Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 07:43:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjj_31622/05_2023/7fjj_31622_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjj_31622/05_2023/7fjj_31622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjj_31622/05_2023/7fjj_31622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjj_31622/05_2023/7fjj_31622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjj_31622/05_2023/7fjj_31622_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fjj_31622/05_2023/7fjj_31622_updated.pdb" } resolution = 3.6 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 48 5.49 5 Mg 1 5.21 5 S 266 5.16 5 C 24803 2.51 5 N 6854 2.21 5 O 7491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A GLU 880": "OE1" <-> "OE2" Residue "A GLU 996": "OE1" <-> "OE2" Residue "A ARG 998": "NH1" <-> "NH2" Residue "A ARG 1069": "NH1" <-> "NH2" Residue "A GLU 1118": "OE1" <-> "OE2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A GLU 1143": "OE1" <-> "OE2" Residue "A GLU 1170": "OE1" <-> "OE2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A GLU 1179": "OE1" <-> "OE2" Residue "A TYR 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1206": "OE1" <-> "OE2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B GLU 660": "OE1" <-> "OE2" Residue "B GLU 726": "OE1" <-> "OE2" Residue "B ARG 764": "NH1" <-> "NH2" Residue "B ARG 781": "NH1" <-> "NH2" Residue "B ARG 805": "NH1" <-> "NH2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B PHE 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1041": "NH1" <-> "NH2" Residue "B ARG 1052": "NH1" <-> "NH2" Residue "B GLU 1066": "OE1" <-> "OE2" Residue "B ASP 1078": "OD1" <-> "OD2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "G ARG 12": "NH1" <-> "NH2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "I ARG 105": "NH1" <-> "NH2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "L GLU 21": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 152": "NH1" <-> "NH2" Residue "M GLU 234": "OE1" <-> "OE2" Residue "N ARG 156": "NH1" <-> "NH2" Residue "N ARG 332": "NH1" <-> "NH2" Residue "N ARG 336": "NH1" <-> "NH2" Residue "O GLU 5": "OE1" <-> "OE2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 134": "OE1" <-> "OE2" Residue "O ARG 159": "NH1" <-> "NH2" Residue "O ARG 258": "NH1" <-> "NH2" Residue "O GLU 408": "OE1" <-> "OE2" Residue "O ARG 419": "NH1" <-> "NH2" Residue "O GLU 448": "OE1" <-> "OE2" Residue "O GLU 453": "OE1" <-> "OE2" Residue "O GLU 456": "OE1" <-> "OE2" Residue "O GLU 500": "OE1" <-> "OE2" Residue "O GLU 513": "OE1" <-> "OE2" Residue "O ARG 533": "NH1" <-> "NH2" Residue "P GLU 233": "OE1" <-> "OE2" Residue "P GLU 257": "OE1" <-> "OE2" Residue "P GLU 301": "OE1" <-> "OE2" Residue "P GLU 312": "OE1" <-> "OE2" Residue "Q TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q GLU 85": "OE1" <-> "OE2" Residue "Q ARG 105": "NH1" <-> "NH2" Residue "Q ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 39474 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 10675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1360, 10675 Classifications: {'peptide': 1360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 64, 'TRANS': 1295} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8644 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 48, 'TRANS': 1046} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 848 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1612 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 13, 'TRANS': 188} Chain breaks: 1 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3546 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "P" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain: "Q" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 724 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Chain: "X" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "Y" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 447 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 534 SG CYS A 69 89.615 41.744 62.913 1.00 96.02 S ATOM 556 SG CYS A 72 86.543 42.825 61.207 1.00 94.46 S ATOM 604 SG CYS A 79 89.321 45.366 63.663 1.00 88.70 S ATOM 845 SG CYS A 109 55.550 59.165 95.552 1.00104.59 S ATOM 1262 SG CYS A 159 52.070 58.415 95.415 1.00121.42 S ATOM 18906 SG CYS B1080 72.533 50.897 60.201 1.00 81.64 S ATOM 18925 SG CYS B1083 72.336 51.182 63.110 1.00 81.49 S ATOM 18991 SG CYS B1092 74.919 48.487 62.993 1.00 86.49 S ATOM 19019 SG CYS B1095 71.374 48.378 61.889 1.00 88.09 S ATOM 27929 SG CYS I 5 84.894 85.359 142.707 1.00 78.98 S ATOM 27946 SG CYS I 8 85.806 81.730 140.798 1.00 77.78 S ATOM 28076 SG CYS I 25 82.617 82.907 139.506 1.00 86.19 S ATOM 28097 SG CYS I 28 82.817 82.491 143.157 1.00 87.33 S ATOM 28791 SG CYS J 7 146.322 86.188 63.969 1.00 54.01 S ATOM 28815 SG CYS J 10 147.036 87.799 62.436 1.00 57.92 S ATOM 29079 SG CYS J 44 146.725 90.332 63.755 1.00 57.10 S ATOM 29085 SG CYS J 45 149.818 88.459 63.972 1.00 54.89 S ATOM 30128 SG CYS L 19 145.332 46.267 81.772 1.00 81.26 S ATOM 30290 SG CYS L 39 144.718 45.164 85.832 1.00 97.98 S ATOM 37535 SG CYS P 287 59.122 35.207 81.002 1.00121.28 S Time building chain proxies: 20.06, per 1000 atoms: 0.51 Number of scatterers: 39474 At special positions: 0 Unit cell: (182.342, 154.938, 177.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 266 16.00 P 48 15.00 Mg 1 11.99 O 7491 8.00 N 6854 7.00 C 24803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 16.44 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN A1902 " pdb="ZN ZN A1902 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1902 " - pdb=" SG CYS A 72 " pdb=" ZN A1903 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1903 " - pdb=" SG CYS A 109 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 8 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 21 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 177 helices and 44 sheets defined 34.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.544A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 209 Proline residue: A 209 - end of helix No H-bonds generated for 'chain 'A' and resid 205 through 209' Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 279 through 299 Processing helix chain 'A' and resid 303 through 321 Processing helix chain 'A' and resid 342 through 345 No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 351 through 354 No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 561 through 571 removed outlier: 3.529A pdb=" N SER A 570 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.768A pdb=" N VAL A 603 " --> pdb=" O GLN A 599 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 655 No H-bonds generated for 'chain 'A' and resid 652 through 655' Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 673 through 694 Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 707 through 732 Processing helix chain 'A' and resid 747 through 770 Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 844 through 876 removed outlier: 3.504A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 943 through 953 Processing helix chain 'A' and resid 963 through 986 Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1008 through 1024 Processing helix chain 'A' and resid 1033 through 1047 Proline residue: A1044 - end of helix removed outlier: 3.505A pdb=" N GLN A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1095 through 1105 Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1136 through 1139 No H-bonds generated for 'chain 'A' and resid 1136 through 1139' Processing helix chain 'A' and resid 1146 through 1153 Processing helix chain 'A' and resid 1187 through 1196 Processing helix chain 'A' and resid 1232 through 1236 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1251 through 1258 Processing helix chain 'A' and resid 1261 through 1277 removed outlier: 3.501A pdb=" N ILE A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A1271 " --> pdb=" O ILE A1267 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A1274 " --> pdb=" O GLU A1270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1294 removed outlier: 3.724A pdb=" N ASP A1292 " --> pdb=" O MET A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1309 removed outlier: 3.866A pdb=" N ALA A1309 " --> pdb=" O ARG A1305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1305 through 1309' Processing helix chain 'A' and resid 1315 through 1319 Processing helix chain 'A' and resid 1324 through 1333 removed outlier: 3.524A pdb=" N LEU A1328 " --> pdb=" O THR A1324 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A1331 " --> pdb=" O HIS A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1359 Processing helix chain 'B' and resid 24 through 36 removed outlier: 4.088A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 29 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 41 through 52 removed outlier: 4.150A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 152 through 158 removed outlier: 3.737A pdb=" N LYS B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 266 through 274 removed outlier: 3.544A pdb=" N GLU B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 removed outlier: 3.710A pdb=" N TYR B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 315 removed outlier: 3.684A pdb=" N ALA B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 348 Processing helix chain 'B' and resid 365 through 392 Processing helix chain 'B' and resid 402 through 405 No H-bonds generated for 'chain 'B' and resid 402 through 405' Processing helix chain 'B' and resid 408 through 420 removed outlier: 3.512A pdb=" N ILE B 411 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN B 413 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 416 " --> pdb=" O ASN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 528 through 532 Processing helix chain 'B' and resid 552 through 565 removed outlier: 3.520A pdb=" N LEU B 561 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 616 Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.842A pdb=" N ASP B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 661 through 664 Processing helix chain 'B' and resid 667 through 670 No H-bonds generated for 'chain 'B' and resid 667 through 670' Processing helix chain 'B' and resid 675 through 677 No H-bonds generated for 'chain 'B' and resid 675 through 677' Processing helix chain 'B' and resid 680 through 691 removed outlier: 3.657A pdb=" N LYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 728 Processing helix chain 'B' and resid 731 through 733 No H-bonds generated for 'chain 'B' and resid 731 through 733' Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 804 through 806 No H-bonds generated for 'chain 'B' and resid 804 through 806' Processing helix chain 'B' and resid 913 through 915 No H-bonds generated for 'chain 'B' and resid 913 through 915' Processing helix chain 'B' and resid 931 through 937 Proline residue: B 935 - end of helix Processing helix chain 'B' and resid 940 through 955 Processing helix chain 'B' and resid 969 through 978 removed outlier: 3.514A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1041 No H-bonds generated for 'chain 'B' and resid 1039 through 1041' Processing helix chain 'B' and resid 1049 through 1058 Processing helix chain 'B' and resid 1061 through 1068 Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1108 through 1119 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 159 through 162 No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 179 through 184 removed outlier: 4.299A pdb=" N ALA C 182 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 291 through 296 removed outlier: 4.320A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL C 296 " --> pdb=" O LYS C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 291 through 296' Processing helix chain 'C' and resid 318 through 343 Processing helix chain 'D' and resid 13 through 30 removed outlier: 3.526A pdb=" N LYS D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER D 30 " --> pdb=" O GLN D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 41 through 55 removed outlier: 3.663A pdb=" N LYS D 51 " --> pdb=" O TYR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 76 removed outlier: 3.522A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'E' and resid 4 through 24 removed outlier: 3.682A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 52 through 55 No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 120 removed outlier: 3.911A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 162 removed outlier: 3.896A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 75 Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 33 removed outlier: 3.751A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU G 29 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS G 32 " --> pdb=" O GLU G 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'I' and resid 50 through 53 No H-bonds generated for 'chain 'I' and resid 50 through 53' Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 31 through 38 Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.789A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 4.107A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 59 removed outlier: 3.577A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 125 Processing helix chain 'M' and resid 71 through 81 removed outlier: 3.591A pdb=" N GLN M 76 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 153 removed outlier: 4.278A pdb=" N ARG M 152 " --> pdb=" O LYS M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 225 removed outlier: 4.335A pdb=" N GLN M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR M 224 " --> pdb=" O HIS M 220 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU M 225 " --> pdb=" O GLU M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'N' and resid 148 through 150 No H-bonds generated for 'chain 'N' and resid 148 through 150' Processing helix chain 'N' and resid 250 through 256 Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 389 through 395 Processing helix chain 'O' and resid 3 through 16 removed outlier: 3.526A pdb=" N GLN O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 31 Processing helix chain 'O' and resid 36 through 42 Processing helix chain 'O' and resid 47 through 59 Processing helix chain 'O' and resid 79 through 97 removed outlier: 3.898A pdb=" N LEU O 83 " --> pdb=" O CYS O 79 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG O 84 " --> pdb=" O SER O 80 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU O 86 " --> pdb=" O VAL O 82 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix removed outlier: 3.543A pdb=" N THR O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR O 95 " --> pdb=" O TYR O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 112 Processing helix chain 'O' and resid 118 through 132 removed outlier: 4.284A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP O 127 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 153 removed outlier: 3.572A pdb=" N VAL O 149 " --> pdb=" O SER O 145 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA O 152 " --> pdb=" O PHE O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 174 No H-bonds generated for 'chain 'O' and resid 171 through 174' Processing helix chain 'O' and resid 239 through 256 Processing helix chain 'O' and resid 261 through 272 removed outlier: 3.597A pdb=" N GLU O 265 " --> pdb=" O GLN O 261 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL O 267 " --> pdb=" O SER O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 295 Processing helix chain 'O' and resid 305 through 316 Processing helix chain 'O' and resid 338 through 357 removed outlier: 3.678A pdb=" N LEU O 342 " --> pdb=" O LEU O 338 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR O 347 " --> pdb=" O ALA O 343 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 371 removed outlier: 3.539A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU O 368 " --> pdb=" O ARG O 364 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL O 369 " --> pdb=" O ILE O 365 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU O 370 " --> pdb=" O PHE O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 383 No H-bonds generated for 'chain 'O' and resid 380 through 383' Processing helix chain 'O' and resid 388 through 400 removed outlier: 3.653A pdb=" N ASP O 393 " --> pdb=" O LYS O 389 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET O 394 " --> pdb=" O GLU O 390 " (cutoff:3.500A) Processing helix chain 'O' and resid 428 through 455 removed outlier: 3.621A pdb=" N LEU O 435 " --> pdb=" O ALA O 431 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA O 444 " --> pdb=" O TYR O 440 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG O 449 " --> pdb=" O ASN O 445 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR O 454 " --> pdb=" O ARG O 450 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS O 455 " --> pdb=" O GLN O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 464 removed outlier: 3.740A pdb=" N LEU O 461 " --> pdb=" O LYS O 458 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU O 462 " --> pdb=" O ARG O 459 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS O 463 " --> pdb=" O LEU O 460 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER O 464 " --> pdb=" O LEU O 461 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 515 removed outlier: 3.653A pdb=" N LEU O 499 " --> pdb=" O GLU O 495 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 517 through 530 removed outlier: 3.984A pdb=" N TYR O 526 " --> pdb=" O LEU O 522 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 205 No H-bonds generated for 'chain 'P' and resid 202 through 205' Processing helix chain 'P' and resid 220 through 227 Processing helix chain 'P' and resid 242 through 254 removed outlier: 4.825A pdb=" N LYS P 247 " --> pdb=" O ILE P 243 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL P 248 " --> pdb=" O TYR P 244 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU P 249 " --> pdb=" O ASP P 245 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET P 250 " --> pdb=" O GLY P 246 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA P 254 " --> pdb=" O MET P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 286 through 289 No H-bonds generated for 'chain 'P' and resid 286 through 289' Processing helix chain 'P' and resid 292 through 294 No H-bonds generated for 'chain 'P' and resid 292 through 294' Processing helix chain 'P' and resid 304 through 306 No H-bonds generated for 'chain 'P' and resid 304 through 306' Processing helix chain 'P' and resid 308 through 313 Processing helix chain 'Q' and resid 46 through 61 removed outlier: 3.780A pdb=" N THR Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY Q 51 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU Q 52 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU Q 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET Q 57 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU Q 58 " --> pdb=" O GLU Q 55 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS Q 61 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 76 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 254 through 257 removed outlier: 7.508A pdb=" N TYR A 85 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLN A 35 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP A 87 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 174 through 176 removed outlier: 4.075A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 364 through 368 removed outlier: 3.508A pdb=" N THR A 367 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 458 " --> pdb=" O ALA A 478 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 369 through 371 removed outlier: 5.917A pdb=" N PHE A 486 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 391 through 395 Processing sheet with id= G, first strand: chain 'A' and resid 420 through 422 Processing sheet with id= H, first strand: chain 'A' and resid 617 through 620 removed outlier: 6.420A pdb=" N GLN A 641 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1116 through 1120 removed outlier: 3.672A pdb=" N VAL A1173 " --> pdb=" O HIS A1168 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1211 through 1214 Processing sheet with id= K, first strand: chain 'B' and resid 80 through 82 removed outlier: 3.613A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 117 through 119 Processing sheet with id= M, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= N, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= O, first strand: chain 'B' and resid 190 through 193 removed outlier: 6.181A pdb=" N VAL B 199 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 218 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 423 through 426 Processing sheet with id= Q, first strand: chain 'B' and resid 454 through 456 Processing sheet with id= R, first strand: chain 'B' and resid 573 through 577 removed outlier: 6.244A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 547 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 630 through 634 Processing sheet with id= T, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.732A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 1003 through 1009 removed outlier: 4.392A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 927 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU B 757 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 910 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 896 through 898 Processing sheet with id= W, first strand: chain 'B' and resid 1074 through 1080 Processing sheet with id= X, first strand: chain 'C' and resid 13 through 16 removed outlier: 4.618A pdb=" N LEU C 299 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 50 through 57 removed outlier: 6.826A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 230 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.172A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 209 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 91 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 262 through 266 Processing sheet with id= AB, first strand: chain 'C' and resid 167 through 169 Processing sheet with id= AC, first strand: chain 'E' and resid 72 through 75 removed outlier: 7.299A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.823A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AF, first strand: chain 'G' and resid 3 through 13 Processing sheet with id= AG, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.989A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 83 through 87 removed outlier: 4.796A pdb=" N GLU G 83 " --> pdb=" O PHE G 150 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE G 150 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER G 189 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 25 through 31 removed outlier: 5.591A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 13 through 16 Processing sheet with id= AK, first strand: chain 'I' and resid 77 through 82 removed outlier: 3.712A pdb=" N TYR I 95 " --> pdb=" O TRP I 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS I 97 " --> pdb=" O HIS I 104 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS I 104 " --> pdb=" O CYS I 97 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'K' and resid 26 through 30 Processing sheet with id= AM, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= AN, first strand: chain 'M' and resid 14 through 18 Processing sheet with id= AO, first strand: chain 'M' and resid 26 through 29 removed outlier: 6.724A pdb=" N GLY M 131 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLN M 29 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU M 133 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU M 59 " --> pdb=" O SER M 46 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 328 through 331 removed outlier: 5.020A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N LEU N 266 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS N 382 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE N 268 " --> pdb=" O LYS N 382 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL N 384 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN N 270 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER N 386 " --> pdb=" O GLN N 270 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'N' and resid 359 through 364 removed outlier: 6.611A pdb=" N SER N 362 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL N 375 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY N 364 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N MET N 373 " --> pdb=" O GLY N 364 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.675A pdb=" N GLN O 66 " --> pdb=" O GLU O 74 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3417 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: 14.56 Time building geometry restraints manager: 17.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 13163 1.36 - 1.56: 26613 1.56 - 1.75: 97 1.75 - 1.94: 408 1.94 - 2.14: 12 Bond restraints: 40293 Sorted by residual: bond pdb=" C GLN B1082 " pdb=" N CYS B1083 " ideal model delta sigma weight residual 1.334 1.234 0.100 1.27e-02 6.20e+03 6.21e+01 bond pdb=" C PRO A 258 " pdb=" O PRO A 258 " ideal model delta sigma weight residual 1.246 1.194 0.052 8.50e-03 1.38e+04 3.74e+01 bond pdb=" C ARG A 694 " pdb=" O ARG A 694 " ideal model delta sigma weight residual 1.237 1.169 0.068 1.19e-02 7.06e+03 3.27e+01 bond pdb=" C PHE A 559 " pdb=" O PHE A 559 " ideal model delta sigma weight residual 1.234 1.167 0.067 1.18e-02 7.18e+03 3.23e+01 bond pdb=" C PRO A 91 " pdb=" O PRO A 91 " ideal model delta sigma weight residual 1.233 1.172 0.061 1.16e-02 7.43e+03 2.75e+01 ... (remaining 40288 not shown) Histogram of bond angle deviations from ideal: 84.97 - 95.56: 27 95.56 - 106.15: 1580 106.15 - 116.74: 25920 116.74 - 127.33: 26758 127.33 - 137.92: 315 Bond angle restraints: 54600 Sorted by residual: angle pdb=" C CYS B1083 " pdb=" CA CYS B1083 " pdb=" CB CYS B1083 " ideal model delta sigma weight residual 110.95 137.92 -26.97 1.55e+00 4.16e-01 3.03e+02 angle pdb=" N CYS B1083 " pdb=" CA CYS B1083 " pdb=" CB CYS B1083 " ideal model delta sigma weight residual 109.98 93.05 16.93 1.45e+00 4.76e-01 1.36e+02 angle pdb="FE2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.56 -16.86 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE3 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.55 -16.85 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE3 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb="FE4 SF4 P 401 " ideal model delta sigma weight residual 73.70 90.54 -16.84 1.50e+00 4.44e-01 1.26e+02 ... (remaining 54595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.13: 23081 28.13 - 56.27: 1404 56.27 - 84.40: 108 84.40 - 112.53: 4 112.53 - 140.67: 3 Dihedral angle restraints: 24600 sinusoidal: 10497 harmonic: 14103 Sorted by residual: dihedral pdb=" N CYS B1095 " pdb=" C CYS B1095 " pdb=" CA CYS B1095 " pdb=" CB CYS B1095 " ideal model delta harmonic sigma weight residual 122.80 92.21 30.59 0 2.50e+00 1.60e-01 1.50e+02 dihedral pdb=" C CYS B1083 " pdb=" N CYS B1083 " pdb=" CA CYS B1083 " pdb=" CB CYS B1083 " ideal model delta harmonic sigma weight residual -122.60 -143.24 20.64 0 2.50e+00 1.60e-01 6.82e+01 dihedral pdb=" C GLU A 177 " pdb=" N GLU A 177 " pdb=" CA GLU A 177 " pdb=" CB GLU A 177 " ideal model delta harmonic sigma weight residual -122.60 -142.56 19.96 0 2.50e+00 1.60e-01 6.37e+01 ... (remaining 24597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 5089 0.164 - 0.329: 971 0.329 - 0.493: 74 0.493 - 0.657: 11 0.657 - 0.821: 5 Chirality restraints: 6150 Sorted by residual: chirality pdb="FE4 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " both_signs ideal model delta sigma weight residual False 10.55 9.73 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb="FE1 SF4 P 401 " pdb=" S2 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb=" S4 SF4 P 401 " both_signs ideal model delta sigma weight residual False -10.55 -9.74 -0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb="FE2 SF4 P 401 " pdb=" S1 SF4 P 401 " pdb=" S3 SF4 P 401 " pdb=" S4 SF4 P 401 " both_signs ideal model delta sigma weight residual False 10.55 9.75 0.81 2.00e-01 2.50e+01 1.63e+01 ... (remaining 6147 not shown) Planarity restraints: 6872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B1072 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C SER B1072 " 0.079 2.00e-02 2.50e+03 pdb=" O SER B1072 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP B1073 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 693 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C ASN A 693 " 0.067 2.00e-02 2.50e+03 pdb=" O ASN A 693 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG A 694 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 39 " -0.020 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C GLN D 39 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN D 39 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN D 40 " -0.022 2.00e-02 2.50e+03 ... (remaining 6869 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 119 2.41 - 3.03: 23767 3.03 - 3.66: 58658 3.66 - 4.28: 91105 4.28 - 4.90: 149361 Nonbonded interactions: 323010 Sorted by model distance: nonbonded pdb=" OG1 THR H 78 " pdb=" NH2 ARG K 87 " model vdw 1.789 2.520 nonbonded pdb=" OE1 GLU A1112 " pdb=" CD LYS I 47 " model vdw 1.835 3.440 nonbonded pdb=" CE LYS B 721 " pdb=" OE2 GLU B 731 " model vdw 1.837 3.440 nonbonded pdb=" OE1 GLU A1143 " pdb=" OD1 ASP E 2 " model vdw 1.911 3.040 nonbonded pdb=" NZ LYS A 180 " pdb=" OD1 ASN A 182 " model vdw 1.964 2.520 ... (remaining 323005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 13.790 Check model and map are aligned: 0.670 Set scattering table: 0.380 Process input model: 108.880 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 : 0.012 0.146 40293 Z= 0.770 Angle : 1.652 26.973 54600 Z= 1.185 Chirality : 0.126 0.821 6150 Planarity : 0.007 0.073 6872 Dihedral : 16.392 140.668 15484 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.13 % Favored : 94.32 % Rotamer Outliers : 9.73 % Cbeta Deviations : 1.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.42 (0.12), residues: 4791 helix: 0.48 (0.13), residues: 1674 sheet: 0.52 (0.21), residues: 619 loop : -1.01 (0.12), residues: 2498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1746 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 415 poor density : 1331 time to evaluate : 4.721 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 outliers start: 415 outliers final: 87 residues processed: 1592 average time/residue: 0.5792 time to fit residues: 1448.7980 Evaluate side-chains 782 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 695 time to evaluate : 4.928 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 87 outliers final: 1 residues processed: 87 average time/residue: 0.4249 time to fit residues: 71.9265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 406 optimal weight: 1.9990 chunk 364 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 377 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 229 optimal weight: 0.9980 chunk 280 optimal weight: 5.9990 chunk 436 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 HIS A 163 ASN A 203 HIS A 241 ASN A 296 HIS ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 385 HIS A 397 ASN A 422 GLN A 528 ASN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 673 GLN A 791 ASN A 836 ASN A 885 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1213 HIS A1239 HIS A1336 GLN A1371 ASN B 92 ASN B 187 ASN B 215 ASN B 228 ASN B 249 GLN B 260 HIS B 276 GLN B 294 GLN B 320 HIS B 395 GLN B 434 GLN B 517 ASN B 577 ASN B 602 GLN B 608 ASN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 648 HIS B 686 GLN B 692 GLN B 738 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 GLN B1132 ASN C 48 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 13 ASN D 18 GLN D 61 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 133 GLN H 76 ASN I 21 HIS K 38 HIS K 85 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 HIS M 149 HIS M 220 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN O 155 HIS O 261 GLN O 337 ASN O 379 GLN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 415 HIS O 457 ASN O 465 GLN O 507 ASN P 200 GLN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 40293 Z= 0.280 Angle : 0.788 12.175 54600 Z= 0.409 Chirality : 0.047 0.320 6150 Planarity : 0.006 0.066 6872 Dihedral : 10.620 150.588 5751 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer Outliers : 4.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.57 (0.12), residues: 4791 helix: 0.27 (0.12), residues: 1699 sheet: 0.49 (0.20), residues: 640 loop : -1.07 (0.12), residues: 2452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 705 time to evaluate : 5.026 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 outliers start: 208 outliers final: 91 residues processed: 849 average time/residue: 0.5547 time to fit residues: 760.0947 Evaluate side-chains 630 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 539 time to evaluate : 4.983 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 0 residues processed: 91 average time/residue: 0.4169 time to fit residues: 75.0074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 242 optimal weight: 10.0000 chunk 135 optimal weight: 0.0570 chunk 363 optimal weight: 4.9990 chunk 297 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 437 optimal weight: 8.9990 chunk 472 optimal weight: 4.9990 chunk 389 optimal weight: 8.9990 chunk 433 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 351 optimal weight: 5.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 374 ASN A 397 ASN A 425 HIS A 453 HIS A 508 HIS A 511 GLN A 543 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 GLN B 249 GLN B 346 GLN B 381 ASN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN B 913 GLN B 959 HIS B1093 HIS C 139 GLN C 194 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 149 HIS O 34 GLN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 40293 Z= 0.360 Angle : 0.747 10.544 54600 Z= 0.388 Chirality : 0.047 0.239 6150 Planarity : 0.005 0.109 6872 Dihedral : 10.441 151.522 5751 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.82 % Favored : 95.09 % Rotamer Outliers : 3.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.65 (0.12), residues: 4791 helix: 0.31 (0.12), residues: 1704 sheet: 0.26 (0.20), residues: 651 loop : -1.15 (0.12), residues: 2436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 575 time to evaluate : 4.931 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 outliers start: 155 outliers final: 60 residues processed: 691 average time/residue: 0.5347 time to fit residues: 606.2536 Evaluate side-chains 541 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 481 time to evaluate : 4.903 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.3822 time to fit residues: 49.4197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 0.2980 chunk 328 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 439 optimal weight: 9.9990 chunk 464 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 416 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 304 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1213 HIS B 249 GLN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 HIS ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN B 913 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 338 GLN O 310 GLN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 451 GLN ** P 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 40293 Z= 0.316 Angle : 0.707 15.599 54600 Z= 0.359 Chirality : 0.045 0.262 6150 Planarity : 0.005 0.098 6872 Dihedral : 10.291 150.299 5751 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.07 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.55 (0.12), residues: 4791 helix: 0.47 (0.13), residues: 1716 sheet: 0.16 (0.20), residues: 644 loop : -1.11 (0.12), residues: 2431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 548 time to evaluate : 5.075 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 outliers start: 117 outliers final: 57 residues processed: 633 average time/residue: 0.5208 time to fit residues: 542.3237 Evaluate side-chains 532 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 475 time to evaluate : 4.682 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.4309 time to fit residues: 52.3332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 387 optimal weight: 5.9990 chunk 263 optimal weight: 0.7980 chunk 6 optimal weight: 0.0050 chunk 346 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 396 optimal weight: 9.9990 chunk 321 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 417 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN B 913 GLN C 25 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS G 71 HIS ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 407 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 40293 Z= 0.239 Angle : 0.665 11.056 54600 Z= 0.337 Chirality : 0.044 0.283 6150 Planarity : 0.004 0.081 6872 Dihedral : 10.125 150.153 5751 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.91 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.45 (0.12), residues: 4791 helix: 0.64 (0.13), residues: 1707 sheet: 0.03 (0.19), residues: 668 loop : -1.06 (0.12), residues: 2416 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 522 time to evaluate : 4.731 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 outliers start: 87 outliers final: 39 residues processed: 586 average time/residue: 0.5477 time to fit residues: 529.4247 Evaluate side-chains 510 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 471 time to evaluate : 4.988 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.4181 time to fit residues: 36.2125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 156 optimal weight: 2.9990 chunk 418 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 272 optimal weight: 0.0770 chunk 114 optimal weight: 2.9990 chunk 465 optimal weight: 10.0000 chunk 386 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS B 249 GLN B 346 GLN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 213 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 149 HIS ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 40293 Z= 0.246 Angle : 0.659 10.776 54600 Z= 0.333 Chirality : 0.043 0.283 6150 Planarity : 0.004 0.071 6872 Dihedral : 10.044 150.053 5751 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.80 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.39 (0.12), residues: 4791 helix: 0.67 (0.13), residues: 1712 sheet: 0.06 (0.19), residues: 657 loop : -1.01 (0.12), residues: 2422 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 501 time to evaluate : 5.003 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 outliers start: 67 outliers final: 35 residues processed: 546 average time/residue: 0.5330 time to fit residues: 482.5839 Evaluate side-chains 494 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 459 time to evaluate : 4.996 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3993 time to fit residues: 32.2955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 448 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 339 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 391 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 463 optimal weight: 20.0000 chunk 290 optimal weight: 20.0000 chunk 282 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN M 76 GLN M 80 ASN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 40293 Z= 0.283 Angle : 0.675 11.683 54600 Z= 0.341 Chirality : 0.044 0.354 6150 Planarity : 0.005 0.070 6872 Dihedral : 10.022 148.512 5751 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.39 (0.12), residues: 4791 helix: 0.66 (0.13), residues: 1731 sheet: 0.01 (0.19), residues: 657 loop : -1.01 (0.12), residues: 2403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 492 time to evaluate : 5.221 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 outliers start: 66 outliers final: 27 residues processed: 531 average time/residue: 0.5465 time to fit residues: 480.7715 Evaluate side-chains 486 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 459 time to evaluate : 5.231 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4147 time to fit residues: 27.0445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 286 optimal weight: 0.0970 chunk 185 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 89 optimal weight: 0.2980 chunk 294 optimal weight: 0.8980 chunk 315 optimal weight: 0.7980 chunk 229 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 364 optimal weight: 9.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN B 610 HIS ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 ASN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 40293 Z= 0.183 Angle : 0.665 15.457 54600 Z= 0.332 Chirality : 0.043 0.303 6150 Planarity : 0.004 0.064 6872 Dihedral : 9.887 148.724 5751 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.21 (0.12), residues: 4791 helix: 0.84 (0.13), residues: 1711 sheet: 0.19 (0.20), residues: 645 loop : -0.92 (0.13), residues: 2435 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9582 Ramachandran restraints generated. 4791 Oldfield, 0 Emsley, 4791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 520 time to evaluate : 4.952 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 outliers start: 30 outliers final: 11 residues processed: 533 average time/residue: 0.5536 time to fit residues: 484.8243 Evaluate side-chains 475 residues out of total 4275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 464 time to evaluate : 4.201 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.4104 time to fit residues: 14.3290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 421 optimal weight: 5.9990 chunk 444 optimal weight: 6.9990 chunk 405 optimal weight: 9.9990 chunk 432 optimal weight: 10.0000 chunk 260 optimal weight: 0.0050 chunk 188 optimal weight: 0.6980 chunk 339 optimal weight: 9.9990 chunk 132 optimal weight: 0.2980 chunk 390 optimal weight: 0.0870 chunk 408 optimal weight: 10.0000 chunk 430 optimal weight: 8.9990 overall best weight: 1.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: