119 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8729 (p) REVERT: T 163 ILE cc_start: 0.8114 (mm) cc_final: 0.7875 (mt) REVERT: T 369 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7097 (mtpp) REVERT: F 84 SER cc_start: 0.8999 (p) cc_final: 0.8752 (t) REVERT: O 65 GLN cc_start: 0.8390 (pt0) cc_final: 0.7834 (pt0) REVERT: P 57 ILE cc_start: 0.8983 (tp) cc_final: 0.8595 (tp) REVERT: P 99 TYR cc_start: 0.8209 (m-80) cc_final: 0.7788 (m-80) REVERT: U 35 PRO cc_start: 0.8246 (Cg_endo) cc_final: 0.7928 (Cg_exo) REVERT: U 75 TRP cc_start: 0.8252 (p90) cc_final: 0.7916 (p90) REVERT: U 129 ASP cc_start: 0.7206 (m-30) cc_final: 0.6672 (m-30) REVERT: E 164 TYR cc_start: 0.9137 (t80) cc_final: 0.8832 (t80) REVERT: D 54 LYS cc_start: 0.4995 (mmtt) cc_final: 0.3554 (mmtt) REVERT: X 18 ASN cc_start: 0.6216 (p0) cc_final: 0.5937 (p0) REVERT: X 63 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.7958 (tp) REVERT: X 75 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8838 (tt) REVERT: X 95 GLN cc_start: 0.5228 (OUTLIER) cc_final: 0.4724 (tt0) REVERT: X 132 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: c 36 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6944 (mtt90) REVERT: c 71 MET cc_start: 0.7695 (tpp) cc_final: 0.7020 (ttm) REVERT: o 61 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8553 (pp) REVERT: o 212 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7163 (mp0) REVERT: o 216 LEU cc_start: 0.8512 (tt) cc_final: 0.8249 (tp) REVERT: q 46 MET cc_start: 0.5347 (ptt) cc_final: 0.5031 (ptt) REVERT: p 20 GLN cc_start: 0.7605 (mt0) cc_final: 0.7379 (mt0) REVERT: p 24 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.5754 (ptt90) REVERT: p 80 TRP cc_start: 0.6229 (m100) cc_final: 0.5962 (m-10) REVERT: M 91 LEU cc_start: 0.8514 (tt) cc_final: 0.8296 (tp) REVERT: M 197 THR cc_start: 0.5188 (p) cc_final: 0.4931 (p) REVERT: M 328 ILE cc_start: 0.8375 (pt) cc_final: 0.7953 (mp) REVERT: f 54 LYS cc_start: 0.5902 (mttt) cc_final: 0.5197 (tmtt) REVERT: g 72 LEU cc_start: 0.8045 (mt) cc_final: 0.7800 (mt) REVERT: g 99 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7405 (mm-30) REVERT: a 126 MET cc_start: 0.7868 (tmm) cc_final: 0.7458 (tmm) REVERT: a 137 PHE cc_start: 0.8156 (t80) cc_final: 0.7525 (t80) REVERT: a 145 LEU cc_start: 0.8662 (tp) cc_final: 0.8456 (tp) REVERT: a 172 ARG cc_start: 0.7711 (mmm160) cc_final: 0.7329 (mmm160) REVERT: a 186 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5532 (t80) REVERT: a 278 TYR cc_start: 0.3179 (p90) cc_final: 0.2698 (p90) REVERT: a 318 GLN cc_start: 0.6695 (pm20) cc_final: 0.6292 (pm20) REVERT: a 349 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.4662 (m-80) REVERT: a 365 MET cc_start: -0.0512 (mmt) cc_final: -0.1034 (mmm) REVERT: a 392 PHE cc_start: 0.4358 (t80) cc_final: 0.3962 (t80) REVERT: a 463 MET cc_start: 0.7474 (mtm) cc_final: 0.6932 (mtp) REVERT: m 15 LEU cc_start: 0.6248 (pt) cc_final: 0.5078 (tp) REVERT: m 16 MET cc_start: 0.5404 (mmp) cc_final: 0.5112 (mmm) REVERT: t 21 HIS cc_start: 0.4605 (OUTLIER) cc_final: 0.3272 (m-70) outliers start: 269 outliers final: 230 residues processed: 1412 average time/residue: 0.5364 time to fit residues: 1300.5301 Evaluate side-chains 1454 residues out of total 6221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1209 time to evaluate : 5.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 143 TYR Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 232 PHE Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain I residue 310 MET Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 369 THR Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 467 LEU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain I residue 489 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain N residue 72 PHE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 290 TYR Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 99 PHE Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 34 GLU Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 41 LEU Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 71 ASN Chi-restraints excluded: chain j residue 14 CYS Chi-restraints excluded: chain j residue 28 CYS Chi-restraints excluded: chain j residue 34 CYS Chi-restraints excluded: chain j residue 36 LEU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 145 ILE Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 207 VAL Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 369 LYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 58 SER Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 80 SER Chi-restraints excluded: chain U residue 88 GLN Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 149 ARG Chi-restraints excluded: chain U residue 152 SER Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 ASP Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 36 ARG Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain k residue 105 ILE Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain o residue 51 ASP Chi-restraints excluded: chain o residue 61 LEU Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 107 VAL Chi-restraints excluded: chain o residue 141 VAL Chi-restraints excluded: chain o residue 150 CYS Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain q residue 67 VAL Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 134 LEU Chi-restraints excluded: chain q residue 135 HIS Chi-restraints excluded: chain q residue 137 CYS Chi-restraints excluded: chain q residue 138 THR Chi-restraints excluded: chain q residue 210 LEU Chi-restraints excluded: chain q residue 218 ASN Chi-restraints excluded: chain q residue 222 LEU Chi-restraints excluded: chain q residue 229 LYS Chi-restraints excluded: chain p residue 13 PHE Chi-restraints excluded: chain p residue 24 ARG Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 46 MET Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 122 ILE Chi-restraints excluded: chain p residue 134 LEU Chi-restraints excluded: chain p residue 139 VAL Chi-restraints excluded: chain p residue 157 VAL Chi-restraints excluded: chain p residue 222 LEU Chi-restraints excluded: chain p residue 227 PHE Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 336 LEU Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 44 HIS Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 97 HIS Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 147 SER Chi-restraints excluded: chain a residue 165 ILE Chi-restraints excluded: chain a residue 170 VAL Chi-restraints excluded: chain a residue 176 PHE Chi-restraints excluded: chain a residue 186 PHE Chi-restraints excluded: chain a residue 296 LEU Chi-restraints excluded: chain a residue 338 LEU Chi-restraints excluded: chain a residue 349 PHE Chi-restraints excluded: chain a residue 519 LEU Chi-restraints excluded: chain a residue 542 PHE Chi-restraints excluded: chain a residue 563 TRP Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain m residue 54 TRP Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain t residue 21 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 713 random chunks: chunk 449 optimal weight: 4.9990 chunk 602 optimal weight: 0.3980 chunk 173 optimal weight: 0.9990 chunk 521 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 566 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 581 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 GLN X 68 HIS ** c 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 HIS ** q 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 HIS ** a 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 337 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.140328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116993 restraints weight = 138100.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.118213 restraints weight = 78648.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.118574 restraints weight = 50291.183| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.255 59313 Z= 0.515 Angle : 1.641 50.794 80348 Z= 1.037 Chirality : 0.301 6.368 8969 Planarity : 0.005 0.077 10136 Dihedral : 8.541 166.353 8447 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.41 % Favored : 91.56 % Rotamer: Outliers : 3.91 % Allowed : 29.95 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.10), residues: 7252 helix: 0.11 (0.09), residues: 3656 sheet: -2.26 (0.28), residues: 334 loop : -2.11 (0.11), residues: 3262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP M 236 HIS 0.021 0.001 HIS a 152 PHE 0.048 0.002 PHE K 61 TYR 0.044 0.002 TYR H 147 ARG 0.013 0.001 ARG c 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20468.88 seconds wall clock time: 353 minutes 6.47 seconds (21186.47 seconds total)