Starting phenix.real_space_refine on Tue Sep 24 10:05:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/09_2024/7a24_11615.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/09_2024/7a24_11615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/09_2024/7a24_11615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/09_2024/7a24_11615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/09_2024/7a24_11615.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/09_2024/7a24_11615.cif" } resolution = 3.8 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= -0.001 sd= 0.004 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 9 5.49 5 S 333 5.16 5 C 31709 2.51 5 N 8398 2.21 5 O 9018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 258 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49497 Number of models: 1 Model: "" Number of chains: 46 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: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 492 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} 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: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 977 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} 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: "z" Number of atoms: 3992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3992 Classifications: {'peptide': 499} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 469} Chain breaks: 1 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 15 Chain: "i" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 90 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 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: "c" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 13 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2707 SG CYS A 405 55.416 63.028 195.115 1.00 18.90 S ATOM 2727 SG CYS A 408 53.525 66.702 198.356 1.00 17.31 S ATOM 2688 SG CYS A 402 59.327 62.879 201.104 1.00 21.30 S ATOM 3052 SG CYS A 448 53.121 60.273 200.857 1.00 20.05 S ATOM 20774 SG CYS C 179 66.327 70.547 179.591 1.00 15.05 S ATOM 20713 SG CYS C 170 64.164 77.175 179.247 1.00 22.03 S ATOM 20734 SG CYS C 173 70.389 74.847 180.959 1.00 22.61 S ATOM 21102 SG CYS C 221 66.705 64.532 188.387 1.00 19.30 S ATOM 21079 SG CYS C 218 68.231 70.226 191.267 1.00 13.72 S ATOM 21126 SG CYS C 224 72.613 65.536 191.082 1.00 14.17 S ATOM 21447 SG CYS C 268 71.604 67.807 186.059 1.00 19.62 S ATOM 20229 SG CYS C 106 62.805 60.249 188.379 1.00 16.72 S ATOM 20313 SG CYS C 117 59.862 62.005 187.449 1.00 18.39 S ATOM 20440 SG CYS C 134 60.216 55.596 187.846 1.00 21.47 S ATOM 29937 SG CYS B 130 50.395 73.868 216.095 1.00 36.50 S ATOM 29968 SG CYS B 135 48.062 75.165 218.311 1.00 40.45 S ATOM 30241 SG CYS B 171 49.330 68.060 214.837 1.00 39.22 S ATOM 30265 SG CYS B 175 46.526 68.868 216.940 1.00 41.46 S ATOM 31987 SG CYS P 72 67.614 91.605 186.884 1.00 28.54 S ATOM 32173 SG CYS P 97 69.508 88.711 185.761 1.00 25.54 S ATOM 34990 SG CYS E 158 69.341 86.839 147.125 1.00 22.55 S ATOM 34490 SG CYS E 94 66.483 93.425 146.428 1.00 17.23 S ATOM 34484 SG CYS E 93 63.712 89.502 144.692 1.00 18.81 S ATOM 35220 SG CYS E 188 66.213 89.968 151.271 1.00 26.47 S ATOM 36455 SG CYS D 165 64.769 86.643 158.604 1.00 19.17 S ATOM 36429 SG CYS D 162 70.698 89.876 157.681 1.00 11.81 S ATOM 36476 SG CYS D 168 68.042 89.242 163.389 1.00 21.11 S ATOM 36197 SG CYS D 133 70.671 84.229 159.641 1.00 27.13 S ATOM 36505 SG CYS D 172 67.374 88.704 172.130 1.00 21.71 S ATOM 36170 SG CYS D 129 71.211 85.500 167.444 1.00 38.74 S ATOM 36128 SG CYS D 123 74.345 88.110 172.053 1.00 25.74 S ATOM 36147 SG CYS D 126 69.779 83.011 172.986 1.00 18.74 S Time building chain proxies: 21.09, per 1000 atoms: 0.43 Number of scatterers: 49497 At special positions: 0 Unit cell: (136.53, 184.26, 250.86, 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 333 16.00 P 9 15.00 O 9018 8.00 N 8398 7.00 C 31709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 53 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.95 Conformation dependent library (CDL) restraints added in 4.8 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 " 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11584 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 53 sheets defined 47.0% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 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: 3.674A 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: 4.472A 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 53 through 72 removed outlier: 3.861A pdb=" N LEU I 57 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU I 59 " --> pdb=" O GLY I 55 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL I 62 " --> pdb=" O GLY I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 77 removed outlier: 4.135A pdb=" N THR I 77 " --> pdb=" O PRO I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 86 Processing helix chain 'I' and resid 90 through 118 removed outlier: 4.631A pdb=" N ASP I 113 " --> pdb=" O SER I 109 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE I 114 " --> pdb=" O MET I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 142 removed outlier: 3.997A pdb=" N ILE I 126 " --> pdb=" O ALA I 122 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL I 127 " --> pdb=" O PHE I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 164 Processing helix chain 'I' and resid 169 through 202 removed outlier: 3.749A pdb=" N THR I 173 " --> pdb=" O SER I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 214 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 Proline residue: I 269 - end of helix removed outlier: 3.763A pdb=" N TYR I 283 " --> pdb=" O ARG I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 312 removed outlier: 3.583A pdb=" N PHE I 294 " --> pdb=" O LEU I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 336 removed outlier: 4.077A pdb=" N GLY I 333 " --> pdb=" O TYR I 329 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE I 334 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 366 Processing helix chain 'I' and resid 373 through 378 Processing helix chain 'I' and resid 384 through 400 removed outlier: 3.556A pdb=" N TYR I 398 " --> pdb=" O THR I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 421 removed outlier: 3.725A pdb=" N CYS I 408 " --> pdb=" O LEU I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 422 through 448 removed outlier: 3.814A pdb=" N TYR I 439 " --> pdb=" O ILE I 435 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 479 removed outlier: 3.752A pdb=" N PHE I 475 " --> pdb=" O MET I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 497 removed outlier: 3.673A pdb=" N PHE I 487 " --> pdb=" O PRO I 483 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU I 497 " --> pdb=" O MET I 493 " (cutoff:3.500A) 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: 3.616A 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: 4.080A pdb=" N TYR H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 162 removed outlier: 3.764A 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: 3.526A 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: 4.095A 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: 3.578A 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 70 Processing helix chain 'Y' and resid 71 through 85 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: 3.650A pdb=" N GLN Y 96 " --> pdb=" O CYS Y 92 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS Y 103 " --> pdb=" O PHE Y 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 112 removed outlier: 3.698A pdb=" N ALA Z 58 " --> pdb=" O SER Z 54 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N MET Z 61 " --> pdb=" O PHE Z 57 " (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: 3.705A pdb=" N LEU V 19 " --> pdb=" O ILE V 15 " (cutoff:3.500A) removed outlier: 3.867A 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: 3.503A 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 18 Processing helix chain 'i' and resid 35 through 69 Processing helix chain 'j' and resid 14 through 24 Processing helix chain 'j' and resid 30 through 47 removed outlier: 5.081A pdb=" N LEU j 36 " --> pdb=" O LYS j 32 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU j 37 " --> pdb=" O ASP j 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG j 38 " --> pdb=" O CYS j 34 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 71 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: 4.086A 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: 4.369A pdb=" N GLN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.795A 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: 3.781A 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: 3.758A 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: 3.898A 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: 4.114A 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: 3.524A 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: 4.520A 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: 3.576A 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: 4.021A 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: 4.165A 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: 3.773A 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: 3.889A 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: 3.582A 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: 3.687A 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: 3.596A 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 69 Processing helix chain 'D' and resid 73 through 89 removed outlier: 3.600A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) 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: 3.749A 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: 3.567A 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 52 removed outlier: 3.598A pdb=" N THR c 41 " --> pdb=" O PHE c 37 " (cutoff:3.500A) 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: 5.553A 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 81 through 102 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 25 removed outlier: 3.697A pdb=" N LEU p 22 " --> pdb=" O THR p 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU p 25 " --> pdb=" O ALA p 21 " (cutoff:3.500A) Processing helix chain 'p' and resid 33 through 37 Processing helix chain 'p' and resid 193 through 213 removed outlier: 3.595A 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 'z' and resid 131 through 144 Processing helix chain 'z' and resid 171 through 177 Processing helix chain 'z' and resid 194 through 205 Processing helix chain 'z' and resid 219 through 226 Processing helix chain 'z' and resid 237 through 242 Processing helix chain 'z' and resid 262 through 272 Processing helix chain 'z' and resid 301 through 316 removed outlier: 4.614A pdb=" N LYS z 309 " --> pdb=" O LYS z 305 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS z 310 " --> pdb=" O LYS z 306 " (cutoff:3.500A) Processing helix chain 'z' and resid 389 through 402 Processing helix chain 'z' and resid 407 through 424 removed outlier: 4.491A pdb=" N ALA z 411 " --> pdb=" O ASP z 407 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS z 412 " --> pdb=" O VAL z 408 " (cutoff:3.500A) Processing helix chain 'z' and resid 456 through 461 removed outlier: 4.146A pdb=" N SER z 460 " --> pdb=" O LEU z 456 " (cutoff:3.500A) Processing helix chain 'z' and resid 462 through 477 Processing helix chain 'z' and resid 524 through 537 Processing helix chain 'z' and resid 544 through 549 removed outlier: 4.396A pdb=" N PHE z 548 " --> pdb=" O LEU z 544 " (cutoff:3.500A) Processing helix chain 'z' and resid 566 through 571 Processing helix chain 'z' and resid 571 through 577 Processing helix chain 'z' and resid 579 through 590 Processing helix chain 'z' and resid 597 through 604 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: 6.612A 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: 6.699A 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: 6.332A 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: 3.783A pdb=" N ARG S 85 " --> pdb=" O GLU R 121 " (cutoff:3.500A) removed outlier: 6.005A 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: 3.571A pdb=" N THR G 327 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 3.695A 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: 6.497A pdb=" N ARG C 308 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 5.916A 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: 6.945A pdb=" N LEU C 485 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 7.293A 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: 5.758A pdb=" N LEU C 441 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASN C 551 " --> pdb=" O PRO C 512 " (cutoff:3.500A) removed outlier: 5.588A 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: 6.195A 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: 7.229A pdb=" N LEU T 310 " --> pdb=" O LEU T 243 " (cutoff:3.500A) removed outlier: 7.190A 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: 6.438A pdb=" N LEU B 127 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 7.173A 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: 3.631A 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: 6.414A 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) Processing sheet with id=AF3, first strand: chain 'z' and resid 149 through 151 Processing sheet with id=AF4, first strand: chain 'z' and resid 178 through 181 removed outlier: 7.158A pdb=" N VAL z 279 " --> pdb=" O VAL z 248 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL z 248 " --> pdb=" O VAL z 279 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU z 281 " --> pdb=" O LYS z 246 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU z 247 " --> pdb=" O ILE z 255 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'z' and resid 207 through 208 Processing sheet with id=AF6, first strand: chain 'z' and resid 328 through 337 removed outlier: 4.565A pdb=" N GLU z 291 " --> pdb=" O VAL z 337 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG z 428 " --> pdb=" O GLU z 294 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'z' and resid 319 through 322 removed outlier: 3.507A pdb=" N GLU z 486 " --> pdb=" O GLY z 513 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'z' and resid 449 through 450 2038 hydrogen bonds defined for protein. 5874 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: 16.86 Time building geometry restraints manager: 11.70 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: 19992 1.39 - 1.61: 30086 1.61 - 1.84: 485 1.84 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 50643 Sorted by residual: bond pdb=" N PRO E 186 " pdb=" CD PRO E 186 " ideal model delta sigma weight residual 1.473 1.332 0.141 1.40e-02 5.10e+03 1.02e+02 bond pdb=" C PRO H 288 " pdb=" O PRO H 288 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.18e-02 7.18e+03 3.95e+01 bond pdb=" CA SER c 44 " pdb=" CB SER c 44 " ideal model delta sigma weight residual 1.532 1.443 0.089 1.53e-02 4.27e+03 3.39e+01 bond pdb=" O2B NDP T 501 " pdb=" P2B NDP T 501 " ideal model delta sigma weight residual 1.833 1.615 0.218 3.80e-02 6.93e+02 3.30e+01 bond pdb=" CA SER H 307 " pdb=" CB SER H 307 " ideal model delta sigma weight residual 1.532 1.452 0.079 1.57e-02 4.06e+03 2.56e+01 ... (remaining 50638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.86: 68258 4.86 - 9.72: 330 9.72 - 14.57: 25 14.57 - 19.43: 5 19.43 - 24.29: 1 Bond angle restraints: 68619 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 89.96 14.37 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 107.74 132.03 -24.29 1.95e+00 2.62e-01 1.55e+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 89.44 14.89 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 68614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 29481 33.06 - 66.13: 799 66.13 - 99.19: 55 99.19 - 132.25: 5 132.25 - 165.32: 4 Dihedral angle restraints: 30344 sinusoidal: 12325 harmonic: 18019 Sorted by residual: 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 -145.35 22.75 0 2.50e+00 1.60e-01 8.28e+01 dihedral pdb=" CB CYS Q 19 " pdb=" SG CYS Q 19 " pdb=" SG CYS Q 53 " pdb=" CB CYS Q 53 " ideal model delta sinusoidal sigma weight residual -86.00 -158.53 72.53 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS Y 81 " pdb=" SG CYS Y 81 " pdb=" SG CYS Y 92 " pdb=" CB CYS Y 92 " ideal model delta sinusoidal sigma weight residual 93.00 162.31 -69.31 1 1.00e+01 1.00e-02 6.21e+01 ... (remaining 30341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.236: 7592 4.236 - 8.472: 0 8.472 - 12.707: 0 12.707 - 16.943: 0 16.943 - 21.179: 20 Chirality restraints: 7612 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 -10.62 21.18 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 -21.00 2.00e-01 2.50e+01 1.10e+04 ... (remaining 7609 not shown) Planarity restraints: 8730 Sorted by residual: 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=" CA VAL R 119 " 0.021 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C VAL R 119 " -0.076 2.00e-02 2.50e+03 pdb=" O VAL R 119 " 0.029 2.00e-02 2.50e+03 pdb=" N ILE R 120 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP T 501 " 0.025 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C5N NDP T 501 " -0.054 2.00e-02 2.50e+03 pdb=" C6N NDP T 501 " 0.056 2.00e-02 2.50e+03 pdb=" N1N NDP T 501 " -0.027 2.00e-02 2.50e+03 ... (remaining 8727 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.66: 5 1.66 - 2.47: 324 2.47 - 3.28: 59561 3.28 - 4.09: 131233 4.09 - 4.90: 246460 Warning: very small nonbonded interaction distances. Nonbonded interactions: 437583 Sorted by model distance: nonbonded pdb=" C GLN z 128 " pdb=" OD1 ASN z 170 " model vdw 0.850 3.270 nonbonded pdb=" O GLN z 128 " pdb=" OD1 ASN z 170 " model vdw 0.903 3.040 nonbonded pdb=" N PRO z 129 " pdb=" OD1 ASN z 170 " model vdw 1.415 3.120 nonbonded pdb=" O GLN z 128 " pdb=" CG ASN z 170 " model vdw 1.482 3.270 nonbonded pdb=" C GLN z 128 " pdb=" CG ASN z 170 " model vdw 1.509 3.500 ... (remaining 437578 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' 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: 1.970 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: 0.040 Extract box with map and model: 1.360 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 102.760 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.200 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4708 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 : 0.009 0.218 50643 Z= 0.589 Angle : 1.160 24.289 68619 Z= 0.815 Chirality : 1.077 21.179 7612 Planarity : 0.006 0.114 8730 Dihedral : 15.349 165.318 18742 Min Nonbonded Distance : 0.850 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.57 % Favored : 90.09 % Rotamer: Outliers : 2.62 % Allowed : 10.02 % Favored : 87.35 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.10 (0.10), residues: 6177 helix: -1.03 (0.09), residues: 2799 sheet: -2.76 (0.27), residues: 338 loop : -3.05 (0.10), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 106 HIS 0.012 0.001 HIS q 107 PHE 0.032 0.002 PHE D 185 TYR 0.024 0.002 TYR G 72 ARG 0.008 0.001 ARG S 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1863 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1724 time to evaluate : 4.156 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: A 182 ARG cc_start: 0.6297 (ttt180) cc_final: 0.6092 (ttp80) REVERT: A 360 MET cc_start: 0.5068 (mmm) cc_final: 0.4208 (mtp) REVERT: I 148 MET cc_start: 0.7615 (ttp) cc_final: 0.7394 (ptm) REVERT: I 181 ILE cc_start: 0.7778 (mt) cc_final: 0.7401 (tp) REVERT: I 209 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6769 (tt) REVERT: I 214 THR cc_start: 0.5371 (OUTLIER) cc_final: 0.5061 (p) REVERT: I 272 SER cc_start: 0.8425 (t) cc_final: 0.6690 (p) REVERT: I 290 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7765 (pt) REVERT: I 292 GLN cc_start: 0.3426 (mm110) cc_final: 0.2971 (mp10) REVERT: I 438 PHE cc_start: 0.3036 (OUTLIER) cc_final: 0.1782 (t80) REVERT: J 2 MET cc_start: 0.1852 (tmm) cc_final: 0.1112 (ttt) REVERT: J 105 ILE cc_start: 0.8901 (mm) cc_final: 0.8657 (mt) REVERT: J 116 LEU cc_start: 0.7812 (mt) cc_final: 0.7157 (mt) REVERT: N 22 ASN cc_start: 0.5679 (t0) cc_final: 0.5423 (t0) REVERT: N 126 VAL cc_start: 0.5921 (p) cc_final: 0.5392 (p) REVERT: H 62 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7164 (mt-10) REVERT: H 229 PHE cc_start: 0.5449 (m-80) cc_final: 0.5051 (m-10) REVERT: V 10 LEU cc_start: 0.4333 (tp) cc_final: 0.4074 (mt) REVERT: S 70 ILE cc_start: 0.6539 (pt) cc_final: 0.5979 (pt) REVERT: S 84 ILE cc_start: 0.6421 (mp) cc_final: 0.5834 (mm) REVERT: S 100 GLU cc_start: 0.7931 (tt0) cc_final: 0.7385 (tm-30) REVERT: i 66 LYS cc_start: 0.6440 (ttpp) cc_final: 0.6234 (tttm) REVERT: G 198 ILE cc_start: 0.5575 (mt) cc_final: 0.4809 (mt) REVERT: G 257 CYS cc_start: 0.6806 (m) cc_final: 0.6560 (m) REVERT: C 74 ILE cc_start: 0.4162 (mt) cc_final: 0.3733 (mt) REVERT: C 83 VAL cc_start: 0.4399 (m) cc_final: 0.4063 (m) REVERT: C 270 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.6970 (t) REVERT: C 478 PHE cc_start: 0.7264 (m-80) cc_final: 0.7018 (m-10) REVERT: C 719 VAL cc_start: 0.7690 (t) cc_final: 0.7130 (t) REVERT: T 170 VAL cc_start: 0.5696 (m) cc_final: 0.5373 (p) REVERT: F 75 TYR cc_start: 0.6767 (m-80) cc_final: 0.6378 (m-80) REVERT: F 179 ASP cc_start: 0.7265 (t0) cc_final: 0.7050 (t70) REVERT: B 53 ASN cc_start: 0.3607 (m-40) cc_final: 0.3058 (m-40) REVERT: R 132 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6377 (tm-30) REVERT: E 89 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.6990 (t80) REVERT: E 188 CYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7401 (t) REVERT: D 90 PRO cc_start: 0.0109 (Cg_exo) cc_final: -0.0173 (Cg_endo) REVERT: D 201 LEU cc_start: 0.6201 (mt) cc_final: 0.5848 (mt) REVERT: c 47 VAL cc_start: 0.7539 (t) cc_final: 0.7332 (t) REVERT: k 83 VAL cc_start: 0.4949 (t) cc_final: 0.4586 (t) REVERT: o 184 PRO cc_start: 0.6887 (Cg_exo) cc_final: 0.6432 (Cg_endo) REVERT: q 13 PHE cc_start: 0.5593 (m-80) cc_final: 0.5293 (m-10) REVERT: q 16 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.5342 (tpp80) REVERT: q 57 LYS cc_start: 0.4498 (mmtt) cc_final: 0.4103 (ttmm) REVERT: q 66 SER cc_start: 0.6514 (m) cc_final: 0.5298 (t) REVERT: q 94 VAL cc_start: 0.6623 (t) cc_final: 0.6392 (t) REVERT: p 13 PHE cc_start: 0.5159 (m-80) cc_final: 0.4926 (m-80) REVERT: p 14 TRP cc_start: 0.6339 (m-10) cc_final: 0.5596 (t60) REVERT: p 50 ASP cc_start: 0.3564 (m-30) cc_final: 0.3242 (m-30) REVERT: z 107 GLU cc_start: 0.5305 (OUTLIER) cc_final: 0.4961 (mm-30) REVERT: z 182 LYS cc_start: 0.1143 (OUTLIER) cc_final: 0.0568 (pttt) REVERT: z 183 GLU cc_start: 0.1968 (tt0) cc_final: 0.1630 (mt-10) REVERT: z 370 TYR cc_start: 0.3185 (t80) cc_final: 0.2300 (t80) REVERT: z 381 ASP cc_start: 0.2280 (t0) cc_final: 0.1762 (t0) REVERT: z 385 PRO cc_start: 0.0011 (Cg_endo) cc_final: -0.0859 (Cg_exo) REVERT: z 510 SER cc_start: 0.1151 (OUTLIER) cc_final: 0.0377 (p) REVERT: z 546 ASP cc_start: 0.3749 (t0) cc_final: 0.2438 (t0) outliers start: 139 outliers final: 38 residues processed: 1829 average time/residue: 0.5409 time to fit residues: 1595.3142 Evaluate side-chains 995 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 945 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 155 GLN Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 438 PHE Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 39 MET Chi-restraints excluded: chain i residue 50 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 46 HIS Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain R residue 132 GLN Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain q residue 16 ARG Chi-restraints excluded: chain z residue 107 GLU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 170 ASN Chi-restraints excluded: chain z residue 182 LYS Chi-restraints excluded: chain z residue 249 THR Chi-restraints excluded: chain z residue 317 HIS Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 387 ILE Chi-restraints excluded: chain z residue 403 ASP Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 510 SER Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 513 optimal weight: 5.9990 chunk 460 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 310 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 476 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 354 optimal weight: 0.6980 chunk 552 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS I 117 GLN I 208 GLN ** I 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 GLN I 384 ASN N 25 HIS N 73 HIS H 104 ASN K 27 ASN ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 HIS Y 87 ASN Z 63 GLN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN V 34 HIS V 39 HIS V 42 HIS S 77 GLN ** i 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 HIS ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 HIS G 277 GLN G 364 GLN ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 479 ASN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 ASN ** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 GLN C 606 HIS C 716 GLN T 143 ASN T 182 GLN T 209 ASN T 254 GLN T 291 HIS F 54 GLN ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 HIS O 77 ASN P 77 ASN P 92 ASN U 46 ASN U 85 ASN U 134 HIS E 121 GLN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN E 166 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 62 GLN ** c 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN o 55 GLN o 103 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 33 ASN q 72 HIS q 99 ASN ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 135 HIS ** q 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 218 ASN p 30 GLN p 42 HIS p 72 HIS p 135 HIS ** p 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 241 GLN z 388 GLN z 415 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5390 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.284 50643 Z= 0.604 Angle : 1.793 52.058 68619 Z= 1.134 Chirality : 0.332 7.035 7612 Planarity : 0.007 0.115 8730 Dihedral : 9.621 171.936 7110 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.84 % Favored : 92.07 % Rotamer: Outliers : 5.27 % Allowed : 17.80 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.57 (0.10), residues: 6177 helix: -0.74 (0.09), residues: 2829 sheet: -2.54 (0.26), residues: 368 loop : -2.59 (0.10), residues: 2980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 44 HIS 0.028 0.003 HIS G 154 PHE 0.036 0.003 PHE I 39 TYR 0.030 0.003 TYR O 57 ARG 0.015 0.001 ARG B 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1058 time to evaluate : 4.274 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: A 360 MET cc_start: 0.5986 (mmm) cc_final: 0.4956 (mtp) REVERT: I 131 LEU cc_start: 0.9013 (mt) cc_final: 0.8761 (mt) REVERT: I 148 MET cc_start: 0.7250 (ttp) cc_final: 0.6770 (ttp) REVERT: I 181 ILE cc_start: 0.7674 (mt) cc_final: 0.7199 (tp) REVERT: I 209 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.6973 (tt) REVERT: I 214 THR cc_start: 0.5135 (OUTLIER) cc_final: 0.4909 (p) REVERT: I 290 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7605 (pt) REVERT: I 401 ILE cc_start: 0.7340 (mm) cc_final: 0.6878 (tp) REVERT: I 411 PHE cc_start: 0.5763 (OUTLIER) cc_final: 0.4655 (t80) REVERT: I 438 PHE cc_start: 0.3078 (OUTLIER) cc_final: 0.2046 (t80) REVERT: I 471 MET cc_start: 0.5961 (mtm) cc_final: 0.5674 (mtp) REVERT: J 2 MET cc_start: 0.1803 (tmm) cc_final: 0.0702 (ttt) REVERT: N 126 VAL cc_start: 0.6643 (OUTLIER) cc_final: 0.6289 (p) REVERT: H 13 ILE cc_start: 0.5621 (OUTLIER) cc_final: 0.5292 (mt) REVERT: H 76 MET cc_start: 0.5419 (ppp) cc_final: 0.5078 (tmm) REVERT: H 211 GLU cc_start: 0.6455 (mm-30) cc_final: 0.6221 (mm-30) REVERT: K 44 SER cc_start: 0.7393 (OUTLIER) cc_final: 0.7020 (t) REVERT: S 100 GLU cc_start: 0.7944 (tt0) cc_final: 0.7556 (tm-30) REVERT: i 18 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6829 (ttm) REVERT: i 19 TYR cc_start: 0.4164 (OUTLIER) cc_final: 0.3092 (p90) REVERT: i 29 MET cc_start: 0.5725 (ppp) cc_final: 0.5514 (ppp) REVERT: j 23 GLU cc_start: 0.5881 (tm-30) cc_final: 0.5482 (tm-30) REVERT: j 25 MET cc_start: 0.7679 (tpp) cc_final: 0.7312 (tpp) REVERT: G 206 ILE cc_start: 0.7864 (mm) cc_final: 0.7597 (mm) REVERT: G 310 ILE cc_start: 0.5708 (OUTLIER) cc_final: 0.5442 (mt) REVERT: G 363 LEU cc_start: 0.9243 (tp) cc_final: 0.8994 (tp) REVERT: C 168 LEU cc_start: 0.5755 (mp) cc_final: 0.5527 (mp) REVERT: C 186 MET cc_start: 0.6559 (tmm) cc_final: 0.6337 (tmm) REVERT: C 327 TRP cc_start: 0.7262 (m100) cc_final: 0.6996 (m100) REVERT: C 587 ASP cc_start: 0.3920 (m-30) cc_final: 0.3495 (t0) REVERT: T 170 VAL cc_start: 0.5617 (m) cc_final: 0.5387 (p) REVERT: F 18 TRP cc_start: 0.6334 (m-10) cc_final: 0.5898 (m-10) REVERT: F 35 THR cc_start: 0.5954 (p) cc_final: 0.5702 (t) REVERT: F 111 TRP cc_start: 0.7545 (m100) cc_final: 0.6736 (m100) REVERT: F 131 ARG cc_start: 0.4440 (OUTLIER) cc_final: 0.4147 (mmt90) REVERT: F 179 ASP cc_start: 0.7384 (t0) cc_final: 0.7115 (t70) REVERT: R 76 MET cc_start: 0.6246 (mtp) cc_final: 0.5928 (ttm) REVERT: E 87 MET cc_start: 0.8233 (tmm) cc_final: 0.7690 (tmm) REVERT: E 93 CYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7884 (p) REVERT: E 121 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: D 167 PHE cc_start: 0.6953 (m-10) cc_final: 0.6654 (m-80) REVERT: o 172 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7293 (p) REVERT: o 246 LYS cc_start: 0.5660 (mmpt) cc_final: 0.4958 (mmtm) REVERT: q 16 ARG cc_start: 0.6428 (OUTLIER) cc_final: 0.6153 (mmp80) REVERT: q 57 LYS cc_start: 0.4396 (mmtt) cc_final: 0.3889 (ttmm) REVERT: q 141 ASP cc_start: 0.4702 (t0) cc_final: 0.4398 (m-30) REVERT: q 191 LYS cc_start: 0.4837 (tptp) cc_final: 0.4062 (mmtm) REVERT: p 14 TRP cc_start: 0.5852 (m-10) cc_final: 0.5246 (t60) REVERT: z 182 LYS cc_start: 0.0726 (OUTLIER) cc_final: 0.0044 (pttt) REVERT: z 415 GLN cc_start: 0.6416 (mm110) cc_final: 0.5465 (tt0) REVERT: z 570 GLN cc_start: 0.0309 (OUTLIER) cc_final: -0.0180 (mt0) REVERT: z 599 MET cc_start: 0.0311 (mpp) cc_final: -0.0057 (mmt) outliers start: 279 outliers final: 137 residues processed: 1238 average time/residue: 0.5090 time to fit residues: 1060.7468 Evaluate side-chains 993 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 838 time to evaluate : 4.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 247 HIS Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 438 PHE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 236 MET Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Y residue 19 THR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain S residue 34 GLU Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 35 HIS Chi-restraints excluded: chain i residue 39 MET Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 157 PHE Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 310 ILE Chi-restraints excluded: chain G residue 347 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 654 TRP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 215 THR Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 93 CYS Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain c residue 41 THR Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain n residue 94 VAL Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 146 LEU Chi-restraints excluded: chain o residue 172 THR Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 16 ARG Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain q residue 201 SER Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 182 LYS Chi-restraints excluded: chain z residue 317 HIS Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 337 VAL Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 540 THR Chi-restraints excluded: chain z residue 570 GLN Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 306 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 459 optimal weight: 0.3980 chunk 375 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 553 optimal weight: 20.0000 chunk 597 optimal weight: 20.0000 chunk 492 optimal weight: 0.0060 chunk 548 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 443 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 ASN H 104 ASN ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 HIS Y 72 GLN Z 90 GLN ** i 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 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** C 165 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 GLN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 GLN C 484 HIS ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 83 GLN B 84 ASN O 49 HIS ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 ASN ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 184 ASN ** q 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 30 GLN p 209 ASN ** p 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 128 GLN z 190 GLN z 357 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5329 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.271 50643 Z= 0.569 Angle : 1.722 50.778 68619 Z= 1.102 Chirality : 0.328 6.424 7612 Planarity : 0.005 0.068 8730 Dihedral : 8.634 176.438 7073 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.43 % Favored : 92.47 % Rotamer: Outliers : 4.29 % Allowed : 20.46 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.15 (0.10), residues: 6177 helix: -0.34 (0.09), residues: 2822 sheet: -2.48 (0.23), residues: 441 loop : -2.39 (0.11), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 19 HIS 0.013 0.001 HIS U 138 PHE 0.044 0.002 PHE D 183 TYR 0.034 0.002 TYR c 49 ARG 0.010 0.001 ARG Q 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 952 time to evaluate : 4.152 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: I 68 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7036 (mt) REVERT: I 131 LEU cc_start: 0.8937 (mt) cc_final: 0.8683 (mt) REVERT: I 209 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7096 (tt) REVERT: I 272 SER cc_start: 0.8703 (p) cc_final: 0.8183 (p) REVERT: I 290 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7659 (pt) REVERT: I 401 ILE cc_start: 0.6715 (mm) cc_final: 0.6447 (tp) REVERT: I 411 PHE cc_start: 0.5752 (OUTLIER) cc_final: 0.4807 (t80) REVERT: J 2 MET cc_start: 0.1603 (tmm) cc_final: 0.0728 (ttt) REVERT: J 116 LEU cc_start: 0.6795 (mp) cc_final: 0.6562 (mp) REVERT: N 126 VAL cc_start: 0.6961 (OUTLIER) cc_final: 0.6616 (p) REVERT: H 27 GLU cc_start: 0.5992 (mt-10) cc_final: 0.5238 (mt-10) REVERT: H 76 MET cc_start: 0.5399 (ppp) cc_final: 0.4963 (tmm) REVERT: S 100 GLU cc_start: 0.7768 (tt0) cc_final: 0.7398 (tm-30) REVERT: i 19 TYR cc_start: 0.3887 (OUTLIER) cc_final: 0.3084 (p90) REVERT: i 29 MET cc_start: 0.5701 (ppp) cc_final: 0.5187 (ppp) REVERT: i 66 LYS cc_start: 0.7210 (pptt) cc_final: 0.6940 (ptpp) REVERT: j 25 MET cc_start: 0.7332 (tpp) cc_final: 0.7035 (tpp) REVERT: j 29 ARG cc_start: 0.5172 (mmt180) cc_final: 0.4544 (mmm-85) REVERT: G 257 CYS cc_start: 0.7728 (m) cc_final: 0.7436 (m) REVERT: G 363 LEU cc_start: 0.9088 (tp) cc_final: 0.8678 (tp) REVERT: G 366 LEU cc_start: 0.8531 (tp) cc_final: 0.8315 (tt) REVERT: G 369 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7298 (ttm) REVERT: C 484 HIS cc_start: 0.6162 (OUTLIER) cc_final: 0.3614 (t-90) REVERT: C 742 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5767 (mp) REVERT: T 297 MET cc_start: 0.5268 (ttt) cc_final: 0.5012 (ttt) REVERT: T 325 MET cc_start: 0.2153 (mmt) cc_final: 0.1197 (mmm) REVERT: T 344 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.5504 (mm) REVERT: F 111 TRP cc_start: 0.7684 (m100) cc_final: 0.6975 (m100) REVERT: F 179 ASP cc_start: 0.7387 (t0) cc_final: 0.7117 (t70) REVERT: B 180 MET cc_start: 0.5097 (tmm) cc_final: 0.4476 (tmm) REVERT: B 211 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5238 (tp30) REVERT: R 132 GLN cc_start: 0.6345 (OUTLIER) cc_final: 0.5966 (tm-30) REVERT: D 78 ARG cc_start: 0.5816 (mmt180) cc_final: 0.5598 (mmp-170) REVERT: X 41 MET cc_start: 0.6026 (mtp) cc_final: 0.5772 (mtp) REVERT: X 96 ARG cc_start: 0.6540 (ttp80) cc_final: 0.6065 (ptt-90) REVERT: c 62 MET cc_start: 0.4224 (ttp) cc_final: 0.3706 (tmm) REVERT: Q 18 LEU cc_start: 0.5097 (pp) cc_final: 0.4794 (pp) REVERT: Q 66 MET cc_start: 0.4338 (tpp) cc_final: 0.3849 (tpp) REVERT: o 172 THR cc_start: 0.7560 (p) cc_final: 0.7276 (p) REVERT: o 246 LYS cc_start: 0.5418 (mmpt) cc_final: 0.4794 (mmtm) REVERT: q 16 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5949 (mmp80) REVERT: q 57 LYS cc_start: 0.4237 (mmtt) cc_final: 0.3708 (ttmm) REVERT: q 191 LYS cc_start: 0.4950 (tptp) cc_final: 0.4664 (tptp) REVERT: p 14 TRP cc_start: 0.5597 (m-10) cc_final: 0.5097 (t60) REVERT: p 199 PHE cc_start: 0.4760 (t80) cc_final: 0.4432 (t80) REVERT: z 182 LYS cc_start: 0.1079 (OUTLIER) cc_final: 0.0592 (pttt) REVERT: z 260 GLU cc_start: 0.4862 (tm-30) cc_final: 0.4418 (mp0) REVERT: z 415 GLN cc_start: 0.6610 (mm110) cc_final: 0.5648 (tt0) REVERT: z 516 MET cc_start: 0.0697 (ppp) cc_final: 0.0134 (pmm) REVERT: z 570 GLN cc_start: 0.0489 (OUTLIER) cc_final: -0.0069 (mt0) REVERT: z 599 MET cc_start: 0.0684 (mpp) cc_final: 0.0468 (mmt) outliers start: 227 outliers final: 112 residues processed: 1103 average time/residue: 0.5034 time to fit residues: 943.7237 Evaluate side-chains 927 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 800 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 117 GLN Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 415 PHE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 455 TRP Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 34 GLU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain S residue 73 HIS Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 369 MET Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 268 CYS Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 484 HIS Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 344 ILE Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain R residue 132 GLN Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 240 GLU Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 8 PHE Chi-restraints excluded: chain q residue 14 TRP Chi-restraints excluded: chain q residue 16 ARG Chi-restraints excluded: chain q residue 40 SER Chi-restraints excluded: chain q residue 100 ILE Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 182 LYS Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 255 ILE Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 570 GLN Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 546 optimal weight: 20.0000 chunk 415 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 263 optimal weight: 9.9990 chunk 371 optimal weight: 1.9990 chunk 555 optimal weight: 8.9990 chunk 587 optimal weight: 0.0770 chunk 290 optimal weight: 7.9990 chunk 526 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 overall best weight: 3.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 33 ASN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 373 HIS ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN U 41 GLN ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 212 GLN ** p 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 119 HIS z 357 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.257 50643 Z= 0.597 Angle : 1.745 51.149 68619 Z= 1.112 Chirality : 0.328 6.473 7612 Planarity : 0.006 0.058 8730 Dihedral : 8.510 178.570 7058 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.11 % Favored : 91.81 % Rotamer: Outliers : 5.51 % Allowed : 21.26 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.32 % Twisted General : 0.02 % 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: -2.07 (0.10), residues: 6177 helix: -0.31 (0.10), residues: 2787 sheet: -2.29 (0.25), residues: 393 loop : -2.32 (0.11), residues: 2997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP K 19 HIS 0.042 0.002 HIS C 484 PHE 0.038 0.003 PHE D 183 TYR 0.030 0.003 TYR T 180 ARG 0.018 0.001 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 875 time to evaluate : 4.263 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 172 MET cc_start: 0.4970 (tmm) cc_final: 0.4469 (ttt) REVERT: A 218 VAL cc_start: 0.7400 (OUTLIER) cc_final: 0.7199 (t) REVERT: A 315 MET cc_start: 0.5649 (mpp) cc_final: 0.5386 (mpp) REVERT: I 181 ILE cc_start: 0.7761 (pt) cc_final: 0.7507 (tp) REVERT: I 209 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7050 (tt) REVERT: I 214 THR cc_start: 0.5033 (OUTLIER) cc_final: 0.4803 (p) REVERT: I 290 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7640 (pt) REVERT: J 2 MET cc_start: 0.1786 (tmm) cc_final: 0.1343 (ttt) REVERT: J 8 ILE cc_start: 0.3779 (pt) cc_final: 0.3425 (tt) REVERT: J 10 ILE cc_start: 0.4779 (tt) cc_final: 0.4459 (mt) REVERT: J 85 LEU cc_start: 0.6608 (mt) cc_final: 0.6371 (mt) REVERT: H 13 ILE cc_start: 0.6252 (OUTLIER) cc_final: 0.5946 (mt) REVERT: H 76 MET cc_start: 0.5644 (ppp) cc_final: 0.5163 (tmm) REVERT: H 293 ASP cc_start: 0.7968 (t0) cc_final: 0.7086 (t0) REVERT: Z 49 MET cc_start: 0.2041 (tpp) cc_final: 0.1543 (tpp) REVERT: S 100 GLU cc_start: 0.7896 (tt0) cc_final: 0.7541 (tm-30) REVERT: S 114 LEU cc_start: 0.4158 (mt) cc_final: 0.3948 (tt) REVERT: i 19 TYR cc_start: 0.4394 (OUTLIER) cc_final: 0.3611 (p90) REVERT: i 66 LYS cc_start: 0.7396 (pptt) cc_final: 0.7103 (ptpt) REVERT: j 25 MET cc_start: 0.7568 (tpp) cc_final: 0.7097 (tpp) REVERT: G 14 ASN cc_start: 0.7878 (m-40) cc_final: 0.7526 (t0) REVERT: G 203 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7994 (mp) REVERT: G 257 CYS cc_start: 0.7762 (m) cc_final: 0.7522 (m) REVERT: G 282 MET cc_start: 0.3871 (ppp) cc_final: 0.3623 (ppp) REVERT: G 363 LEU cc_start: 0.9077 (tp) cc_final: 0.8787 (tp) REVERT: G 388 VAL cc_start: 0.7501 (t) cc_final: 0.7233 (m) REVERT: C 150 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6540 (tp) REVERT: C 195 PHE cc_start: 0.5559 (t80) cc_final: 0.5121 (t80) REVERT: C 205 LYS cc_start: 0.6404 (mptt) cc_final: 0.5981 (mttt) REVERT: C 326 GLU cc_start: 0.6505 (mp0) cc_final: 0.6257 (mp0) REVERT: C 458 ILE cc_start: 0.7973 (mm) cc_final: 0.7752 (mm) REVERT: C 484 HIS cc_start: 0.5763 (OUTLIER) cc_final: 0.5110 (t-170) REVERT: C 742 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6145 (mp) REVERT: T 325 MET cc_start: 0.2593 (mmt) cc_final: 0.2185 (mmt) REVERT: T 344 ILE cc_start: 0.6240 (OUTLIER) cc_final: 0.5770 (mt) REVERT: T 378 LEU cc_start: 0.7365 (mt) cc_final: 0.7149 (mt) REVERT: F 106 PRO cc_start: 0.8063 (Cg_exo) cc_final: 0.7780 (Cg_endo) REVERT: F 179 ASP cc_start: 0.7473 (t0) cc_final: 0.7239 (t70) REVERT: B 211 GLU cc_start: 0.5719 (OUTLIER) cc_final: 0.4938 (tp30) REVERT: P 100 CYS cc_start: 0.5157 (t) cc_final: 0.4705 (t) REVERT: U 100 ILE cc_start: 0.4899 (OUTLIER) cc_final: 0.4442 (pt) REVERT: E 87 MET cc_start: 0.8073 (tmm) cc_final: 0.7856 (tmm) REVERT: E 212 PHE cc_start: 0.4468 (t80) cc_final: 0.4052 (t80) REVERT: D 76 MET cc_start: 0.5809 (mpp) cc_final: 0.5339 (mtm) REVERT: X 96 ARG cc_start: 0.6909 (ttp80) cc_final: 0.6114 (ptt-90) REVERT: k 116 TYR cc_start: 0.4487 (t80) cc_final: 0.3929 (t80) REVERT: o 172 THR cc_start: 0.7710 (p) cc_final: 0.7433 (p) REVERT: o 246 LYS cc_start: 0.5715 (mmpt) cc_final: 0.5100 (mmtm) REVERT: q 16 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5966 (mmp80) REVERT: q 57 LYS cc_start: 0.4203 (mmtt) cc_final: 0.3388 (ttmm) REVERT: z 182 LYS cc_start: 0.0843 (OUTLIER) cc_final: 0.0373 (pttt) REVERT: z 370 TYR cc_start: 0.2475 (t80) cc_final: 0.1783 (t80) REVERT: z 415 GLN cc_start: 0.6473 (mm110) cc_final: 0.5546 (tt0) REVERT: z 516 MET cc_start: 0.0740 (ppp) cc_final: 0.0316 (pmm) REVERT: z 570 GLN cc_start: 0.0566 (OUTLIER) cc_final: 0.0043 (mt0) outliers start: 292 outliers final: 172 residues processed: 1074 average time/residue: 0.4873 time to fit residues: 894.3897 Evaluate side-chains 970 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 782 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 247 HIS Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 455 TRP Chi-restraints excluded: chain I residue 459 GLU Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 190 PHE Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 15 VAL Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 34 GLU Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 484 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 64 SER Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 282 LEU Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 344 ILE Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain c residue 41 THR Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 97 VAL Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 8 PHE Chi-restraints excluded: chain q residue 10 SER Chi-restraints excluded: chain q residue 16 ARG Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 145 ILE Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 192 LEU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 182 LYS Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 570 GLN Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 489 optimal weight: 5.9990 chunk 333 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 437 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 501 optimal weight: 10.0000 chunk 406 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 300 optimal weight: 10.0000 chunk 527 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS I 53 ASN I 326 HIS J 32 ASN H 104 ASN H 294 GLN ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 10 ASN Y 72 GLN Z 68 ASN W 13 GLN i 35 HIS ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 108 HIS T 160 ASN ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN U 63 GLN ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 HIS ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 212 GLN ** z 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.252 50643 Z= 0.583 Angle : 1.731 51.060 68619 Z= 1.105 Chirality : 0.327 6.446 7612 Planarity : 0.005 0.064 8730 Dihedral : 8.305 176.437 7056 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.48 % Favored : 92.44 % Rotamer: Outliers : 5.17 % Allowed : 22.64 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.32 % Twisted General : 0.00 % 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: -1.95 (0.10), residues: 6177 helix: -0.21 (0.10), residues: 2779 sheet: -2.23 (0.24), residues: 423 loop : -2.23 (0.11), residues: 2975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 216 HIS 0.019 0.002 HIS G 154 PHE 0.041 0.002 PHE C 334 TYR 0.025 0.002 TYR E 164 ARG 0.015 0.001 ARG X 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 860 time to evaluate : 4.201 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 181 ILE cc_start: 0.7601 (pt) cc_final: 0.7388 (tp) REVERT: I 209 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.6994 (tt) REVERT: I 272 SER cc_start: 0.8770 (p) cc_final: 0.8461 (p) REVERT: I 290 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7598 (pt) REVERT: I 411 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.4891 (t80) REVERT: J 8 ILE cc_start: 0.3101 (pt) cc_final: 0.2900 (tt) REVERT: J 10 ILE cc_start: 0.5180 (tt) cc_final: 0.4860 (mt) REVERT: H 76 MET cc_start: 0.5908 (ppp) cc_final: 0.5433 (tmm) REVERT: H 289 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6301 (mtp85) REVERT: Z 49 MET cc_start: 0.2232 (tpp) cc_final: 0.1920 (tpp) REVERT: Z 100 GLU cc_start: 0.5808 (mm-30) cc_final: 0.5478 (mt-10) REVERT: S 100 GLU cc_start: 0.8147 (tt0) cc_final: 0.7492 (tm-30) REVERT: i 19 TYR cc_start: 0.4373 (OUTLIER) cc_final: 0.3512 (p90) REVERT: j 25 MET cc_start: 0.7596 (tpp) cc_final: 0.7231 (tpp) REVERT: G 14 ASN cc_start: 0.7926 (m-40) cc_final: 0.7587 (t0) REVERT: G 203 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8083 (mp) REVERT: G 363 LEU cc_start: 0.9002 (tp) cc_final: 0.8783 (tp) REVERT: C 81 TYR cc_start: 0.4868 (m-80) cc_final: 0.4525 (m-10) REVERT: C 164 MET cc_start: 0.5080 (tmm) cc_final: 0.4663 (tmm) REVERT: C 742 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6185 (mp) REVERT: T 325 MET cc_start: 0.2448 (mmt) cc_final: 0.2029 (mmt) REVERT: T 344 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5558 (mt) REVERT: F 106 PRO cc_start: 0.8193 (Cg_exo) cc_final: 0.7951 (Cg_endo) REVERT: F 179 ASP cc_start: 0.7561 (t0) cc_final: 0.7327 (t70) REVERT: B 211 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5225 (tp30) REVERT: U 100 ILE cc_start: 0.4465 (OUTLIER) cc_final: 0.4088 (pt) REVERT: D 80 LEU cc_start: 0.6697 (mt) cc_final: 0.5912 (tp) REVERT: X 96 ARG cc_start: 0.6672 (ttp80) cc_final: 0.5978 (ptt-90) REVERT: c 49 TYR cc_start: 0.5226 (t80) cc_final: 0.4837 (t80) REVERT: k 116 TYR cc_start: 0.4489 (t80) cc_final: 0.3918 (t80) REVERT: o 172 THR cc_start: 0.7903 (p) cc_final: 0.7641 (p) REVERT: o 246 LYS cc_start: 0.5685 (mmpt) cc_final: 0.4997 (mmtm) REVERT: q 16 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.6072 (mmp80) REVERT: q 57 LYS cc_start: 0.4212 (mmtt) cc_final: 0.3228 (ttmm) REVERT: z 182 LYS cc_start: 0.0729 (OUTLIER) cc_final: 0.0212 (pttt) REVERT: z 183 GLU cc_start: 0.1117 (OUTLIER) cc_final: -0.0464 (tp30) REVERT: z 205 TYR cc_start: 0.2410 (m-10) cc_final: 0.1884 (m-10) REVERT: z 245 MET cc_start: 0.2730 (ppp) cc_final: 0.2318 (ppp) REVERT: z 370 TYR cc_start: 0.2491 (t80) cc_final: 0.1794 (t80) REVERT: z 415 GLN cc_start: 0.6615 (mm110) cc_final: 0.5668 (tt0) REVERT: z 516 MET cc_start: 0.0677 (ppp) cc_final: 0.0312 (pmm) REVERT: z 570 GLN cc_start: 0.0546 (OUTLIER) cc_final: -0.0003 (mt0) outliers start: 274 outliers final: 171 residues processed: 1051 average time/residue: 0.4896 time to fit residues: 879.8789 Evaluate side-chains 957 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 772 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 326 HIS Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 63 MET Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain T residue 282 LEU Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 344 ILE Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 41 THR Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain n residue 94 VAL Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 8 PHE Chi-restraints excluded: chain q residue 10 SER Chi-restraints excluded: chain q residue 16 ARG Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 106 VAL Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 192 LEU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 182 LYS Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 231 THR Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 570 GLN Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 197 optimal weight: 9.9990 chunk 529 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 345 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 588 optimal weight: 4.9990 chunk 488 optimal weight: 30.0000 chunk 272 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 308 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN W 13 GLN ** S 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 HIS G 48 HIS ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 HIS C 726 ASN ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 ASN ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 ** p 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 212 GLN ** z 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 388 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.254 50643 Z= 0.605 Angle : 1.748 51.031 68619 Z= 1.114 Chirality : 0.327 6.458 7612 Planarity : 0.006 0.113 8730 Dihedral : 8.356 176.744 7050 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 25.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.56 % Favored : 91.36 % Rotamer: Outliers : 5.61 % Allowed : 23.39 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.65 % Twisted General : 0.00 % 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: -2.07 (0.10), residues: 6177 helix: -0.40 (0.09), residues: 2797 sheet: -2.27 (0.25), residues: 404 loop : -2.22 (0.11), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP E 216 HIS 0.064 0.002 HIS I 326 PHE 0.040 0.003 PHE c 29 TYR 0.028 0.002 TYR S 72 ARG 0.031 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 841 time to evaluate : 5.559 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 354 ILE cc_start: 0.4098 (OUTLIER) cc_final: 0.3431 (tp) REVERT: A 417 MET cc_start: 0.3177 (mmm) cc_final: 0.2283 (ptm) REVERT: I 209 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7041 (tt) REVERT: I 214 THR cc_start: 0.5071 (OUTLIER) cc_final: 0.4821 (p) REVERT: I 290 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7614 (pt) REVERT: J 8 ILE cc_start: 0.2987 (pt) cc_final: 0.2724 (tt) REVERT: N 171 MET cc_start: 0.5583 (tpp) cc_final: 0.5218 (tpp) REVERT: H 13 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6429 (mt) REVERT: H 76 MET cc_start: 0.6097 (ppp) cc_final: 0.5684 (tmm) REVERT: H 289 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6459 (mtp85) REVERT: S 100 GLU cc_start: 0.8277 (tt0) cc_final: 0.7624 (tm-30) REVERT: i 19 TYR cc_start: 0.4607 (OUTLIER) cc_final: 0.3643 (p90) REVERT: j 25 MET cc_start: 0.7812 (tpp) cc_final: 0.7366 (tpp) REVERT: G 14 ASN cc_start: 0.8046 (m-40) cc_final: 0.7650 (t0) REVERT: G 363 LEU cc_start: 0.8980 (tp) cc_final: 0.8602 (tp) REVERT: C 81 TYR cc_start: 0.4797 (m-80) cc_final: 0.4555 (m-10) REVERT: C 205 LYS cc_start: 0.7631 (mmtt) cc_final: 0.6130 (mmtp) REVERT: C 484 HIS cc_start: 0.5883 (OUTLIER) cc_final: 0.4553 (t70) REVERT: C 742 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6291 (mp) REVERT: T 121 MET cc_start: 0.2890 (tpp) cc_final: 0.2620 (mmm) REVERT: T 325 MET cc_start: 0.2215 (mmt) cc_final: 0.1782 (mmt) REVERT: F 106 PRO cc_start: 0.8243 (Cg_exo) cc_final: 0.8042 (Cg_endo) REVERT: F 179 ASP cc_start: 0.7633 (t0) cc_final: 0.7402 (t70) REVERT: B 181 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6901 (pt) REVERT: B 211 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.5078 (tp30) REVERT: O 64 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7680 (t) REVERT: P 54 MET cc_start: 0.7116 (tpp) cc_final: 0.6233 (tpt) REVERT: U 100 ILE cc_start: 0.4335 (OUTLIER) cc_final: 0.3914 (pt) REVERT: D 114 ARG cc_start: 0.5522 (mtp180) cc_final: 0.5302 (mmm160) REVERT: X 96 ARG cc_start: 0.6699 (ttp80) cc_final: 0.6017 (ptt-90) REVERT: Q 79 GLU cc_start: 0.3015 (tm-30) cc_final: 0.2312 (mp0) REVERT: k 116 TYR cc_start: 0.4555 (t80) cc_final: 0.3847 (t80) REVERT: o 172 THR cc_start: 0.8132 (p) cc_final: 0.7768 (p) REVERT: o 246 LYS cc_start: 0.5808 (mmpt) cc_final: 0.5072 (mmtm) REVERT: q 57 LYS cc_start: 0.4114 (mmtt) cc_final: 0.2928 (ttmm) REVERT: z 182 LYS cc_start: 0.0842 (OUTLIER) cc_final: 0.0303 (pttt) REVERT: z 205 TYR cc_start: 0.2523 (m-10) cc_final: 0.2016 (m-10) REVERT: z 245 MET cc_start: 0.2750 (ppp) cc_final: 0.2288 (ppp) REVERT: z 415 GLN cc_start: 0.6455 (mm110) cc_final: 0.5526 (tt0) REVERT: z 516 MET cc_start: 0.0823 (ppp) cc_final: 0.0400 (pmm) REVERT: z 570 GLN cc_start: 0.0701 (OUTLIER) cc_final: 0.0172 (mt0) outliers start: 297 outliers final: 212 residues processed: 1047 average time/residue: 0.4801 time to fit residues: 864.5956 Evaluate side-chains 993 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 766 time to evaluate : 4.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 241 ILE Chi-restraints excluded: chain I residue 247 HIS Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain I residue 459 GLU Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain Y residue 85 TYR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 63 MET Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 268 MET Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 484 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 737 GLN Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 83 TYR Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 190 VAL Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain T residue 282 LEU Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 41 THR Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain k residue 87 MET Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain n residue 94 VAL Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 133 THR Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 10 SER Chi-restraints excluded: chain q residue 102 ASP Chi-restraints excluded: chain q residue 106 VAL Chi-restraints excluded: chain q residue 147 MET Chi-restraints excluded: chain q residue 175 ILE Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 192 LEU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 182 LYS Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 393 THR Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 429 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 570 GLN Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 567 optimal weight: 30.0000 chunk 66 optimal weight: 0.5980 chunk 335 optimal weight: 6.9990 chunk 429 optimal weight: 0.8980 chunk 332 optimal weight: 8.9990 chunk 495 optimal weight: 10.0000 chunk 328 optimal weight: 1.9990 chunk 586 optimal weight: 8.9990 chunk 366 optimal weight: 2.9990 chunk 357 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 464 ASN ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 13 GLN S 73 HIS ** G 23 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** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 HIS ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 77 ASN ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 212 GLN z 110 HIS z 317 HIS z 388 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.253 50643 Z= 0.569 Angle : 1.725 50.779 68619 Z= 1.101 Chirality : 0.326 6.383 7612 Planarity : 0.005 0.061 8730 Dihedral : 8.095 174.683 7046 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.40 % Favored : 92.52 % Rotamer: Outliers : 4.76 % Allowed : 24.73 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.65 % Twisted General : 0.02 % 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: -1.85 (0.10), residues: 6177 helix: -0.19 (0.10), residues: 2790 sheet: -2.01 (0.25), residues: 398 loop : -2.16 (0.11), residues: 2989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP E 216 HIS 0.027 0.001 HIS C 484 PHE 0.029 0.002 PHE R 60 TYR 0.027 0.002 TYR I 352 ARG 0.009 0.001 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 845 time to evaluate : 4.192 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 172 MET cc_start: 0.5113 (ttp) cc_final: 0.4809 (ttt) REVERT: A 417 MET cc_start: 0.2745 (mmm) cc_final: 0.1986 (ptm) REVERT: I 209 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7009 (tt) REVERT: I 214 THR cc_start: 0.4887 (OUTLIER) cc_final: 0.4605 (p) REVERT: I 272 SER cc_start: 0.8572 (p) cc_final: 0.8108 (p) REVERT: I 290 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7634 (pt) REVERT: I 411 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.4745 (t80) REVERT: J 8 ILE cc_start: 0.2974 (OUTLIER) cc_final: 0.2515 (tt) REVERT: N 171 MET cc_start: 0.5382 (tpp) cc_final: 0.4966 (tpp) REVERT: H 74 PHE cc_start: 0.4007 (p90) cc_final: 0.3597 (p90) REVERT: H 76 MET cc_start: 0.6137 (ppp) cc_final: 0.5689 (tmm) REVERT: H 144 MET cc_start: 0.7604 (mmm) cc_final: 0.7271 (mmm) REVERT: H 289 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6368 (mtp85) REVERT: S 100 GLU cc_start: 0.7943 (tt0) cc_final: 0.7337 (pt0) REVERT: i 19 TYR cc_start: 0.4373 (OUTLIER) cc_final: 0.2800 (p90) REVERT: j 25 MET cc_start: 0.7741 (tpp) cc_final: 0.7273 (tpp) REVERT: G 14 ASN cc_start: 0.8040 (m-40) cc_final: 0.7703 (t0) REVERT: G 44 ILE cc_start: 0.7146 (mm) cc_final: 0.6808 (mm) REVERT: G 251 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7592 (t) REVERT: C 53 ILE cc_start: 0.6564 (mm) cc_final: 0.5875 (mt) REVERT: C 205 LYS cc_start: 0.7307 (mmtt) cc_final: 0.5607 (mttt) REVERT: C 373 HIS cc_start: 0.3836 (OUTLIER) cc_final: 0.3525 (m-70) REVERT: C 742 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6220 (mp) REVERT: T 180 TYR cc_start: 0.3864 (OUTLIER) cc_final: 0.2906 (t80) REVERT: T 325 MET cc_start: 0.2329 (mmt) cc_final: 0.1999 (mmt) REVERT: F 106 PRO cc_start: 0.8413 (Cg_exo) cc_final: 0.8178 (Cg_endo) REVERT: F 116 TRP cc_start: 0.7627 (t60) cc_final: 0.7003 (t60) REVERT: F 179 ASP cc_start: 0.7628 (t0) cc_final: 0.7387 (t70) REVERT: B 132 THR cc_start: 0.5461 (OUTLIER) cc_final: 0.5043 (m) REVERT: O 64 THR cc_start: 0.8020 (p) cc_final: 0.7635 (t) REVERT: P 54 MET cc_start: 0.7005 (tpp) cc_final: 0.6140 (tpt) REVERT: R 132 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6487 (tm-30) REVERT: U 100 ILE cc_start: 0.3996 (OUTLIER) cc_final: 0.3722 (pt) REVERT: E 216 TRP cc_start: 0.3316 (m-10) cc_final: 0.2483 (p-90) REVERT: X 96 ARG cc_start: 0.6452 (ttp80) cc_final: 0.5920 (ptt-90) REVERT: c 94 GLU cc_start: 0.4217 (tp30) cc_final: 0.3973 (mt-10) REVERT: Q 71 CYS cc_start: 0.5257 (OUTLIER) cc_final: 0.4941 (t) REVERT: Q 79 GLU cc_start: 0.3001 (tm-30) cc_final: 0.2267 (mp0) REVERT: k 116 TYR cc_start: 0.4455 (t80) cc_final: 0.3797 (t80) REVERT: k 118 HIS cc_start: 0.3932 (t-90) cc_final: 0.3622 (t70) REVERT: o 105 ILE cc_start: 0.6092 (mm) cc_final: 0.5772 (mm) REVERT: o 172 THR cc_start: 0.8218 (p) cc_final: 0.7846 (p) REVERT: o 246 LYS cc_start: 0.5883 (mmpt) cc_final: 0.5116 (mmtm) REVERT: q 57 LYS cc_start: 0.4056 (mmtt) cc_final: 0.2931 (ttmm) REVERT: p 199 PHE cc_start: 0.4697 (t80) cc_final: 0.4475 (t80) REVERT: z 205 TYR cc_start: 0.2251 (m-10) cc_final: 0.1839 (m-10) REVERT: z 245 MET cc_start: 0.2756 (ppp) cc_final: 0.2263 (ppp) REVERT: z 415 GLN cc_start: 0.6481 (mm110) cc_final: 0.5512 (tt0) REVERT: z 516 MET cc_start: 0.0802 (ppp) cc_final: 0.0382 (pmm) REVERT: z 570 GLN cc_start: 0.0690 (OUTLIER) cc_final: 0.0165 (mt0) outliers start: 252 outliers final: 182 residues processed: 1016 average time/residue: 0.4768 time to fit residues: 831.1074 Evaluate side-chains 970 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 772 time to evaluate : 4.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 459 GLU Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 63 MET Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 373 HIS Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 TYR Chi-restraints excluded: chain T residue 282 LEU Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 298 TYR Chi-restraints excluded: chain T residue 300 MET Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 132 GLN Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain k residue 87 MET Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 80 LEU Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 10 SER Chi-restraints excluded: chain q residue 106 VAL Chi-restraints excluded: chain q residue 147 MET Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 142 GLU Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain p residue 192 LEU Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 429 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 570 GLN Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 362 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 349 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 372 optimal weight: 7.9990 chunk 399 optimal weight: 0.7980 chunk 289 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 460 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 13 GLN S 73 HIS ** G 23 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 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 HIS C 686 ASN ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 ASN U 85 ASN ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 ASN D 182 ASN ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 212 GLN z 388 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.7115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.250 50643 Z= 0.568 Angle : 1.726 50.858 68619 Z= 1.102 Chirality : 0.326 6.398 7612 Planarity : 0.005 0.083 8730 Dihedral : 7.953 176.686 7041 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.92 % Favored : 92.00 % Rotamer: Outliers : 4.70 % Allowed : 25.75 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.65 % Twisted General : 0.02 % 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: -1.77 (0.10), residues: 6177 helix: -0.13 (0.10), residues: 2791 sheet: -2.11 (0.25), residues: 394 loop : -2.08 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP E 216 HIS 0.034 0.002 HIS C 373 PHE 0.030 0.002 PHE E 212 TYR 0.027 0.002 TYR I 352 ARG 0.013 0.001 ARG o 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 829 time to evaluate : 4.218 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: A 417 MET cc_start: 0.3022 (mmm) cc_final: 0.2343 (ptm) REVERT: I 110 MET cc_start: 0.7623 (mmp) cc_final: 0.6849 (mmm) REVERT: I 209 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.6990 (tt) REVERT: I 214 THR cc_start: 0.4891 (OUTLIER) cc_final: 0.4622 (p) REVERT: I 290 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7591 (pt) REVERT: J 8 ILE cc_start: 0.2736 (OUTLIER) cc_final: 0.2477 (tt) REVERT: J 76 THR cc_start: 0.8704 (p) cc_final: 0.8438 (p) REVERT: H 13 ILE cc_start: 0.6246 (OUTLIER) cc_final: 0.5881 (mt) REVERT: H 74 PHE cc_start: 0.4194 (p90) cc_final: 0.3646 (p90) REVERT: H 76 MET cc_start: 0.5873 (ppp) cc_final: 0.5458 (tmm) REVERT: H 289 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6366 (mtp85) REVERT: V 26 GLN cc_start: 0.5368 (mm-40) cc_final: 0.4677 (mp10) REVERT: S 100 GLU cc_start: 0.7904 (tt0) cc_final: 0.7370 (tm-30) REVERT: i 19 TYR cc_start: 0.4208 (OUTLIER) cc_final: 0.3004 (p90) REVERT: j 25 MET cc_start: 0.7790 (tpp) cc_final: 0.7461 (tpp) REVERT: G 14 ASN cc_start: 0.8086 (m-40) cc_final: 0.7781 (t0) REVERT: G 28 LEU cc_start: 0.8651 (tp) cc_final: 0.8439 (pt) REVERT: G 44 ILE cc_start: 0.7200 (mm) cc_final: 0.6745 (mm) REVERT: G 251 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7658 (t) REVERT: C 53 ILE cc_start: 0.6683 (mm) cc_final: 0.6062 (mt) REVERT: C 83 VAL cc_start: 0.5647 (m) cc_final: 0.5430 (m) REVERT: C 205 LYS cc_start: 0.7212 (mmtt) cc_final: 0.5550 (mttm) REVERT: C 484 HIS cc_start: 0.5591 (OUTLIER) cc_final: 0.4822 (t70) REVERT: C 632 ASN cc_start: 0.6428 (p0) cc_final: 0.6211 (p0) REVERT: C 742 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6215 (mp) REVERT: T 180 TYR cc_start: 0.3973 (OUTLIER) cc_final: 0.2926 (t80) REVERT: T 300 MET cc_start: 0.3889 (OUTLIER) cc_final: 0.3648 (tmm) REVERT: T 325 MET cc_start: 0.2409 (mmt) cc_final: 0.1996 (mmt) REVERT: F 57 ILE cc_start: 0.6356 (mm) cc_final: 0.5896 (mm) REVERT: F 106 PRO cc_start: 0.8400 (Cg_exo) cc_final: 0.8163 (Cg_endo) REVERT: F 116 TRP cc_start: 0.7667 (t60) cc_final: 0.7065 (t60) REVERT: F 179 ASP cc_start: 0.7606 (t0) cc_final: 0.7369 (t70) REVERT: B 132 THR cc_start: 0.5263 (OUTLIER) cc_final: 0.4846 (m) REVERT: O 64 THR cc_start: 0.7946 (p) cc_final: 0.7564 (t) REVERT: O 89 MET cc_start: 0.2905 (tpp) cc_final: 0.2416 (tpp) REVERT: P 54 MET cc_start: 0.7073 (tpp) cc_final: 0.6204 (tpt) REVERT: R 132 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: U 59 ASN cc_start: 0.2295 (OUTLIER) cc_final: 0.1648 (m-40) REVERT: U 100 ILE cc_start: 0.3933 (OUTLIER) cc_final: 0.3636 (pt) REVERT: U 122 GLU cc_start: 0.5006 (tp30) cc_final: 0.4798 (tm-30) REVERT: E 87 MET cc_start: 0.8097 (tmm) cc_final: 0.7699 (tmm) REVERT: E 120 ARG cc_start: 0.6407 (mmt180) cc_final: 0.5124 (mtt90) REVERT: E 193 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6006 (tm-30) REVERT: D 52 LEU cc_start: 0.8022 (tt) cc_final: 0.7692 (mm) REVERT: D 80 LEU cc_start: 0.6830 (mt) cc_final: 0.6333 (tp) REVERT: X 96 ARG cc_start: 0.6413 (ttp80) cc_final: 0.5886 (ptt-90) REVERT: c 94 GLU cc_start: 0.4470 (tp30) cc_final: 0.4100 (mt-10) REVERT: Q 71 CYS cc_start: 0.5357 (OUTLIER) cc_final: 0.4840 (t) REVERT: Q 79 GLU cc_start: 0.3014 (tm-30) cc_final: 0.2333 (mp0) REVERT: k 116 TYR cc_start: 0.4672 (t80) cc_final: 0.3950 (t80) REVERT: k 118 HIS cc_start: 0.3792 (t-90) cc_final: 0.3575 (t70) REVERT: o 172 THR cc_start: 0.8243 (p) cc_final: 0.7853 (p) REVERT: o 246 LYS cc_start: 0.5903 (mmpt) cc_final: 0.5172 (mmtm) REVERT: q 57 LYS cc_start: 0.4067 (mmtt) cc_final: 0.2932 (ttmm) REVERT: q 145 ILE cc_start: 0.3263 (mt) cc_final: 0.2983 (mm) REVERT: p 199 PHE cc_start: 0.4545 (t80) cc_final: 0.4297 (t80) REVERT: z 205 TYR cc_start: 0.2134 (m-10) cc_final: 0.1830 (m-10) REVERT: z 245 MET cc_start: 0.2733 (ppp) cc_final: 0.2253 (ppp) REVERT: z 370 TYR cc_start: 0.1899 (t80) cc_final: 0.1276 (t80) REVERT: z 516 MET cc_start: 0.0807 (ppp) cc_final: 0.0386 (pmm) REVERT: z 570 GLN cc_start: 0.0712 (OUTLIER) cc_final: 0.0177 (mt0) outliers start: 249 outliers final: 195 residues processed: 1004 average time/residue: 0.4740 time to fit residues: 817.2476 Evaluate side-chains 980 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 766 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 94 PHE Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 321 PHE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 30 CYS Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 63 MET Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 484 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 112 MET Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 TYR Chi-restraints excluded: chain T residue 282 LEU Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 298 TYR Chi-restraints excluded: chain T residue 300 MET Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 132 GLN Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 59 ASN Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain n residue 94 VAL Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 10 SER Chi-restraints excluded: chain q residue 106 VAL Chi-restraints excluded: chain q residue 147 MET Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 125 ASN Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 142 GLU Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain p residue 175 ILE Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 429 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 570 GLN Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 533 optimal weight: 6.9990 chunk 561 optimal weight: 3.9990 chunk 512 optimal weight: 8.9990 chunk 546 optimal weight: 10.0000 chunk 328 optimal weight: 20.0000 chunk 237 optimal weight: 1.9990 chunk 428 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 493 optimal weight: 0.6980 chunk 516 optimal weight: 4.9990 chunk 544 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 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 13 GLN S 73 HIS G 23 HIS ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 182 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 HIS C 484 HIS ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 212 GLN z 125 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 moved from start: 0.7412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.250 50643 Z= 0.575 Angle : 1.734 50.957 68619 Z= 1.106 Chirality : 0.326 6.411 7612 Planarity : 0.006 0.094 8730 Dihedral : 7.946 177.989 7041 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.13 % Favored : 91.79 % Rotamer: Outliers : 4.47 % Allowed : 26.20 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.65 % Twisted General : 0.02 % 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: -1.72 (0.10), residues: 6177 helix: -0.09 (0.10), residues: 2779 sheet: -2.08 (0.25), residues: 392 loop : -2.05 (0.11), residues: 3006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP E 216 HIS 0.032 0.001 HIS G 154 PHE 0.040 0.002 PHE D 183 TYR 0.038 0.002 TYR O 140 ARG 0.018 0.001 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 800 time to evaluate : 4.258 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: 0.7417 (mtt) cc_final: 0.6926 (mtt) REVERT: A 315 MET cc_start: 0.5341 (mpp) cc_final: 0.4792 (mpp) REVERT: A 417 MET cc_start: 0.3146 (mmm) cc_final: 0.2423 (ptm) REVERT: I 209 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7018 (tt) REVERT: I 214 THR cc_start: 0.5051 (OUTLIER) cc_final: 0.4768 (p) REVERT: I 290 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7546 (pt) REVERT: J 8 ILE cc_start: 0.2400 (OUTLIER) cc_final: 0.2137 (tt) REVERT: H 13 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5859 (mt) REVERT: H 74 PHE cc_start: 0.4258 (p90) cc_final: 0.3760 (p90) REVERT: H 76 MET cc_start: 0.5924 (ppp) cc_final: 0.5513 (tmm) REVERT: H 178 TRP cc_start: 0.4150 (m-10) cc_final: 0.3947 (m-10) REVERT: H 289 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6512 (mtp85) REVERT: S 100 GLU cc_start: 0.8057 (tt0) cc_final: 0.7392 (pt0) REVERT: i 19 TYR cc_start: 0.4288 (OUTLIER) cc_final: 0.3041 (p90) REVERT: j 25 MET cc_start: 0.7870 (tpp) cc_final: 0.7588 (tpp) REVERT: G 14 ASN cc_start: 0.8035 (m-40) cc_final: 0.7781 (t0) REVERT: G 28 LEU cc_start: 0.8697 (tp) cc_final: 0.8494 (pt) REVERT: G 44 ILE cc_start: 0.7070 (mm) cc_final: 0.6619 (mm) REVERT: G 251 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7806 (t) REVERT: C 53 ILE cc_start: 0.6741 (mm) cc_final: 0.6141 (mt) REVERT: C 83 VAL cc_start: 0.5584 (m) cc_final: 0.5361 (m) REVERT: C 163 LEU cc_start: 0.5718 (mt) cc_final: 0.5470 (mt) REVERT: C 205 LYS cc_start: 0.7297 (mmtt) cc_final: 0.5867 (mttt) REVERT: C 484 HIS cc_start: 0.5536 (OUTLIER) cc_final: 0.4250 (t-90) REVERT: C 632 ASN cc_start: 0.6497 (p0) cc_final: 0.6290 (p0) REVERT: C 742 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6314 (mp) REVERT: T 180 TYR cc_start: 0.4122 (OUTLIER) cc_final: 0.3041 (t80) REVERT: T 325 MET cc_start: 0.2512 (mmt) cc_final: 0.2051 (mmt) REVERT: F 57 ILE cc_start: 0.6378 (mm) cc_final: 0.6043 (mm) REVERT: F 106 PRO cc_start: 0.8163 (Cg_exo) cc_final: 0.7953 (Cg_endo) REVERT: F 116 TRP cc_start: 0.7715 (t60) cc_final: 0.7107 (t60) REVERT: F 179 ASP cc_start: 0.7618 (t0) cc_final: 0.7392 (t70) REVERT: B 109 GLU cc_start: 0.5893 (pt0) cc_final: 0.5445 (pt0) REVERT: B 132 THR cc_start: 0.5162 (OUTLIER) cc_final: 0.4853 (m) REVERT: B 181 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6787 (pt) REVERT: O 64 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7696 (t) REVERT: P 54 MET cc_start: 0.7169 (tpp) cc_final: 0.6285 (tpt) REVERT: R 132 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6583 (tm-30) REVERT: E 120 ARG cc_start: 0.6150 (mmt180) cc_final: 0.5045 (mtt90) REVERT: E 193 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6009 (tm-30) REVERT: D 52 LEU cc_start: 0.8011 (tt) cc_final: 0.7653 (mm) REVERT: X 96 ARG cc_start: 0.6601 (ttp80) cc_final: 0.5904 (ptt-90) REVERT: c 94 GLU cc_start: 0.4494 (tp30) cc_final: 0.4128 (mt-10) REVERT: Q 71 CYS cc_start: 0.5859 (OUTLIER) cc_final: 0.5618 (t) REVERT: Q 79 GLU cc_start: 0.3401 (tm-30) cc_final: 0.2705 (mp0) REVERT: k 116 TYR cc_start: 0.4738 (t80) cc_final: 0.3972 (t80) REVERT: o 172 THR cc_start: 0.8215 (p) cc_final: 0.7790 (p) REVERT: o 246 LYS cc_start: 0.6186 (mmpt) cc_final: 0.5338 (mttp) REVERT: q 57 LYS cc_start: 0.4038 (mmtt) cc_final: 0.2817 (ttmm) REVERT: q 145 ILE cc_start: 0.3590 (mt) cc_final: 0.3200 (mm) REVERT: p 199 PHE cc_start: 0.4612 (t80) cc_final: 0.4329 (t80) REVERT: z 205 TYR cc_start: 0.2052 (m-10) cc_final: 0.1794 (m-10) REVERT: z 245 MET cc_start: 0.2742 (ppp) cc_final: 0.2216 (ppp) REVERT: z 516 MET cc_start: 0.0823 (ppp) cc_final: 0.0417 (pmm) REVERT: z 570 GLN cc_start: 0.0706 (OUTLIER) cc_final: 0.0153 (mt0) outliers start: 237 outliers final: 186 residues processed: 973 average time/residue: 0.4779 time to fit residues: 797.5206 Evaluate side-chains 961 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 757 time to evaluate : 4.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 94 PHE Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 63 MET Chi-restraints excluded: chain j residue 45 LEU Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 410 CYS Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 484 HIS Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 112 MET Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 TYR Chi-restraints excluded: chain T residue 282 LEU Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 298 TYR Chi-restraints excluded: chain T residue 307 TYR Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 132 GLN Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 10 SER Chi-restraints excluded: chain q residue 106 VAL Chi-restraints excluded: chain q residue 147 MET Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 142 GLU Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 429 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 570 GLN Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 358 optimal weight: 5.9990 chunk 577 optimal weight: 8.9990 chunk 352 optimal weight: 0.7980 chunk 273 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 chunk 605 optimal weight: 0.3980 chunk 557 optimal weight: 5.9990 chunk 482 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 372 optimal weight: 2.9990 chunk 295 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 HIS S 80 ASN i 35 HIS G 23 HIS ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 HIS T 160 ASN ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 ASN ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 182 ASN ** X 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 118 HIS ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 212 GLN z 388 GLN z 541 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5816 moved from start: 0.7663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.250 50643 Z= 0.574 Angle : 1.742 50.853 68619 Z= 1.108 Chirality : 0.326 6.415 7612 Planarity : 0.006 0.095 8730 Dihedral : 7.869 177.425 7039 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.08 % Favored : 91.84 % Rotamer: Outliers : 4.25 % Allowed : 26.52 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.65 % Twisted General : 0.02 % 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: -1.75 (0.10), residues: 6177 helix: -0.14 (0.10), residues: 2787 sheet: -1.98 (0.25), residues: 405 loop : -2.05 (0.11), residues: 2985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP O 74 HIS 0.046 0.002 HIS C 484 PHE 0.034 0.002 PHE D 183 TYR 0.044 0.002 TYR z 322 ARG 0.010 0.001 ARG N 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12354 Ramachandran restraints generated. 6177 Oldfield, 0 Emsley, 6177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 787 time to evaluate : 4.213 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 417 MET cc_start: 0.3091 (mmm) cc_final: 0.2522 (ptm) REVERT: I 209 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7029 (tt) REVERT: I 214 THR cc_start: 0.5028 (OUTLIER) cc_final: 0.4751 (p) REVERT: I 290 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7496 (pt) REVERT: J 8 ILE cc_start: 0.2651 (OUTLIER) cc_final: 0.2259 (tt) REVERT: H 13 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.6015 (mt) REVERT: H 74 PHE cc_start: 0.4188 (p90) cc_final: 0.3716 (p90) REVERT: H 76 MET cc_start: 0.5953 (ppp) cc_final: 0.5591 (tmm) REVERT: H 144 MET cc_start: 0.7848 (mmm) cc_final: 0.7192 (tpp) REVERT: H 178 TRP cc_start: 0.4353 (m-10) cc_final: 0.4071 (m-10) REVERT: H 278 PHE cc_start: 0.5881 (t80) cc_final: 0.5313 (t80) REVERT: H 289 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6673 (mtp85) REVERT: Y 27 MET cc_start: 0.6638 (tpp) cc_final: 0.5236 (ptp) REVERT: S 100 GLU cc_start: 0.7953 (tt0) cc_final: 0.7406 (tm-30) REVERT: i 19 TYR cc_start: 0.4209 (OUTLIER) cc_final: 0.2529 (p90) REVERT: j 25 MET cc_start: 0.7886 (tpp) cc_final: 0.7637 (tpp) REVERT: G 14 ASN cc_start: 0.7990 (m-40) cc_final: 0.7780 (t0) REVERT: G 44 ILE cc_start: 0.7310 (mm) cc_final: 0.6901 (mm) REVERT: G 47 LEU cc_start: 0.7510 (tp) cc_final: 0.7271 (tp) REVERT: G 251 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7838 (t) REVERT: G 314 GLU cc_start: 0.7463 (mp0) cc_final: 0.7196 (mp0) REVERT: C 53 ILE cc_start: 0.6749 (mm) cc_final: 0.6131 (mt) REVERT: C 83 VAL cc_start: 0.5384 (m) cc_final: 0.5171 (m) REVERT: C 163 LEU cc_start: 0.5812 (mt) cc_final: 0.5492 (mt) REVERT: C 205 LYS cc_start: 0.7282 (mmtt) cc_final: 0.5744 (mttm) REVERT: C 742 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6359 (mp) REVERT: T 180 TYR cc_start: 0.4169 (OUTLIER) cc_final: 0.3187 (t80) REVERT: T 298 TYR cc_start: 0.4366 (OUTLIER) cc_final: 0.3393 (m-80) REVERT: T 325 MET cc_start: 0.2546 (mmt) cc_final: 0.2075 (mmt) REVERT: F 57 ILE cc_start: 0.6451 (mm) cc_final: 0.6058 (mm) REVERT: F 106 PRO cc_start: 0.8192 (Cg_exo) cc_final: 0.7966 (Cg_endo) REVERT: F 116 TRP cc_start: 0.7779 (t60) cc_final: 0.7162 (t60) REVERT: F 179 ASP cc_start: 0.7611 (t0) cc_final: 0.7397 (t70) REVERT: B 109 GLU cc_start: 0.6025 (pt0) cc_final: 0.5519 (pt0) REVERT: B 132 THR cc_start: 0.5133 (OUTLIER) cc_final: 0.4829 (m) REVERT: B 136 MET cc_start: 0.4615 (tpt) cc_final: 0.4303 (tpt) REVERT: B 181 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6739 (pt) REVERT: O 64 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7687 (t) REVERT: P 54 MET cc_start: 0.7316 (tpp) cc_final: 0.6462 (tpt) REVERT: R 103 MET cc_start: 0.5096 (mtt) cc_final: 0.4805 (mtt) REVERT: R 132 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6586 (tm-30) REVERT: E 87 MET cc_start: 0.8156 (tmm) cc_final: 0.7761 (tmm) REVERT: E 120 ARG cc_start: 0.6303 (mmt180) cc_final: 0.5107 (mtt90) REVERT: E 193 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6035 (tm-30) REVERT: D 52 LEU cc_start: 0.8087 (tt) cc_final: 0.7614 (mm) REVERT: D 80 LEU cc_start: 0.6305 (mt) cc_final: 0.5704 (tt) REVERT: D 93 THR cc_start: 0.6106 (t) cc_final: 0.5774 (m) REVERT: X 96 ARG cc_start: 0.6549 (ttp80) cc_final: 0.5858 (ptt-90) REVERT: c 94 GLU cc_start: 0.4545 (tp30) cc_final: 0.4148 (mt-10) REVERT: Q 79 GLU cc_start: 0.3524 (tm-30) cc_final: 0.2778 (mp0) REVERT: k 116 TYR cc_start: 0.4766 (t80) cc_final: 0.3992 (t80) REVERT: o 172 THR cc_start: 0.8279 (p) cc_final: 0.7890 (p) REVERT: o 246 LYS cc_start: 0.6258 (mmpt) cc_final: 0.5483 (mttp) REVERT: q 57 LYS cc_start: 0.3942 (mmtt) cc_final: 0.2695 (ttmt) REVERT: p 199 PHE cc_start: 0.4574 (t80) cc_final: 0.4317 (t80) REVERT: z 205 TYR cc_start: 0.2059 (m-10) cc_final: 0.1794 (m-10) REVERT: z 245 MET cc_start: 0.3045 (ppp) cc_final: 0.2504 (ppp) REVERT: z 516 MET cc_start: 0.0848 (ppp) cc_final: 0.0441 (pmm) REVERT: z 570 GLN cc_start: 0.0686 (OUTLIER) cc_final: 0.0165 (mt0) outliers start: 225 outliers final: 189 residues processed: 955 average time/residue: 0.4905 time to fit residues: 806.8255 Evaluate side-chains 960 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 754 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 83 TRP Chi-restraints excluded: chain I residue 120 PHE Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 209 LEU Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 336 CYS Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 411 PHE Chi-restraints excluded: chain I residue 427 LEU Chi-restraints excluded: chain I residue 451 THR Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 94 PHE Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 229 PHE Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 42 HIS Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain S residue 47 LEU Chi-restraints excluded: chain i residue 7 MET Chi-restraints excluded: chain i residue 19 TYR Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 31 HIS Chi-restraints excluded: chain i residue 63 MET Chi-restraints excluded: chain j residue 45 LEU Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 380 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 672 SER Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 112 MET Chi-restraints excluded: chain T residue 118 VAL Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 180 TYR Chi-restraints excluded: chain T residue 282 LEU Chi-restraints excluded: chain T residue 286 ASP Chi-restraints excluded: chain T residue 298 TYR Chi-restraints excluded: chain T residue 307 TYR Chi-restraints excluded: chain T residue 342 ASP Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 132 GLN Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 165 CYS Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain X residue 26 VAL Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 83 ASN Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain o residue 88 ASP Chi-restraints excluded: chain o residue 118 VAL Chi-restraints excluded: chain o residue 241 VAL Chi-restraints excluded: chain o residue 244 PHE Chi-restraints excluded: chain q residue 10 SER Chi-restraints excluded: chain q residue 147 MET Chi-restraints excluded: chain q residue 177 SER Chi-restraints excluded: chain p residue 42 HIS Chi-restraints excluded: chain p residue 91 THR Chi-restraints excluded: chain p residue 99 ASN Chi-restraints excluded: chain p residue 103 ASN Chi-restraints excluded: chain p residue 108 VAL Chi-restraints excluded: chain p residue 133 VAL Chi-restraints excluded: chain p residue 142 GLU Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain z residue 111 THR Chi-restraints excluded: chain z residue 112 VAL Chi-restraints excluded: chain z residue 183 GLU Chi-restraints excluded: chain z residue 284 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 368 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 409 HIS Chi-restraints excluded: chain z residue 413 VAL Chi-restraints excluded: chain z residue 429 VAL Chi-restraints excluded: chain z residue 520 THR Chi-restraints excluded: chain z residue 570 GLN Chi-restraints excluded: chain z residue 595 LEU Chi-restraints excluded: chain z residue 597 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 383 optimal weight: 0.0980 chunk 513 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 444 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 483 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 496 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 13 GLN S 73 HIS S 80 ASN i 35 HIS G 23 HIS ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 GLN ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 202 GLN ** 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 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 212 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.180204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.162926 restraints weight = 125740.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.162013 restraints weight = 100483.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.163280 restraints weight = 85008.412| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.7807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.254 50643 Z= 0.562 Angle : 1.736 50.740 68619 Z= 1.105 Chirality : 0.326 6.386 7612 Planarity : 0.006 0.085 8730 Dihedral : 7.707 177.655 7039 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.50 % Favored : 92.42 % Rotamer: Outliers : 3.40 % Allowed : 27.69 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.65 % Twisted General : 0.02 % 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: -1.60 (0.10), residues: 6177 helix: -0.02 (0.10), residues: 2769 sheet: -1.83 (0.26), residues: 384 loop : -1.99 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 310 HIS 0.021 0.001 HIS G 154 PHE 0.035 0.002 PHE D 98 TYR 0.037 0.002 TYR z 322 ARG 0.017 0.001 ARG N 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13718.80 seconds wall clock time: 237 minutes 25.28 seconds (14245.28 seconds total)