Starting phenix.real_space_refine (version: dev) on Sat Apr 9 20:57:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/04_2022/7a24_11615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/04_2022/7a24_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_11615/04_2022/7a24_11615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/04_2022/7a24_11615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/04_2022/7a24_11615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a24_11615/04_2022/7a24_11615_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "Y TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 28, 'CIS': 1, '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: {'SF4': 2, 'FES': 1} 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: {'BCT': 1, ' ZN': 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: 25.91, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 22.08 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Iron sulfur cluster 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 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... running ksdssp... Secondary structure from input PDB file: 224 helices and 32 sheets defined 41.1% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 232 through 240 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 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 268 through 279 Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 406 through 422 removed outlier: 4.269A pdb=" N GLY A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.472A pdb=" N GLY A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N HIS A 445 " --> pdb=" O GLN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 479 Proline residue: A 457 - end of helix Proline residue: A 467 - end of helix Processing helix chain 'I' and resid 20 through 40 Processing helix chain 'I' and resid 54 through 71 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 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 80 through 85 Processing helix chain 'I' and resid 91 through 117 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 123 through 141 removed outlier: 3.501A pdb=" N VAL I 127 " --> pdb=" O PHE I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 164 Processing helix chain 'I' and resid 170 through 201 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 224 through 240 Processing helix chain 'I' and resid 244 through 246 No H-bonds generated for 'chain 'I' and resid 244 through 246' Processing helix chain 'I' and resid 250 through 256 Processing helix chain 'I' and resid 259 through 282 Proline residue: I 269 - end of helix Processing helix chain 'I' and resid 290 through 311 removed outlier: 3.583A pdb=" N PHE I 294 " --> pdb=" O LEU I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 315 through 335 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 339 through 366 Processing helix chain 'I' and resid 374 through 377 No H-bonds generated for 'chain 'I' and resid 374 through 377' Processing helix chain 'I' and resid 385 through 399 removed outlier: 3.556A pdb=" N TYR I 398 " --> pdb=" O THR I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 420 Processing helix chain 'I' and resid 423 through 447 removed outlier: 3.814A pdb=" N TYR I 439 " --> pdb=" O ILE I 435 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 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 484 through 496 Processing helix chain 'J' and resid 3 through 28 removed outlier: 3.783A pdb=" N ALA J 6 " --> pdb=" O LEU J 3 " (cutoff:3.500A) Proline residue: J 7 - end of helix removed outlier: 3.504A pdb=" N ILE J 10 " --> pdb=" O PRO J 7 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU J 12 " --> pdb=" O PHE J 9 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER J 15 " --> pdb=" O LEU J 12 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL J 25 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Proline residue: J 26 - end of helix Processing helix chain 'J' and resid 59 through 83 removed outlier: 4.522A pdb=" N VAL J 64 " --> pdb=" O PHE J 61 " (cutoff:3.500A) Proline residue: J 80 - end of helix Processing helix chain 'J' and resid 92 through 113 Processing helix chain 'N' and resid 5 through 17 removed outlier: 3.717A pdb=" N VAL N 17 " --> pdb=" O GLY N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 43 Processing helix chain 'N' and resid 47 through 58 Processing helix chain 'N' and resid 61 through 70 Processing helix chain 'N' and resid 136 through 144 removed outlier: 4.828A pdb=" N LEU N 143 " --> pdb=" O THR N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 170 removed outlier: 4.793A pdb=" N VAL N 154 " --> pdb=" O TRP N 151 " (cutoff:3.500A) Proline residue: N 155 - end of helix removed outlier: 4.084A pdb=" N LEU N 169 " --> pdb=" O ALA N 166 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR N 170 " --> pdb=" O ILE N 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 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 50 through 59 Processing helix chain 'H' and resid 77 through 89 removed outlier: 4.549A pdb=" N TRP H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 removed outlier: 4.080A pdb=" N TYR H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 161 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 167 through 172 Processing helix chain 'H' and resid 179 through 182 No H-bonds generated for 'chain 'H' and resid 179 through 182' Processing helix chain 'H' and resid 184 through 197 removed outlier: 3.654A pdb=" N ALA H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 215 removed outlier: 4.236A pdb=" N VAL H 213 " --> pdb=" O GLU H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 242 Processing helix chain 'H' and resid 265 through 285 Processing helix chain 'H' and resid 296 through 299 No H-bonds generated for 'chain 'H' and resid 296 through 299' Processing helix chain 'H' and resid 305 through 320 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) Processing helix chain 'K' and resid 3 through 23 removed outlier: 4.097A pdb=" N SER K 10 " --> pdb=" O TYR K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 41 Processing helix chain 'K' and resid 43 through 52 Processing helix chain 'K' and resid 57 through 83 removed outlier: 4.347A pdb=" N ALA K 71 " --> pdb=" O THR K 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 20 Processing helix chain 'Y' and resid 22 through 27 Processing helix chain 'Y' and resid 30 through 42 Processing helix chain 'Y' and resid 47 through 69 removed outlier: 5.618A pdb=" N ASP Y 51 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL Y 60 " --> pdb=" O THR Y 57 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Y 61 " --> pdb=" O ARG Y 58 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS Y 68 " --> pdb=" O LYS Y 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 72 through 84 Processing helix chain 'Y' and resid 90 through 102 removed outlier: 3.915A pdb=" N ARG Y 93 " --> pdb=" O ASP Y 90 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS Y 94 " --> pdb=" O LEU Y 91 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU Y 95 " --> pdb=" O CYS Y 92 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE Y 99 " --> pdb=" O GLN Y 96 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL Y 102 " --> pdb=" O PHE Y 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 111 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 4 through 28 removed outlier: 3.582A pdb=" N LEU V 10 " --> pdb=" O GLU V 7 " (cutoff:3.500A) Proline residue: V 11 - end of helix removed outlier: 4.616A pdb=" N GLY V 17 " --> pdb=" O ILE V 14 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET V 18 " --> pdb=" O ILE V 15 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N CYS V 20 " --> pdb=" O GLY V 17 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN V 24 " --> pdb=" O ILE V 21 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER V 25 " --> pdb=" O MET V 22 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN V 26 " --> pdb=" O GLY V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 33 No H-bonds generated for 'chain 'V' and resid 30 through 33' Processing helix chain 'V' and resid 44 through 56 Processing helix chain 'W' and resid 5 through 13 Processing helix chain 'W' and resid 15 through 18 No H-bonds generated for 'chain 'W' and resid 15 through 18' Processing helix chain 'W' and resid 25 through 28 No H-bonds generated for 'chain 'W' and resid 25 through 28' Processing helix chain 'W' and resid 30 through 37 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 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 91 through 100 Processing helix chain 'i' and resid 8 through 17 Processing helix chain 'i' and resid 36 through 68 Processing helix chain 'j' and resid 15 through 25 Processing helix chain 'j' and resid 31 through 46 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 48 through 70 Processing helix chain 'G' and resid 51 through 57 removed outlier: 4.845A pdb=" N GLU G 56 " --> pdb=" O GLU G 52 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR G 57 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 69 removed outlier: 3.858A pdb=" N ASP G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 3.795A pdb=" N GLU G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 125 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) removed outlier: 3.916A pdb=" N HIS G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 148 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 171 through 179 Processing helix chain 'G' and resid 182 through 191 Processing helix chain 'G' and resid 197 through 203 Processing helix chain 'G' and resid 211 through 216 Processing helix chain 'G' and resid 241 through 243 No H-bonds generated for 'chain 'G' and resid 241 through 243' Processing helix chain 'G' and resid 257 through 280 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 299 through 304 Processing helix chain 'G' and resid 306 through 316 Processing helix chain 'G' and resid 362 through 369 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 375 through 384 removed outlier: 3.919A pdb=" N VAL G 379 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE G 381 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE G 382 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 391 No H-bonds generated for 'chain 'G' and resid 389 through 391' Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 149 through 162 Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.614A pdb=" N SER C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 264 through 267 No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 330 through 333 No H-bonds generated for 'chain 'C' and resid 330 through 333' Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 361 through 373 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 390 through 402 Processing helix chain 'C' and resid 422 through 425 removed outlier: 3.526A pdb=" N TYR C 425 " --> pdb=" O ARG C 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 422 through 425' Processing helix chain 'C' and resid 433 through 436 Processing helix chain 'C' and resid 452 through 463 Processing helix chain 'C' and resid 490 through 496 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 518 through 521 Processing helix chain 'C' and resid 526 through 540 Processing helix chain 'C' and resid 557 through 564 removed outlier: 4.273A pdb=" N ALA C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 613 No H-bonds generated for 'chain 'C' and resid 610 through 613' Processing helix chain 'C' and resid 653 through 663 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 685 through 687 No H-bonds generated for 'chain 'C' and resid 685 through 687' Processing helix chain 'C' and resid 700 through 702 No H-bonds generated for 'chain 'C' and resid 700 through 702' Processing helix chain 'C' and resid 727 through 730 No H-bonds generated for 'chain 'C' and resid 727 through 730' Processing helix chain 'T' and resid 79 through 90 removed outlier: 4.165A pdb=" N TYR T 83 " --> pdb=" O PHE T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 110 Processing helix chain 'T' and resid 131 through 134 No H-bonds generated for 'chain 'T' and resid 131 through 134' Processing helix chain 'T' and resid 157 through 160 No H-bonds generated for 'chain 'T' and resid 157 through 160' Processing helix chain 'T' and resid 164 through 173 Processing helix chain 'T' and resid 195 through 210 Processing helix chain 'T' and resid 246 through 249 removed outlier: 3.591A pdb=" N GLY T 249 " --> pdb=" O ILE T 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 246 through 249' Processing helix chain 'T' and resid 258 through 270 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 300 removed outlier: 3.579A pdb=" N ASP T 299 " --> pdb=" O GLU T 295 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 318 Processing helix chain 'T' and resid 341 through 348 Processing helix chain 'T' and resid 360 through 363 Processing helix chain 'T' and resid 373 through 381 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 9 through 13 Processing helix chain 'F' and resid 38 through 43 Processing helix chain 'F' and resid 106 through 118 removed outlier: 3.530A pdb=" N GLY F 109 " --> pdb=" O PRO F 106 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP F 110 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET F 118 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 69 through 83 removed outlier: 4.229A pdb=" N ILE B 74 " --> pdb=" O SER B 71 " (cutoff:3.500A) Proline residue: B 75 - end of helix Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 133 through 138 removed outlier: 4.322A pdb=" N ARG B 138 " --> pdb=" O PRO B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'O' and resid 47 through 49 No H-bonds generated for 'chain 'O' and resid 47 through 49' Processing helix chain 'O' and resid 111 through 120 Processing helix chain 'O' and resid 140 through 142 No H-bonds generated for 'chain 'O' and resid 140 through 142' Processing helix chain 'P' and resid 41 through 44 No H-bonds generated for 'chain 'P' and resid 41 through 44' Processing helix chain 'P' and resid 53 through 58 Processing helix chain 'R' and resid 29 through 46 removed outlier: 3.996A pdb=" N GLN R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ALA R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 70 Processing helix chain 'R' and resid 74 through 80 Processing helix chain 'R' and resid 86 through 103 Processing helix chain 'U' and resid 38 through 44 Processing helix chain 'U' and resid 96 through 98 No H-bonds generated for 'chain 'U' and resid 96 through 98' Processing helix chain 'U' and resid 105 through 110 removed outlier: 5.108A pdb=" N SER U 110 " --> pdb=" O ASP U 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 93 through 101 Processing helix chain 'E' and resid 136 through 145 removed outlier: 3.764A pdb=" N GLN E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 160 No H-bonds generated for 'chain 'E' and resid 157 through 160' Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 192 through 207 removed outlier: 3.596A pdb=" N LYS E 204 " --> pdb=" O LEU E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 215 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 74 through 88 removed outlier: 3.502A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 190 through 193 No H-bonds generated for 'chain 'D' and resid 190 through 193' Processing helix chain 'D' and resid 201 through 218 removed outlier: 3.594A pdb=" N GLY D 204 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 205 " --> pdb=" O GLU D 202 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR D 209 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA D 212 " --> pdb=" O THR D 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 44 Proline residue: X 38 - end of helix Processing helix chain 'X' and resid 52 through 65 Processing helix chain 'X' and resid 72 through 90 Processing helix chain 'X' and resid 99 through 102 No H-bonds generated for 'chain 'X' and resid 99 through 102' Processing helix chain 'X' and resid 123 through 127 Processing helix chain 'c' and resid 33 through 53 removed outlier: 3.598A pdb=" N THR c 41 " --> pdb=" O PHE c 37 " (cutoff:3.500A) Processing helix chain 'c' and resid 59 through 85 Processing helix chain 'c' and resid 95 through 99 Processing helix chain 'Q' and resid 26 through 42 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 79 through 93 removed outlier: 3.605A pdb=" N GLY Q 93 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 55 Processing helix chain 'k' and resid 79 through 92 Processing helix chain 'k' and resid 99 through 104 removed outlier: 4.542A pdb=" N LYS k 104 " --> pdb=" O LYS k 100 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 115 Processing helix chain 'n' and resid 82 through 101 Processing helix chain 'o' and resid 207 through 230 Proline residue: o 214 - end of helix removed outlier: 4.038A pdb=" N GLU o 230 " --> pdb=" O ASP o 226 " (cutoff:3.500A) Processing helix chain 'o' and resid 237 through 246 Processing helix chain 'q' and resid 10 through 22 Processing helix chain 'q' and resid 25 through 27 No H-bonds generated for 'chain 'q' and resid 25 through 27' Processing helix chain 'q' and resid 194 through 213 Processing helix chain 'q' and resid 216 through 218 No H-bonds generated for 'chain 'q' and resid 216 through 218' Processing helix chain 'q' and resid 221 through 231 removed outlier: 3.961A pdb=" N LYS q 229 " --> pdb=" O ILE q 225 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL q 230 " --> pdb=" O GLU q 226 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU q 231 " --> pdb=" O PHE q 227 " (cutoff:3.500A) Processing helix chain 'p' and resid 7 through 24 removed outlier: 3.697A pdb=" N LEU p 22 " --> pdb=" O THR p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 34 through 36 No H-bonds generated for 'chain 'p' and resid 34 through 36' Processing helix chain 'p' and resid 194 through 212 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 221 through 228 Processing helix chain 'z' and resid 132 through 145 Processing helix chain 'z' and resid 172 through 176 Processing helix chain 'z' and resid 195 through 204 Processing helix chain 'z' and resid 220 through 225 Processing helix chain 'z' and resid 238 through 241 No H-bonds generated for 'chain 'z' and resid 238 through 241' Processing helix chain 'z' and resid 263 through 271 Processing helix chain 'z' and resid 301 through 315 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 390 through 401 Processing helix chain 'z' and resid 408 through 423 removed outlier: 3.641A pdb=" N LYS z 412 " --> pdb=" O VAL z 408 " (cutoff:3.500A) Processing helix chain 'z' and resid 455 through 460 Proline residue: z 459 - end of helix No H-bonds generated for 'chain 'z' and resid 455 through 460' Processing helix chain 'z' and resid 463 through 476 Processing helix chain 'z' and resid 525 through 536 Processing helix chain 'z' and resid 545 through 548 No H-bonds generated for 'chain 'z' and resid 545 through 548' Processing helix chain 'z' and resid 567 through 570 No H-bonds generated for 'chain 'z' and resid 567 through 570' Processing helix chain 'z' and resid 572 through 576 Processing helix chain 'z' and resid 580 through 589 Processing helix chain 'z' and resid 598 through 603 Processing sheet with id= A, first strand: chain 'A' and resid 135 through 138 removed outlier: 6.535A pdb=" N ALA A 176 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL A 138 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR A 178 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU A 217 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 179 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR A 219 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A 181 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS A 221 " --> pdb=" O ILE A 181 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, 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= C, 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= D, first strand: chain 'G' and resid 29 through 33 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= E, first strand: chain 'C' and resid 74 through 78 Processing sheet with id= F, first strand: chain 'C' and resid 211 through 213 Processing sheet with id= G, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= H, 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= I, first strand: chain 'C' and resid 348 through 350 Processing sheet with id= J, first strand: chain 'C' and resid 439 through 443 removed outlier: 6.669A pdb=" N LYS C 468 " --> pdb=" O PHE C 440 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU C 442 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY C 470 " --> pdb=" O LEU C 442 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'T' and resid 140 through 143 removed outlier: 6.906A pdb=" N ARG T 179 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ASN T 143 " --> pdb=" O ARG T 179 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE T 181 " --> pdb=" O ASN T 143 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 242 through 246 removed outlier: 6.682A pdb=" N ARG T 306 " --> pdb=" O LEU T 243 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU T 245 " --> pdb=" O ARG T 306 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL T 308 " --> pdb=" O LEU T 245 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.341A pdb=" N ASN F 29 " --> pdb=" O ARG F 85 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP F 58 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 127 through 130 Processing sheet with id= O, first strand: chain 'B' and resid 180 through 182 Processing sheet with id= P, first strand: chain 'O' and resid 54 through 58 Processing sheet with id= Q, 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= R, first strand: chain 'U' and resid 60 through 63 Processing sheet with id= S, first strand: chain 'E' and resid 126 through 128 removed outlier: 6.076A pdb=" N ILE E 153 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE E 183 " --> pdb=" O SER E 154 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 110 through 113 Processing sheet with id= U, first strand: chain 'D' and resid 138 through 144 removed outlier: 6.185A pdb=" N GLU D 143 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR D 152 " --> pdb=" O GLU D 143 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Q' and resid 47 through 50 removed outlier: 3.664A pdb=" N GLN Q 59 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'o' and resid 84 through 86 removed outlier: 7.157A pdb=" N ILE o 105 " --> pdb=" O THR o 85 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'o' and resid 118 through 120 Processing sheet with id= Y, first strand: chain 'q' and resid 92 through 94 removed outlier: 6.790A pdb=" N THR q 120 " --> pdb=" O SER q 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'q' and resid 179 through 182 removed outlier: 5.386A pdb=" N GLY q 182 " --> pdb=" O PHE q 188 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE q 188 " --> pdb=" O GLY q 182 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'p' and resid 53 through 55 removed outlier: 5.835A pdb=" N VAL p 71 " --> pdb=" O ILE p 54 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'p' and resid 179 through 181 removed outlier: 4.010A pdb=" N ARG p 190 " --> pdb=" O VAL p 180 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'z' and resid 149 through 151 removed outlier: 5.511A pdb=" N GLY z 167 " --> pdb=" O ARG z 150 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'z' and resid 178 through 181 removed outlier: 6.580A pdb=" N LYS z 246 " --> pdb=" O ALA z 280 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL z 282 " --> pdb=" O SER z 244 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER z 244 " --> pdb=" O VAL z 282 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU z 247 " --> pdb=" O ILE z 255 " (cutoff:3.500A) Processing sheet with id= AE, 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= AF, 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) 1672 hydrogen bonds defined for protein. 4557 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: 15.72 Time building geometry restraints manager: 23.08 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: 73.14 - 85.37: 72 85.37 - 97.61: 9 97.61 - 109.84: 7932 109.84 - 122.07: 51673 122.07 - 134.30: 8933 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: 29416 33.06 - 66.13: 778 66.13 - 99.19: 42 99.19 - 132.25: 0 132.25 - 165.32: 3 Dihedral angle restraints: 30239 sinusoidal: 12220 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 30236 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: 331 2.47 - 3.28: 59937 3.28 - 4.09: 132019 4.09 - 4.90: 246732 Warning: very small nonbonded interaction distances. Nonbonded interactions: 439024 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 439019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 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. 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: 3.710 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: 0.060 Extract box with map and model: 15.360 Check model and map are aligned: 0.700 Convert atoms to be neutral: 0.390 Process input model: 136.780 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4683 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= 0.587 Angle : 1.160 24.289 68619 Z= 0.815 Chirality : 1.077 21.179 7612 Planarity : 0.006 0.114 8730 Dihedral : 14.937 165.318 18637 Min Nonbonded Distance : 0.850 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.57 % Favored : 90.09 % Rotamer Outliers : 2.62 % 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 *********************** 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 : 5.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 38 residues processed: 1829 average time/residue: 0.6388 time to fit residues: 1897.5427 Evaluate side-chains 961 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 923 time to evaluate : 5.782 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 2 residues processed: 38 average time/residue: 0.4408 time to fit residues: 39.5238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 513 optimal weight: 6.9990 chunk 460 optimal weight: 0.0670 chunk 255 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 310 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 chunk 476 optimal weight: 7.9990 chunk 184 optimal weight: 50.0000 chunk 289 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 552 optimal weight: 8.9990 overall best weight: 2.9524 ------------------------------------------------------------------------------- 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** I 80 HIS ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 117 GLN I 208 GLN I 291 GLN I 312 GLN I 384 ASN N 25 HIS N 73 HIS ** H 104 ASN ** 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 45 ASN Y 68 HIS Y 87 ASN Z 63 GLN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN V 39 HIS V 42 HIS ** i 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 HIS G 277 GLN G 364 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 GLN C 522 ASN ** C 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 GLN C 569 GLN C 606 HIS C 716 GLN T 117 GLN ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 84 ASN ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 HIS O 77 ASN O 149 ASN P 77 ASN P 92 ASN ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 ASN U 88 GLN U 134 HIS ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN E 166 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 62 GLN X 102 GLN Q 35 ASN o 77 ASN o 103 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 221 ASN q 33 ASN q 72 HIS q 99 ASN ** q 101 GLN ** 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 212 GLN q 218 ASN ** p 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 72 HIS ** p 160 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 415 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5257 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.276 50643 Z= 0.602 Angle : 1.778 52.063 68619 Z= 1.127 Chirality : 0.332 6.746 7612 Planarity : 0.008 0.117 8730 Dihedral : 7.532 168.757 6913 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 26.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer Outliers : 4.80 % 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: -2.66 (0.10), residues: 6177 helix: -0.84 (0.09), residues: 2769 sheet: -2.41 (0.24), residues: 405 loop : -2.59 (0.10), residues: 3003 *********************** 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 1302 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1048 time to evaluate : 6.098 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 outliers start: 254 outliers final: 130 residues processed: 1214 average time/residue: 0.6333 time to fit residues: 1302.8426 Evaluate side-chains 971 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 841 time to evaluate : 5.283 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 0 residues processed: 130 average time/residue: 0.4511 time to fit residues: 120.3265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 306 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 459 optimal weight: 1.9990 chunk 375 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 553 optimal weight: 30.0000 chunk 597 optimal weight: 20.0000 chunk 492 optimal weight: 0.8980 chunk 548 optimal weight: 0.7980 chunk 188 optimal weight: 0.4980 chunk 443 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** I 326 HIS ** H 104 ASN ** 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** Z 90 GLN ** i 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 HIS G 43 HIS ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 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 342 GLN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 HIS R 122 ASN ** U 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 85 ASN U 88 GLN E 145 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 102 GLN ** Q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 103 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 221 ASN ** q 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** p 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 110 HIS z 119 HIS z 190 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.269 50643 Z= 0.597 Angle : 1.725 50.817 68619 Z= 1.103 Chirality : 0.327 6.407 7612 Planarity : 0.007 0.109 8730 Dihedral : 7.179 171.850 6913 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.41 % Favored : 92.47 % Rotamer Outliers : 2.68 % 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: -2.26 (0.10), residues: 6177 helix: -0.48 (0.10), residues: 2756 sheet: -2.41 (0.25), residues: 403 loop : -2.38 (0.10), residues: 3018 *********************** 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 1103 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 961 time to evaluate : 5.729 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 outliers start: 142 outliers final: 57 residues processed: 1059 average time/residue: 0.6048 time to fit residues: 1081.5346 Evaluate side-chains 874 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 817 time to evaluate : 5.733 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.4790 time to fit residues: 58.4366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 546 optimal weight: 10.0000 chunk 415 optimal weight: 5.9990 chunk 287 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 371 optimal weight: 7.9990 chunk 555 optimal weight: 8.9990 chunk 587 optimal weight: 9.9990 chunk 290 optimal weight: 20.0000 chunk 526 optimal weight: 0.3980 chunk 158 optimal weight: 9.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 243 GLN ** 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 322 GLN K 27 ASN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 ASN ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS ** i 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 HIS G 80 HIS ** G 113 ASN ** 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 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 94 GLN ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 291 HIS ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN U 41 GLN U 45 HIS ** U 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 GLN ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 ASN ** X 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 118 HIS ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 103 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 221 ASN ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 ASN ** 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** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 30 GLN ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 107 HIS z 357 GLN z 388 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.254 50643 Z= 0.708 Angle : 1.854 51.317 68619 Z= 1.160 Chirality : 0.330 6.565 7612 Planarity : 0.009 0.124 8730 Dihedral : 7.898 179.014 6913 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 34.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.83 % Favored : 90.06 % Rotamer Outliers : 5.21 % 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: -2.77 (0.10), residues: 6177 helix: -1.01 (0.09), residues: 2691 sheet: -2.36 (0.24), residues: 408 loop : -2.56 (0.10), residues: 3078 *********************** 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 1193 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 917 time to evaluate : 5.882 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 outliers start: 276 outliers final: 142 residues processed: 1100 average time/residue: 0.5878 time to fit residues: 1100.3101 Evaluate side-chains 908 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 766 time to evaluate : 6.072 Switching outliers to nearest non-outliers outliers start: 142 outliers final: 0 residues processed: 142 average time/residue: 0.4477 time to fit residues: 128.5305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 489 optimal weight: 20.0000 chunk 333 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 437 optimal weight: 0.9980 chunk 242 optimal weight: 0.9980 chunk 501 optimal weight: 8.9990 chunk 406 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 300 optimal weight: 2.9990 chunk 527 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN ** V 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 GLN C 165 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 291 HIS ** F 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN O 49 HIS U 46 ASN ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN c 28 ASN ** c 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 55 GLN ** o 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 103 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 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** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.276 50643 Z= 0.609 Angle : 1.761 51.171 68619 Z= 1.119 Chirality : 0.327 6.368 7612 Planarity : 0.007 0.115 8730 Dihedral : 7.385 171.858 6913 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 27.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.77 % Favored : 92.15 % Rotamer Outliers : 2.93 % 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: -2.36 (0.10), residues: 6177 helix: -0.64 (0.09), residues: 2714 sheet: -2.31 (0.24), residues: 412 loop : -2.35 (0.11), residues: 3051 *********************** 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 1029 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 874 time to evaluate : 5.935 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 outliers start: 155 outliers final: 67 residues processed: 976 average time/residue: 0.5896 time to fit residues: 981.0378 Evaluate side-chains 828 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 761 time to evaluate : 5.669 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.4497 time to fit residues: 64.9660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 197 optimal weight: 2.9990 chunk 529 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 345 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 588 optimal weight: 0.7980 chunk 488 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 308 optimal weight: 10.0000 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 353 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 180 GLN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 ASN ** V 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 30 HIS ** i 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 HIS G 48 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** 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 84 ASN ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 HIS ** U 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 HIS ** c 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 83 GLN o 103 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 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** ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.6880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.260 50643 Z= 0.647 Angle : 1.778 51.266 68619 Z= 1.128 Chirality : 0.327 6.457 7612 Planarity : 0.007 0.162 8730 Dihedral : 7.446 170.689 6913 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 30.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.44 % Favored : 90.46 % Rotamer Outliers : 3.08 % 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: -2.45 (0.10), residues: 6177 helix: -0.72 (0.09), residues: 2700 sheet: -2.38 (0.23), residues: 423 loop : -2.38 (0.11), residues: 3054 *********************** 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 1001 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 838 time to evaluate : 5.587 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 outliers start: 163 outliers final: 88 residues processed: 940 average time/residue: 0.6172 time to fit residues: 990.4444 Evaluate side-chains 846 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 758 time to evaluate : 5.708 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 0.5315 time to fit residues: 94.0888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 567 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 chunk 429 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 495 optimal weight: 8.9990 chunk 328 optimal weight: 9.9990 chunk 586 optimal weight: 20.0000 chunk 366 optimal weight: 1.9990 chunk 357 optimal weight: 0.9990 chunk 270 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 291 GLN H 294 GLN K 59 GLN ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 HIS i 35 HIS j 47 HIS ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** c 80 ASN o 103 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 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** ** p 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 373 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.360 50643 Z= 0.632 Angle : 1.766 50.898 68619 Z= 1.124 Chirality : 0.326 6.401 7612 Planarity : 0.007 0.168 8730 Dihedral : 7.238 168.680 6913 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 27.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.09 % Favored : 91.82 % Rotamer Outliers : 1.83 % 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: -2.25 (0.10), residues: 6177 helix: -0.55 (0.10), residues: 2708 sheet: -2.29 (0.24), residues: 422 loop : -2.27 (0.11), residues: 3047 *********************** 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 931 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 834 time to evaluate : 5.496 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 outliers start: 97 outliers final: 50 residues processed: 895 average time/residue: 0.6186 time to fit residues: 933.9811 Evaluate side-chains 813 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 763 time to evaluate : 5.701 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.4943 time to fit residues: 53.1993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 362 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 372 optimal weight: 0.9990 chunk 399 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 460 optimal weight: 10.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 HIS Y 72 GLN i 35 HIS ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 201 GLN ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 103 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 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** ** p 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 592 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.7325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.404 50643 Z= 0.656 Angle : 1.763 50.882 68619 Z= 1.123 Chirality : 0.326 6.434 7612 Planarity : 0.007 0.172 8730 Dihedral : 7.056 166.764 6913 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 26.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.29 % Favored : 91.63 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.02 % 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: -2.11 (0.10), residues: 6177 helix: -0.45 (0.10), residues: 2699 sheet: -2.26 (0.24), residues: 414 loop : -2.17 (0.11), residues: 3064 *********************** 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 893 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 820 time to evaluate : 5.872 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 outliers start: 73 outliers final: 32 residues processed: 854 average time/residue: 0.6150 time to fit residues: 890.5143 Evaluate side-chains 777 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 745 time to evaluate : 5.679 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4971 time to fit residues: 37.0297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 533 optimal weight: 10.0000 chunk 561 optimal weight: 50.0000 chunk 512 optimal weight: 5.9990 chunk 546 optimal weight: 20.0000 chunk 328 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 428 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 493 optimal weight: 8.9990 chunk 516 optimal weight: 0.4980 chunk 544 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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** N 22 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS S 73 HIS i 35 HIS G 23 HIS ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** 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 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 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** ** p 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.7612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.965 50643 Z= 0.830 Angle : 1.845 82.315 68619 Z= 1.150 Chirality : 0.326 6.427 7612 Planarity : 0.008 0.185 8730 Dihedral : 7.102 166.303 6913 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 28.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.73 % Favored : 91.16 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.10), residues: 6177 helix: -0.54 (0.10), residues: 2721 sheet: -2.20 (0.24), residues: 414 loop : -2.18 (0.11), residues: 3042 *********************** 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 853 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 794 time to evaluate : 5.791 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 outliers start: 59 outliers final: 33 residues processed: 818 average time/residue: 0.6281 time to fit residues: 874.4620 Evaluate side-chains 779 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 746 time to evaluate : 5.668 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5837 time to fit residues: 42.3661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 358 optimal weight: 7.9990 chunk 577 optimal weight: 20.0000 chunk 352 optimal weight: 8.9990 chunk 273 optimal weight: 0.0060 chunk 401 optimal weight: 0.0370 chunk 605 optimal weight: 8.9990 chunk 557 optimal weight: 7.9990 chunk 482 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 372 optimal weight: 0.9990 chunk 295 optimal weight: 10.0000 overall best weight: 3.0080 ------------------------------------------------------------------------------- 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** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 HIS ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 GLN ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** 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 ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 81 ASN ** 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 171 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** ** q 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.7669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.015 1.112 50643 Z= 1.049 Angle : 1.930 106.100 68619 Z= 1.178 Chirality : 0.327 6.415 7612 Planarity : 0.008 0.172 8730 Dihedral : 7.110 166.247 6913 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 31.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.90 % Favored : 91.02 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 6177 helix: -0.54 (0.10), residues: 2713 sheet: -2.21 (0.24), residues: 414 loop : -2.17 (0.11), residues: 3050 ********************** 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 787 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 757 time to evaluate : 6.316 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 outliers start: 30 outliers final: 19 residues processed: 770 average time/residue: 0.6290 time to fit residues: 835.0204 Evaluate side-chains 763 residues out of total 5298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 744 time to evaluate : 5.688 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5181 time to fit residues: 25.1368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 608 random chunks: chunk 383 optimal weight: 0.3980 chunk 513 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 444 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 483 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 496 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 0.0270 overall best weight: 0.6040 ------------------------------------------------------------------------------- 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** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 HIS i 35 HIS G 78 GLN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 GLN ** T 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** 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 ** n 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 103 ASN ** o 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 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** ** p 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 110 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.177397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.159530 restraints weight = 127260.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.158956 restraints weight = 101826.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.160062 restraints weight = 79990.508| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.7687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.045 50643 Z= 0.878 Angle : 1.876 101.174 68619 Z= 1.158 Chirality : 0.327 6.452 7612 Planarity : 0.008 0.194 8730 Dihedral : 7.074 165.717 6913 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.56 % Favored : 91.37 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.10), residues: 6177 helix: -0.52 (0.10), residues: 2712 sheet: -2.10 (0.24), residues: 405 loop : -2.13 (0.11), residues: 3060 =============================================================================== Job complete usr+sys time: 15646.98 seconds wall clock time: 281 minutes 13.90 seconds (16873.90 seconds total)