Starting phenix.real_space_refine on Sat Feb 24 07:12:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1o_14451/02_2024/7z1o_14451_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1o_14451/02_2024/7z1o_14451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1o_14451/02_2024/7z1o_14451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1o_14451/02_2024/7z1o_14451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1o_14451/02_2024/7z1o_14451_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1o_14451/02_2024/7z1o_14451_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 66 5.49 5 Mg 1 5.21 5 S 217 5.16 5 C 26659 2.51 5 N 7301 2.21 5 O 8124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 304": "OD1" <-> "OD2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 671": "OD1" <-> "OD2" Residue "A GLU 759": "OE1" <-> "OE2" Residue "A ASP 779": "OD1" <-> "OD2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A GLU 860": "OE1" <-> "OE2" Residue "A ASP 895": "OD1" <-> "OD2" Residue "A GLU 971": "OE1" <-> "OE2" Residue "A TYR 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1099": "OE1" <-> "OE2" Residue "A GLU 1151": "OE1" <-> "OE2" Residue "A TYR 1177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1194": "OD1" <-> "OD2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "A GLU 1409": "OE1" <-> "OE2" Residue "B ASP 265": "OD1" <-> "OD2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B ASP 639": "OD1" <-> "OD2" Residue "B TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 882": "OD1" <-> "OD2" Residue "B TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 145": "OD1" <-> "OD2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "H TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 16": "OD1" <-> "OD2" Residue "J ASP 55": "OD1" <-> "OD2" Residue "M PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 239": "OE1" <-> "OE2" Residue "O TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 328": "OD1" <-> "OD2" Residue "O GLU 350": "OE1" <-> "OE2" Residue "O GLU 470": "OE1" <-> "OE2" Residue "P TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42375 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 11228 Classifications: {'peptide': 1436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 66, 'TRANS': 1369} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8693 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 41, 'TRANS': 1059} Chain breaks: 1 Chain: "C" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2647 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "D" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1185 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1594 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1083 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 1 Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 872 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain breaks: 1 Chain: "N" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1196 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain breaks: 2 Chain: "O" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4562 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Chain: "P" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1159 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain breaks: 1 Chain: "R" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna3p': 10} Chain: "S" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "T" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 597 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 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: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 500 SG CYS A 67 114.110 78.495 108.016 1.00 53.58 S ATOM 518 SG CYS A 70 112.829 74.993 107.055 1.00 54.80 S ATOM 565 SG CYS A 77 111.387 78.163 105.337 1.00 45.88 S ATOM 803 SG CYS A 107 82.264 100.569 137.711 1.00 40.77 S ATOM 826 SG CYS A 110 83.280 97.430 139.680 1.00 44.92 S ATOM 1192 SG CYS A 154 79.582 98.500 139.471 1.00 53.98 S ATOM 1216 SG CYS A 157 82.129 100.405 141.529 1.00 54.88 S ATOM 19494 SG CYS B1095 99.299 70.114 117.025 1.00 43.11 S ATOM 19517 SG CYS B1098 98.719 73.893 117.473 1.00 43.33 S ATOM 19583 SG CYS B1107 102.124 72.680 116.902 1.00 47.69 S ATOM 19603 SG CYS B1110 100.483 71.830 120.205 1.00 48.48 S ATOM 28899 SG CYS I 5 63.942 153.726 108.724 1.00 74.07 S ATOM 28918 SG CYS I 8 67.645 152.759 107.959 1.00 74.28 S ATOM 29046 SG CYS I 26 65.881 150.974 110.707 1.00 75.01 S ATOM 29069 SG CYS I 29 66.581 154.746 111.006 1.00 77.94 S ATOM 29396 SG CYS I 69 15.258 125.229 101.551 1.00162.84 S ATOM 29646 SG CYS I 100 15.666 124.848 97.072 1.00150.09 S ATOM 29667 SG CYS I 103 17.487 126.778 98.789 1.00153.60 S ATOM 29786 SG CYS J 7 93.922 91.311 38.742 1.00 32.27 S ATOM 29809 SG CYS J 10 93.339 88.437 36.224 1.00 34.22 S ATOM 30089 SG CYS J 45 90.475 90.804 37.376 1.00 33.82 S ATOM 30095 SG CYS J 46 93.278 91.781 34.951 1.00 34.66 S ATOM 31152 SG CYS L 31 127.336 110.667 59.172 1.00 59.34 S ATOM 31172 SG CYS L 34 129.174 111.554 56.007 1.00 61.23 S ATOM 31276 SG CYS L 48 131.164 110.964 59.159 1.00 66.10 S ATOM 31299 SG CYS L 51 129.028 114.069 58.915 1.00 67.77 S Time building chain proxies: 22.04, per 1000 atoms: 0.52 Number of scatterers: 42375 At special positions: 0 Unit cell: (148.863, 193.626, 196.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 217 16.00 P 66 15.00 Mg 1 11.99 O 8124 8.00 N 7301 7.00 C 26659 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: 16.54 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1110 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 26 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 100 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 69 " pdb=" ZN J 100 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 33 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 189 helices and 48 sheets defined 35.4% alpha, 13.0% beta 14 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 19.42 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 134 through 149 Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 209 through 214 removed outlier: 3.861A pdb=" N ARG A 213 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.937A pdb=" N GLN A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) 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 253 through 256 Processing helix chain 'A' and resid 284 through 305 Processing helix chain 'A' and resid 309 through 327 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 363 through 366 No H-bonds generated for 'chain 'A' and resid 363 through 366' Processing helix chain 'A' and resid 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 451 through 454 No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 677 through 685 Processing helix chain 'A' and resid 687 through 707 removed outlier: 4.035A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 747 removed outlier: 4.079A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 784 removed outlier: 3.594A pdb=" N GLU A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 858 through 893 removed outlier: 4.409A pdb=" N THR A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 956 through 972 Proline residue: A 969 - end of helix Processing helix chain 'A' and resid 986 through 988 No H-bonds generated for 'chain 'A' and resid 986 through 988' Processing helix chain 'A' and resid 992 through 994 No H-bonds generated for 'chain 'A' and resid 992 through 994' Processing helix chain 'A' and resid 999 through 1025 Processing helix chain 'A' and resid 1052 through 1059 Processing helix chain 'A' and resid 1064 through 1080 Processing helix chain 'A' and resid 1089 through 1101 Proline residue: A1100 - end of helix Processing helix chain 'A' and resid 1123 through 1130 Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 3.521A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1190 through 1196 Processing helix chain 'A' and resid 1202 through 1211 Processing helix chain 'A' and resid 1255 through 1269 Proline residue: A1268 - end of helix Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1319 through 1325 Processing helix chain 'A' and resid 1328 through 1346 removed outlier: 3.755A pdb=" N HIS A1346 " --> pdb=" O THR A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 Processing helix chain 'A' and resid 1373 through 1379 Processing helix chain 'A' and resid 1383 through 1387 Processing helix chain 'A' and resid 1392 through 1402 Processing helix chain 'A' and resid 1411 through 1417 Processing helix chain 'A' and resid 1424 through 1426 No H-bonds generated for 'chain 'A' and resid 1424 through 1426' Processing helix chain 'A' and resid 1439 through 1441 No H-bonds generated for 'chain 'A' and resid 1439 through 1441' Processing helix chain 'A' and resid 1447 through 1451 Processing helix chain 'B' and resid 41 through 54 removed outlier: 4.396A pdb=" N TRP B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS B 46 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 59 through 70 Processing helix chain 'B' and resid 72 through 79 Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 277 through 292 removed outlier: 4.988A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 removed outlier: 4.232A pdb=" N LYS B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 343 through 361 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 380 through 407 removed outlier: 3.644A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 421 Processing helix chain 'B' and resid 423 through 438 removed outlier: 3.704A pdb=" N ASN B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 527 through 536 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 624 through 632 Processing helix chain 'B' and resid 637 through 643 Processing helix chain 'B' and resid 651 through 655 Processing helix chain 'B' and resid 663 through 665 No H-bonds generated for 'chain 'B' and resid 663 through 665' Processing helix chain 'B' and resid 677 through 680 Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 691 through 693 No H-bonds generated for 'chain 'B' and resid 691 through 693' Processing helix chain 'B' and resid 696 through 708 removed outlier: 4.405A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 743 Processing helix chain 'B' and resid 764 through 766 No H-bonds generated for 'chain 'B' and resid 764 through 766' Processing helix chain 'B' and resid 775 through 779 Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing helix chain 'B' and resid 946 through 950 Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 955 through 970 Processing helix chain 'B' and resid 984 through 993 Processing helix chain 'B' and resid 1031 through 1033 No H-bonds generated for 'chain 'B' and resid 1031 through 1033' Processing helix chain 'B' and resid 1054 through 1056 No H-bonds generated for 'chain 'B' and resid 1054 through 1056' Processing helix chain 'B' and resid 1064 through 1073 Processing helix chain 'B' and resid 1076 through 1083 Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 122 through 125 No H-bonds generated for 'chain 'C' and resid 122 through 125' Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.838A pdb=" N THR C 178 " --> pdb=" O GLN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 310 through 330 Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 53 through 67 Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.806A pdb=" N SER D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 147 through 158 Processing helix chain 'E' and resid 2 through 25 removed outlier: 3.943A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 125 removed outlier: 4.065A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Proline residue: E 125 - end of helix Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 117 through 126 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 34 Processing helix chain 'G' and resid 163 through 174 removed outlier: 3.512A pdb=" N GLU G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 92 removed outlier: 3.924A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 89 through 92' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 removed outlier: 3.770A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.741A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 63 removed outlier: 3.538A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 removed outlier: 4.536A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 141 Processing helix chain 'M' and resid 133 through 139 Processing helix chain 'M' and resid 184 through 198 Processing helix chain 'M' and resid 230 through 239 Processing helix chain 'M' and resid 252 through 265 removed outlier: 4.283A pdb=" N ASP M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 279 removed outlier: 3.572A pdb=" N ILE M 278 " --> pdb=" O GLN M 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 199 Processing helix chain 'N' and resid 209 through 211 No H-bonds generated for 'chain 'N' and resid 209 through 211' Processing helix chain 'N' and resid 216 through 222 removed outlier: 3.562A pdb=" N GLU N 221 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 296 Processing helix chain 'O' and resid 28 through 34 Processing helix chain 'O' and resid 39 through 41 No H-bonds generated for 'chain 'O' and resid 39 through 41' Processing helix chain 'O' and resid 44 through 56 Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 76 through 82 Processing helix chain 'O' and resid 88 through 100 Processing helix chain 'O' and resid 124 through 131 Processing helix chain 'O' and resid 133 through 143 Processing helix chain 'O' and resid 151 through 166 Processing helix chain 'O' and resid 171 through 177 removed outlier: 4.180A pdb=" N SER O 177 " --> pdb=" O ASP O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 196 Processing helix chain 'O' and resid 211 through 224 Processing helix chain 'O' and resid 234 through 258 Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 284 through 302 removed outlier: 3.840A pdb=" N THR O 302 " --> pdb=" O ASN O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 318 Processing helix chain 'O' and resid 329 through 332 Processing helix chain 'O' and resid 339 through 355 removed outlier: 3.779A pdb=" N GLU O 354 " --> pdb=" O GLU O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 367 Processing helix chain 'O' and resid 450 through 461 Processing helix chain 'O' and resid 480 through 500 removed outlier: 3.851A pdb=" N MET O 484 " --> pdb=" O TYR O 480 " (cutoff:3.500A) Proline residue: O 485 - end of helix Processing helix chain 'O' and resid 502 through 513 Processing helix chain 'O' and resid 519 through 525 Processing helix chain 'O' and resid 530 through 543 removed outlier: 3.767A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR O 543 " --> pdb=" O SER O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 570 through 598 Processing helix chain 'O' and resid 600 through 606 Processing helix chain 'O' and resid 615 through 618 No H-bonds generated for 'chain 'O' and resid 615 through 618' Processing helix chain 'O' and resid 621 through 648 Processing helix chain 'P' and resid 172 through 190 Processing helix chain 'P' and resid 218 through 228 Processing helix chain 'P' and resid 237 through 249 Processing helix chain 'P' and resid 265 through 271 removed outlier: 3.707A pdb=" N MET P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 296 through 298 No H-bonds generated for 'chain 'P' and resid 296 through 298' Processing helix chain 'Q' and resid 42 through 44 No H-bonds generated for 'chain 'Q' and resid 42 through 44' Processing helix chain 'Q' and resid 49 through 66 Processing helix chain 'Q' and resid 129 through 131 No H-bonds generated for 'chain 'Q' and resid 129 through 131' Processing helix chain 'Q' and resid 134 through 136 No H-bonds generated for 'chain 'Q' and resid 134 through 136' Processing sheet with id= A, first strand: chain 'A' and resid 15 through 17 Processing sheet with id= B, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= C, first strand: chain 'A' and resid 163 through 166 Processing sheet with id= D, first strand: chain 'A' and resid 376 through 380 Processing sheet with id= E, first strand: chain 'A' and resid 381 through 383 removed outlier: 6.066A pdb=" N PHE A 498 " --> pdb=" O SER A 382 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.855A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 626 through 629 removed outlier: 3.553A pdb=" N ILE A 653 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 661 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG A 655 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1140 through 1144 removed outlier: 3.707A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1222 through 1225 removed outlier: 4.455A pdb=" N SER A1182 " --> pdb=" O VAL A1234 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 82 through 84 removed outlier: 5.476A pdb=" N TYR B 92 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 126 through 128 Processing sheet with id= L, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= M, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= N, first strand: chain 'B' and resid 205 through 210 removed outlier: 4.459A pdb=" N VAL B 216 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 441 through 444 Processing sheet with id= P, first strand: chain 'B' and resid 589 through 593 removed outlier: 6.382A pdb=" N GLY B 554 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE B 601 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 553 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 563 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 557 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 609 through 613 Processing sheet with id= R, first strand: chain 'B' and resid 724 through 728 removed outlier: 4.011A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 1018 through 1024 removed outlier: 4.225A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 942 " --> pdb=" O ALA B 758 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 846 through 848 Processing sheet with id= U, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id= V, first strand: chain 'B' and resid 771 through 774 removed outlier: 7.595A pdb=" N LEU B 773 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE B 925 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.526A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.603A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 226 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.409A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 256 through 258 Processing sheet with id= AA, first strand: chain 'C' and resid 161 through 163 Processing sheet with id= AB, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.928A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.781A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 133 through 135 Processing sheet with id= AE, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.660A pdb=" N THR G 47 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE G 77 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N CYS G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.524A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS G 91 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N SER G 100 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ILE G 89 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU G 197 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU G 153 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA G 195 " --> pdb=" O GLU G 153 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.811A pdb=" N THR G 122 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA G 127 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.855A pdb=" N THR G 71 " --> pdb=" O LEU G 52 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.174A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 12 through 15 removed outlier: 4.667A pdb=" N TYR I 31 " --> pdb=" O CYS I 26 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 64 through 66 Processing sheet with id= AL, first strand: chain 'K' and resid 47 through 49 Processing sheet with id= AM, first strand: chain 'L' and resid 29 through 31 Processing sheet with id= AN, first strand: chain 'M' and resid 76 through 79 removed outlier: 6.415A pdb=" N VAL M 168 " --> pdb=" O LYS M 77 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER M 79 " --> pdb=" O VAL M 168 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU M 170 " --> pdb=" O SER M 79 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'M' and resid 180 through 182 removed outlier: 4.331A pdb=" N THR M 147 " --> pdb=" O PHE M 182 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU M 118 " --> pdb=" O LYS M 113 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA M 109 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE M 107 " --> pdb=" O PRO M 124 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 152 through 154 removed outlier: 7.330A pdb=" N LEU M 85 " --> pdb=" O GLU M 174 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL M 176 " --> pdb=" O LEU M 85 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL M 87 " --> pdb=" O VAL M 176 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN M 178 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN M 89 " --> pdb=" O GLN M 178 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'N' and resid 306 through 308 removed outlier: 4.464A pdb=" N ILE N 382 " --> pdb=" O LEU N 371 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU N 371 " --> pdb=" O ILE N 382 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'N' and resid 393 through 398 removed outlier: 3.962A pdb=" N GLY N 410 " --> pdb=" O VAL N 394 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA N 396 " --> pdb=" O LEU N 408 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU N 408 " --> pdb=" O ALA N 396 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER N 398 " --> pdb=" O ALA N 406 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ALA N 406 " --> pdb=" O SER N 398 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'O' and resid 106 through 110 Processing sheet with id= AT, first strand: chain 'O' and resid 168 through 170 Processing sheet with id= AU, first strand: chain 'O' and resid 547 through 551 Processing sheet with id= AV, first strand: chain 'P' and resid 253 through 257 removed outlier: 3.721A pdb=" N VAL P 256 " --> pdb=" O CYS P 260 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS P 260 " --> pdb=" O VAL P 256 " (cutoff:3.500A) 1418 hydrogen bonds defined for protein. 4083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 20.53 Time building geometry restraints manager: 16.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13402 1.34 - 1.46: 7764 1.46 - 1.58: 21622 1.58 - 1.70: 138 1.70 - 1.82: 352 Bond restraints: 43278 Sorted by residual: bond pdb=" C LEU A1267 " pdb=" N PRO A1268 " ideal model delta sigma weight residual 1.334 1.363 -0.029 8.40e-03 1.42e+04 1.20e+01 bond pdb=" C15 1N7 C 401 " pdb=" C16 1N7 C 401 " ideal model delta sigma weight residual 1.530 1.594 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C16 1N7 C 401 " pdb=" C17 1N7 C 401 " ideal model delta sigma weight residual 1.527 1.590 -0.063 2.00e-02 2.50e+03 9.84e+00 bond pdb=" C15 1N7 A2003 " pdb=" C16 1N7 A2003 " ideal model delta sigma weight residual 1.530 1.592 -0.062 2.00e-02 2.50e+03 9.76e+00 bond pdb=" C19 1N7 A2003 " pdb=" C2 1N7 A2003 " ideal model delta sigma weight residual 1.551 1.613 -0.062 2.00e-02 2.50e+03 9.52e+00 ... (remaining 43273 not shown) Histogram of bond angle deviations from ideal: 94.95 - 102.78: 303 102.78 - 110.62: 12797 110.62 - 118.45: 21196 118.45 - 126.29: 23769 126.29 - 134.12: 668 Bond angle restraints: 58733 Sorted by residual: angle pdb=" CA PRO O 473 " pdb=" N PRO O 473 " pdb=" CD PRO O 473 " ideal model delta sigma weight residual 112.00 103.76 8.24 1.40e+00 5.10e-01 3.46e+01 angle pdb=" CA PRO O 256 " pdb=" N PRO O 256 " pdb=" CD PRO O 256 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" N ILE A 550 " pdb=" CA ILE A 550 " pdb=" C ILE A 550 " ideal model delta sigma weight residual 113.53 108.68 4.85 9.80e-01 1.04e+00 2.45e+01 angle pdb=" N ALA D 129 " pdb=" CA ALA D 129 " pdb=" C ALA D 129 " ideal model delta sigma weight residual 114.04 108.09 5.95 1.24e+00 6.50e-01 2.30e+01 angle pdb=" C GLU P 314 " pdb=" N TRP P 315 " pdb=" CA TRP P 315 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 ... (remaining 58728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.48: 25365 27.48 - 54.95: 1027 54.95 - 82.43: 115 82.43 - 109.91: 2 109.91 - 137.39: 2 Dihedral angle restraints: 26511 sinusoidal: 11488 harmonic: 15023 Sorted by residual: dihedral pdb=" CA ASN O 514 " pdb=" C ASN O 514 " pdb=" N LYS O 515 " pdb=" CA LYS O 515 " ideal model delta harmonic sigma weight residual 180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA MET B 469 " pdb=" C MET B 469 " pdb=" N MET B 470 " pdb=" CA MET B 470 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLU O 149 " pdb=" C GLU O 149 " pdb=" N GLU O 150 " pdb=" CA GLU O 150 " ideal model delta harmonic sigma weight residual 180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 26508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5738 0.068 - 0.135: 857 0.135 - 0.203: 30 0.203 - 0.270: 7 0.270 - 0.338: 4 Chirality restraints: 6636 Sorted by residual: chirality pdb=" C9 1N7 C 401 " pdb=" C20 1N7 C 401 " pdb=" C5 1N7 C 401 " pdb=" C8 1N7 C 401 " both_signs ideal model delta sigma weight residual False 2.62 2.96 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C9 1N7 A2003 " pdb=" C20 1N7 A2003 " pdb=" C5 1N7 A2003 " pdb=" C8 1N7 A2003 " both_signs ideal model delta sigma weight residual False 2.62 2.95 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C17 1N7 C 401 " pdb=" C16 1N7 C 401 " pdb=" C18 1N7 C 401 " pdb=" O3 1N7 C 401 " both_signs ideal model delta sigma weight residual False 2.40 2.71 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 6633 not shown) Planarity restraints: 7320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS O 255 " -0.090 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO O 256 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO O 256 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO O 256 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 472 " -0.078 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO O 473 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO O 473 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO O 473 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 124 " -0.051 5.00e-02 4.00e+02 7.68e-02 9.45e+00 pdb=" N PRO E 125 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO E 125 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 125 " -0.043 5.00e-02 4.00e+02 ... (remaining 7317 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 361 2.63 - 3.20: 35772 3.20 - 3.76: 65196 3.76 - 4.33: 91863 4.33 - 4.90: 152679 Nonbonded interactions: 345871 Sorted by model distance: nonbonded pdb=" O3' C R 19 " pdb="MG MG A2002 " model vdw 2.062 2.170 nonbonded pdb=" OD1 ASP A 511 " pdb="MG MG A2002 " model vdw 2.083 2.170 nonbonded pdb=" OD1 ASP A 513 " pdb="MG MG A2002 " model vdw 2.156 2.170 nonbonded pdb=" O VAL O 31 " pdb=" OG SER O 35 " model vdw 2.207 2.440 nonbonded pdb=" OG1 THR B 231 " pdb=" O VAL B 331 " model vdw 2.218 2.440 ... (remaining 345866 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 individual isotropic 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: 2.160 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: 11.060 Check model and map are aligned: 0.640 Set scattering table: 0.390 Process input model: 126.850 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 : 0.004 0.103 43278 Z= 0.235 Angle : 0.654 11.709 58733 Z= 0.349 Chirality : 0.046 0.338 6636 Planarity : 0.005 0.132 7320 Dihedral : 14.182 137.386 16791 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.03 (0.11), residues: 5092 helix: 0.59 (0.11), residues: 1877 sheet: 0.33 (0.20), residues: 697 loop : -0.42 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 185 HIS 0.007 0.001 HIS L 53 PHE 0.027 0.001 PHE B1018 TYR 0.017 0.001 TYR B 416 ARG 0.015 0.000 ARG B 915 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 593 time to evaluate : 5.043 Fit side-chains REVERT: A 775 GLU cc_start: 0.6899 (tp30) cc_final: 0.6681 (mm-30) REVERT: A 819 SER cc_start: 0.8265 (t) cc_final: 0.8046 (m) REVERT: A 890 MET cc_start: 0.7585 (tpp) cc_final: 0.7344 (tpp) REVERT: A 1060 TYR cc_start: 0.7638 (m-80) cc_final: 0.7430 (m-80) REVERT: A 1127 LYS cc_start: 0.7852 (tttm) cc_final: 0.7427 (ttpt) REVERT: A 1210 THR cc_start: 0.8126 (m) cc_final: 0.7908 (m) REVERT: A 1337 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7319 (mtm110) REVERT: B 882 ASP cc_start: 0.7060 (t0) cc_final: 0.6808 (t0) REVERT: B 1084 MET cc_start: 0.8018 (ttp) cc_final: 0.7812 (ttm) REVERT: C 9 TYR cc_start: 0.8608 (p90) cc_final: 0.8300 (p90) REVERT: F 115 THR cc_start: 0.8847 (p) cc_final: 0.8639 (p) REVERT: G 75 VAL cc_start: 0.7387 (t) cc_final: 0.7132 (m) REVERT: H 25 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8167 (ttm-80) REVERT: O 629 MET cc_start: 0.6716 (mmp) cc_final: 0.6399 (mpp) REVERT: Q 65 VAL cc_start: 0.7936 (t) cc_final: 0.7734 (t) outliers start: 0 outliers final: 2 residues processed: 593 average time/residue: 1.6892 time to fit residues: 1204.9469 Evaluate side-chains 493 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 491 time to evaluate : 5.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 722 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 433 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 402 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 299 optimal weight: 7.9990 chunk 465 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN A 821 ASN A1262 GLN B 80 ASN B 237 ASN B 837 GLN C 158 ASN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN O 652 GLN Q 138 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 43278 Z= 0.526 Angle : 0.625 9.438 58733 Z= 0.322 Chirality : 0.048 0.274 6636 Planarity : 0.005 0.083 7320 Dihedral : 11.623 145.449 6494 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.54 % Allowed : 8.70 % Favored : 89.76 % 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: 0.16 (0.11), residues: 5092 helix: 0.86 (0.12), residues: 1883 sheet: 0.16 (0.19), residues: 759 loop : -0.43 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 79 HIS 0.013 0.002 HIS A 427 PHE 0.033 0.002 PHE B1018 TYR 0.020 0.002 TYR E 112 ARG 0.014 0.001 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 525 time to evaluate : 4.652 Fit side-chains REVERT: A 361 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7645 (mm-40) REVERT: A 505 CYS cc_start: 0.7225 (p) cc_final: 0.6877 (p) REVERT: A 583 MET cc_start: 0.8725 (ptp) cc_final: 0.8403 (ptp) REVERT: A 658 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7392 (mm110) REVERT: A 775 GLU cc_start: 0.6830 (tp30) cc_final: 0.6628 (mm-30) REVERT: A 784 GLU cc_start: 0.6989 (tp30) cc_final: 0.6678 (tp30) REVERT: A 909 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.7971 (t0) REVERT: A 1210 THR cc_start: 0.8142 (m) cc_final: 0.7903 (m) REVERT: A 1294 LEU cc_start: 0.8023 (pp) cc_final: 0.7789 (pt) REVERT: B 135 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.6356 (p90) REVERT: B 239 LYS cc_start: 0.8238 (mtpt) cc_final: 0.8013 (mtpt) REVERT: B 628 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.7228 (ttm-80) REVERT: B 882 ASP cc_start: 0.7151 (t0) cc_final: 0.6853 (t0) REVERT: C 9 TYR cc_start: 0.8699 (p90) cc_final: 0.8365 (p90) REVERT: E 50 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.6031 (pp-130) REVERT: E 73 PRO cc_start: 0.8426 (Cg_endo) cc_final: 0.8214 (Cg_exo) REVERT: G 75 VAL cc_start: 0.7473 (t) cc_final: 0.7117 (m) REVERT: G 84 ILE cc_start: 0.8517 (pt) cc_final: 0.8189 (pp) REVERT: M 133 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6772 (mppt) REVERT: M 261 LYS cc_start: 0.7482 (tmmt) cc_final: 0.7198 (tmmm) REVERT: O 144 MET cc_start: 0.7140 (ptp) cc_final: 0.6841 (ptp) REVERT: O 183 MET cc_start: 0.7386 (tpp) cc_final: 0.6986 (mmp) REVERT: O 317 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7211 (mpt-90) REVERT: O 343 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7090 (mppt) REVERT: O 542 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6904 (mmm160) REVERT: O 629 MET cc_start: 0.6664 (mmp) cc_final: 0.6356 (mpp) REVERT: Q 63 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7211 (mtmm) outliers start: 70 outliers final: 27 residues processed: 556 average time/residue: 1.6428 time to fit residues: 1107.4152 Evaluate side-chains 537 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 500 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain O residue 596 LYS Chi-restraints excluded: chain P residue 216 SER Chi-restraints excluded: chain Q residue 63 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 258 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 387 optimal weight: 1.9990 chunk 317 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 466 optimal weight: 0.6980 chunk 504 optimal weight: 1.9990 chunk 415 optimal weight: 9.9990 chunk 462 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 374 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 ASN A 821 ASN A1262 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43278 Z= 0.216 Angle : 0.491 7.847 58733 Z= 0.258 Chirality : 0.042 0.191 6636 Planarity : 0.004 0.066 7320 Dihedral : 11.433 141.131 6489 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.58 % Allowed : 11.01 % Favored : 87.41 % 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: 0.47 (0.12), residues: 5092 helix: 1.27 (0.12), residues: 1878 sheet: 0.22 (0.19), residues: 705 loop : -0.33 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 215 HIS 0.006 0.001 HIS A 427 PHE 0.021 0.001 PHE B 678 TYR 0.016 0.001 TYR B 92 ARG 0.007 0.000 ARG B 874 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 506 time to evaluate : 4.850 Fit side-chains REVERT: A 505 CYS cc_start: 0.7209 (p) cc_final: 0.6932 (p) REVERT: A 658 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7349 (mm110) REVERT: A 774 ARG cc_start: 0.6996 (ttt180) cc_final: 0.6697 (ttt180) REVERT: A 775 GLU cc_start: 0.6822 (tp30) cc_final: 0.6620 (mm-30) REVERT: A 784 GLU cc_start: 0.6979 (tp30) cc_final: 0.6635 (tp30) REVERT: A 909 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.7970 (t0) REVERT: A 915 THR cc_start: 0.8077 (m) cc_final: 0.7840 (t) REVERT: A 1058 GLN cc_start: 0.7878 (mt0) cc_final: 0.7633 (mt0) REVERT: A 1210 THR cc_start: 0.8130 (m) cc_final: 0.7905 (m) REVERT: A 1294 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7745 (pp) REVERT: B 239 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7907 (mtpt) REVERT: B 250 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: B 628 ARG cc_start: 0.7455 (ttp-110) cc_final: 0.7200 (ttm-80) REVERT: B 639 ASP cc_start: 0.6964 (t70) cc_final: 0.6710 (t0) REVERT: C 9 TYR cc_start: 0.8658 (p90) cc_final: 0.8290 (p90) REVERT: C 38 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7898 (ttpp) REVERT: E 73 PRO cc_start: 0.8390 (Cg_endo) cc_final: 0.8189 (Cg_exo) REVERT: G 84 ILE cc_start: 0.8481 (pt) cc_final: 0.8184 (pp) REVERT: G 167 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5620 (mp0) REVERT: H 25 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.8013 (ttt90) REVERT: M 261 LYS cc_start: 0.7467 (tmmt) cc_final: 0.7188 (tppt) REVERT: O 144 MET cc_start: 0.6938 (ptp) cc_final: 0.6640 (ptp) REVERT: O 183 MET cc_start: 0.7321 (tpp) cc_final: 0.6925 (mmp) REVERT: O 317 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7179 (mpt-90) REVERT: O 343 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7047 (mppt) REVERT: O 542 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6835 (mmm160) REVERT: O 629 MET cc_start: 0.6771 (mmp) cc_final: 0.6369 (mpp) REVERT: Q 65 VAL cc_start: 0.8150 (t) cc_final: 0.7916 (t) outliers start: 72 outliers final: 26 residues processed: 534 average time/residue: 1.6340 time to fit residues: 1058.0703 Evaluate side-chains 525 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 491 time to evaluate : 4.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain P residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 461 optimal weight: 7.9990 chunk 350 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 468 optimal weight: 0.0980 chunk 495 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 443 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN A1131 ASN A1262 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 43278 Z= 0.425 Angle : 0.562 8.620 58733 Z= 0.291 Chirality : 0.045 0.200 6636 Planarity : 0.005 0.066 7320 Dihedral : 11.539 141.063 6489 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.29 % Allowed : 11.87 % Favored : 85.85 % 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: 0.38 (0.12), residues: 5092 helix: 1.18 (0.12), residues: 1880 sheet: 0.13 (0.19), residues: 727 loop : -0.36 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 258 HIS 0.010 0.001 HIS A 427 PHE 0.020 0.002 PHE B1018 TYR 0.018 0.002 TYR A 326 ARG 0.009 0.001 ARG O 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 514 time to evaluate : 4.736 Fit side-chains REVERT: A 361 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7664 (mm-40) REVERT: A 774 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6752 (ttt180) REVERT: A 784 GLU cc_start: 0.7025 (tp30) cc_final: 0.6630 (tp30) REVERT: A 909 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.7974 (t0) REVERT: A 1173 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7647 (t) REVERT: A 1210 THR cc_start: 0.8126 (m) cc_final: 0.7905 (m) REVERT: A 1294 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7697 (pp) REVERT: A 1380 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6778 (mmp-170) REVERT: A 1409 GLU cc_start: 0.6859 (pt0) cc_final: 0.6501 (pm20) REVERT: B 109 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7396 (mtmm) REVERT: B 239 LYS cc_start: 0.8236 (mppt) cc_final: 0.7921 (mtpt) REVERT: B 628 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.7176 (ttm-80) REVERT: B 639 ASP cc_start: 0.7047 (t70) cc_final: 0.6789 (t0) REVERT: B 882 ASP cc_start: 0.7105 (t0) cc_final: 0.6791 (t0) REVERT: C 9 TYR cc_start: 0.8714 (p90) cc_final: 0.8370 (p90) REVERT: C 38 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7915 (ttpp) REVERT: E 75 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7941 (mtt) REVERT: G 84 ILE cc_start: 0.8560 (pt) cc_final: 0.8241 (pp) REVERT: G 167 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5582 (mp0) REVERT: H 55 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7543 (pp) REVERT: K 71 THR cc_start: 0.8184 (t) cc_final: 0.7947 (m) REVERT: M 133 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7227 (mptt) REVERT: M 261 LYS cc_start: 0.7564 (tmmt) cc_final: 0.7236 (tppt) REVERT: M 282 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7283 (t) REVERT: O 317 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7027 (mpt-90) REVERT: O 343 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7097 (mppt) REVERT: O 542 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6887 (mmm160) REVERT: O 629 MET cc_start: 0.6755 (mmp) cc_final: 0.6430 (mpp) REVERT: O 653 MET cc_start: 0.7148 (mmt) cc_final: 0.4955 (mmt) outliers start: 104 outliers final: 46 residues processed: 555 average time/residue: 1.6340 time to fit residues: 1105.6540 Evaluate side-chains 564 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 503 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1381 ASP Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 722 ASP Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain O residue 192 VAL Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 362 ASN Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain P residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 412 optimal weight: 6.9990 chunk 281 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 369 optimal weight: 9.9990 chunk 204 optimal weight: 0.3980 chunk 423 optimal weight: 2.9990 chunk 342 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 445 optimal weight: 0.1980 chunk 125 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN A1131 ASN A1262 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43278 Z= 0.186 Angle : 0.481 7.954 58733 Z= 0.252 Chirality : 0.041 0.191 6636 Planarity : 0.004 0.065 7320 Dihedral : 11.401 140.606 6489 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.96 % Allowed : 13.19 % Favored : 84.86 % 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: 0.61 (0.12), residues: 5092 helix: 1.43 (0.12), residues: 1879 sheet: 0.19 (0.19), residues: 714 loop : -0.26 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 215 HIS 0.005 0.001 HIS A 427 PHE 0.019 0.001 PHE B 678 TYR 0.014 0.001 TYR B 92 ARG 0.008 0.000 ARG B 874 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 503 time to evaluate : 4.734 Fit side-chains REVERT: A 774 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6725 (ttt180) REVERT: A 784 GLU cc_start: 0.7027 (tp30) cc_final: 0.6649 (tp30) REVERT: A 819 SER cc_start: 0.8485 (t) cc_final: 0.8200 (m) REVERT: A 915 THR cc_start: 0.8084 (m) cc_final: 0.7854 (t) REVERT: A 1173 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7591 (t) REVERT: A 1210 THR cc_start: 0.8109 (m) cc_final: 0.7892 (m) REVERT: A 1294 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7658 (pp) REVERT: B 239 LYS cc_start: 0.8197 (mppt) cc_final: 0.7893 (mtpt) REVERT: B 250 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: B 281 ASP cc_start: 0.7312 (m-30) cc_final: 0.6920 (m-30) REVERT: B 639 ASP cc_start: 0.7095 (t70) cc_final: 0.6819 (t0) REVERT: B 882 ASP cc_start: 0.7111 (t0) cc_final: 0.6810 (t0) REVERT: C 9 TYR cc_start: 0.8671 (p90) cc_final: 0.8324 (p90) REVERT: E 69 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7716 (tp) REVERT: G 84 ILE cc_start: 0.8537 (pt) cc_final: 0.8291 (pp) REVERT: G 114 MET cc_start: 0.7246 (ptp) cc_final: 0.7013 (pmm) REVERT: G 167 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5602 (mp0) REVERT: H 55 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7465 (pp) REVERT: M 240 GLU cc_start: 0.7359 (tt0) cc_final: 0.7081 (tt0) REVERT: M 261 LYS cc_start: 0.7540 (tmmt) cc_final: 0.7206 (tppt) REVERT: M 282 VAL cc_start: 0.7694 (OUTLIER) cc_final: 0.7275 (t) REVERT: N 312 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6662 (ttp-170) REVERT: O 317 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7157 (mpt-90) REVERT: O 343 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7039 (mppt) REVERT: O 542 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6818 (mmm160) REVERT: O 629 MET cc_start: 0.6752 (mmp) cc_final: 0.6431 (mpp) REVERT: Q 65 VAL cc_start: 0.8147 (t) cc_final: 0.7907 (t) REVERT: Q 140 MET cc_start: 0.8495 (mtp) cc_final: 0.8274 (mtm) outliers start: 89 outliers final: 36 residues processed: 544 average time/residue: 1.6711 time to fit residues: 1105.8037 Evaluate side-chains 534 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 487 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 722 ASP Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 362 ASN Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain O residue 596 LYS Chi-restraints excluded: chain P residue 216 SER Chi-restraints excluded: chain P residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 166 optimal weight: 3.9990 chunk 446 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 496 optimal weight: 5.9990 chunk 412 optimal weight: 0.7980 chunk 229 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 260 optimal weight: 2.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN A1262 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Q 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 43278 Z= 0.326 Angle : 0.529 8.703 58733 Z= 0.273 Chirality : 0.043 0.198 6636 Planarity : 0.004 0.060 7320 Dihedral : 11.438 140.404 6489 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.62 % Allowed : 13.58 % Favored : 83.80 % 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: 5092 helix: 1.37 (0.12), residues: 1881 sheet: 0.12 (0.19), residues: 722 loop : -0.27 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 215 HIS 0.009 0.001 HIS A 427 PHE 0.020 0.001 PHE O 217 TYR 0.017 0.001 TYR J 44 ARG 0.011 0.000 ARG O 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 502 time to evaluate : 5.043 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7671 (mm-40) REVERT: A 714 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8010 (tp) REVERT: A 784 GLU cc_start: 0.7029 (tp30) cc_final: 0.6616 (tp30) REVERT: A 915 THR cc_start: 0.8105 (m) cc_final: 0.7872 (t) REVERT: A 1158 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7154 (ttmm) REVERT: A 1173 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7625 (t) REVERT: A 1210 THR cc_start: 0.8132 (m) cc_final: 0.7913 (m) REVERT: A 1294 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7721 (pp) REVERT: A 1373 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7361 (ptp-170) REVERT: A 1380 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6732 (mmp-170) REVERT: B 109 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7349 (mtmm) REVERT: B 239 LYS cc_start: 0.8212 (mppt) cc_final: 0.7873 (mtpt) REVERT: B 250 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7250 (mt-10) REVERT: B 281 ASP cc_start: 0.7305 (m-30) cc_final: 0.6893 (m-30) REVERT: B 639 ASP cc_start: 0.7105 (t70) cc_final: 0.6852 (t0) REVERT: B 882 ASP cc_start: 0.7110 (t0) cc_final: 0.6800 (t0) REVERT: C 9 TYR cc_start: 0.8702 (p90) cc_final: 0.8335 (p90) REVERT: E 17 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6851 (ttt-90) REVERT: E 69 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7783 (tp) REVERT: G 84 ILE cc_start: 0.8552 (pt) cc_final: 0.8237 (pp) REVERT: G 167 GLU cc_start: 0.5938 (OUTLIER) cc_final: 0.5577 (mp0) REVERT: H 55 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7514 (pp) REVERT: M 261 LYS cc_start: 0.7559 (tmmt) cc_final: 0.7215 (tppt) REVERT: M 282 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7348 (t) REVERT: N 312 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6675 (ttp-170) REVERT: O 183 MET cc_start: 0.7348 (tpp) cc_final: 0.6952 (mmp) REVERT: O 317 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7124 (mpt-90) REVERT: O 343 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7074 (mppt) REVERT: O 542 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6890 (mmm160) REVERT: O 629 MET cc_start: 0.6748 (mmp) cc_final: 0.6443 (mpp) REVERT: Q 65 VAL cc_start: 0.8291 (t) cc_final: 0.7992 (p) REVERT: Q 140 MET cc_start: 0.8560 (mtp) cc_final: 0.8308 (mtm) outliers start: 119 outliers final: 59 residues processed: 566 average time/residue: 1.6251 time to fit residues: 1123.6920 Evaluate side-chains 570 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 493 time to evaluate : 4.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 1158 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1373 ARG Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1381 ASP Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 722 ASP Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 151 GLU Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 362 ASN Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain O residue 596 LYS Chi-restraints excluded: chain P residue 216 SER Chi-restraints excluded: chain P residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 478 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 362 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 417 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 494 optimal weight: 3.9990 chunk 309 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS C 234 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Q 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 43278 Z= 0.318 Angle : 0.529 9.446 58733 Z= 0.273 Chirality : 0.043 0.195 6636 Planarity : 0.004 0.056 7320 Dihedral : 11.447 140.435 6489 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.46 % Allowed : 14.15 % Favored : 83.38 % 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: 0.54 (0.12), residues: 5092 helix: 1.35 (0.12), residues: 1882 sheet: 0.14 (0.19), residues: 712 loop : -0.27 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 201 HIS 0.008 0.001 HIS A 427 PHE 0.020 0.001 PHE B 678 TYR 0.016 0.001 TYR B 92 ARG 0.011 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 503 time to evaluate : 5.025 Fit side-chains revert: symmetry clash REVERT: A 714 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8025 (tp) REVERT: A 784 GLU cc_start: 0.7043 (tp30) cc_final: 0.6606 (tp30) REVERT: A 819 SER cc_start: 0.8449 (t) cc_final: 0.8180 (m) REVERT: A 915 THR cc_start: 0.8116 (m) cc_final: 0.7890 (t) REVERT: A 1173 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7633 (t) REVERT: A 1210 THR cc_start: 0.8131 (m) cc_final: 0.7914 (m) REVERT: A 1264 ARG cc_start: 0.7455 (ttt180) cc_final: 0.7235 (ttt180) REVERT: A 1294 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7704 (pp) REVERT: A 1373 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7367 (ptp-170) REVERT: B 109 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7365 (mtmm) REVERT: B 239 LYS cc_start: 0.8210 (mppt) cc_final: 0.7859 (mtpt) REVERT: B 250 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: B 281 ASP cc_start: 0.7304 (m-30) cc_final: 0.6889 (m-30) REVERT: B 639 ASP cc_start: 0.6997 (t70) cc_final: 0.6742 (t0) REVERT: B 882 ASP cc_start: 0.7113 (t0) cc_final: 0.6798 (t0) REVERT: C 9 TYR cc_start: 0.8709 (p90) cc_final: 0.8330 (p90) REVERT: E 17 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6941 (ttt-90) REVERT: G 84 ILE cc_start: 0.8571 (pt) cc_final: 0.8261 (pp) REVERT: G 167 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5574 (mp0) REVERT: H 55 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7498 (pp) REVERT: J 66 LEU cc_start: 0.8286 (mp) cc_final: 0.7989 (mm) REVERT: M 261 LYS cc_start: 0.7579 (tmmt) cc_final: 0.7250 (tppt) REVERT: M 282 VAL cc_start: 0.7774 (OUTLIER) cc_final: 0.7354 (t) REVERT: N 312 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6669 (ttp-170) REVERT: O 183 MET cc_start: 0.7355 (tpp) cc_final: 0.6955 (mmp) REVERT: O 317 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7063 (mpt-90) REVERT: O 343 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7074 (mppt) REVERT: O 542 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6907 (mmm160) REVERT: O 629 MET cc_start: 0.6786 (mmp) cc_final: 0.6489 (mpp) outliers start: 112 outliers final: 66 residues processed: 561 average time/residue: 1.5900 time to fit residues: 1094.8471 Evaluate side-chains 580 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 500 time to evaluate : 4.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1373 ARG Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1381 ASP Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 722 ASP Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 151 GLU Chi-restraints excluded: chain O residue 172 GLU Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 362 ASN Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain O residue 596 LYS Chi-restraints excluded: chain P residue 216 SER Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain Q residue 105 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 305 optimal weight: 0.9990 chunk 197 optimal weight: 0.2980 chunk 295 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 314 optimal weight: 3.9990 chunk 336 optimal weight: 0.5980 chunk 244 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 388 optimal weight: 7.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 51 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Q 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43278 Z= 0.174 Angle : 0.485 11.180 58733 Z= 0.251 Chirality : 0.041 0.197 6636 Planarity : 0.004 0.056 7320 Dihedral : 11.351 139.880 6489 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.93 % Allowed : 14.97 % Favored : 83.10 % 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: 0.72 (0.12), residues: 5092 helix: 1.56 (0.12), residues: 1881 sheet: 0.19 (0.19), residues: 713 loop : -0.20 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 215 HIS 0.004 0.001 HIS A 427 PHE 0.019 0.001 PHE O 217 TYR 0.013 0.001 TYR B 92 ARG 0.013 0.000 ARG O 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 495 time to evaluate : 5.151 Fit side-chains revert: symmetry clash REVERT: A 714 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7995 (tp) REVERT: A 774 ARG cc_start: 0.7021 (ttt180) cc_final: 0.6701 (ttt180) REVERT: A 784 GLU cc_start: 0.7056 (tp30) cc_final: 0.6644 (tp30) REVERT: A 819 SER cc_start: 0.8466 (t) cc_final: 0.8187 (m) REVERT: A 1168 ASP cc_start: 0.7307 (m-30) cc_final: 0.7093 (t70) REVERT: A 1173 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7522 (t) REVERT: A 1210 THR cc_start: 0.8121 (m) cc_final: 0.7906 (m) REVERT: A 1294 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7629 (pp) REVERT: A 1373 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7330 (ptp-170) REVERT: B 239 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7816 (mtpt) REVERT: B 250 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: B 281 ASP cc_start: 0.7272 (m-30) cc_final: 0.6858 (m-30) REVERT: B 639 ASP cc_start: 0.7017 (t70) cc_final: 0.6773 (t0) REVERT: B 882 ASP cc_start: 0.7112 (t0) cc_final: 0.6816 (t0) REVERT: C 9 TYR cc_start: 0.8675 (p90) cc_final: 0.8281 (p90) REVERT: D 92 LYS cc_start: 0.6710 (mmpt) cc_final: 0.6478 (mmtm) REVERT: E 69 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7826 (tp) REVERT: G 84 ILE cc_start: 0.8565 (pt) cc_final: 0.8319 (pp) REVERT: G 114 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6882 (pmm) REVERT: G 167 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5635 (mp0) REVERT: M 261 LYS cc_start: 0.7587 (tmmt) cc_final: 0.7261 (tppt) REVERT: M 282 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7368 (t) REVERT: N 312 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6700 (ttp-170) REVERT: O 317 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7185 (mpt-90) REVERT: O 343 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7044 (mppt) REVERT: O 542 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.6857 (mmm160) REVERT: O 629 MET cc_start: 0.6785 (mmp) cc_final: 0.6483 (mpp) REVERT: P 314 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6621 (mt-10) REVERT: Q 65 VAL cc_start: 0.8110 (t) cc_final: 0.7880 (t) outliers start: 88 outliers final: 54 residues processed: 548 average time/residue: 1.6241 time to fit residues: 1083.4090 Evaluate side-chains 559 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 490 time to evaluate : 4.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1373 ARG Chi-restraints excluded: chain A residue 1381 ASP Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 151 GLU Chi-restraints excluded: chain O residue 172 GLU Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 362 ASN Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain O residue 596 LYS Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 314 GLU Chi-restraints excluded: chain Q residue 105 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 449 optimal weight: 4.9990 chunk 473 optimal weight: 3.9990 chunk 432 optimal weight: 1.9990 chunk 460 optimal weight: 7.9990 chunk 277 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 361 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 416 optimal weight: 5.9990 chunk 435 optimal weight: 0.8980 chunk 459 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Q 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 43278 Z= 0.237 Angle : 0.510 12.378 58733 Z= 0.262 Chirality : 0.042 0.201 6636 Planarity : 0.004 0.061 7320 Dihedral : 11.352 139.773 6489 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.18 % Allowed : 15.08 % Favored : 82.75 % 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: 0.72 (0.12), residues: 5092 helix: 1.55 (0.12), residues: 1881 sheet: 0.20 (0.19), residues: 711 loop : -0.20 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 201 HIS 0.006 0.001 HIS A 427 PHE 0.021 0.001 PHE O 217 TYR 0.014 0.001 TYR J 44 ARG 0.013 0.000 ARG O 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 492 time to evaluate : 4.828 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7653 (mm-40) REVERT: A 714 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7992 (tp) REVERT: A 774 ARG cc_start: 0.7022 (ttt180) cc_final: 0.6701 (ttt180) REVERT: A 784 GLU cc_start: 0.7066 (tp30) cc_final: 0.6658 (tp30) REVERT: A 819 SER cc_start: 0.8472 (t) cc_final: 0.8198 (m) REVERT: A 1168 ASP cc_start: 0.7308 (m-30) cc_final: 0.7097 (t70) REVERT: A 1173 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7590 (t) REVERT: A 1210 THR cc_start: 0.8127 (m) cc_final: 0.7909 (m) REVERT: A 1294 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7650 (pp) REVERT: A 1373 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7391 (ptp-170) REVERT: B 109 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7326 (mtmm) REVERT: B 239 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7828 (mtpt) REVERT: B 250 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: B 281 ASP cc_start: 0.7259 (m-30) cc_final: 0.6855 (m-30) REVERT: B 639 ASP cc_start: 0.7022 (t70) cc_final: 0.6781 (t0) REVERT: B 882 ASP cc_start: 0.7101 (t0) cc_final: 0.6797 (t0) REVERT: C 9 TYR cc_start: 0.8697 (p90) cc_final: 0.8305 (p90) REVERT: C 128 ASP cc_start: 0.7111 (p0) cc_final: 0.6898 (p0) REVERT: D 92 LYS cc_start: 0.6742 (mmpt) cc_final: 0.6535 (mmtm) REVERT: D 131 MET cc_start: 0.6624 (tpt) cc_final: 0.6086 (tpt) REVERT: E 69 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7758 (tp) REVERT: G 75 VAL cc_start: 0.7467 (t) cc_final: 0.7191 (m) REVERT: G 84 ILE cc_start: 0.8569 (pt) cc_final: 0.8324 (pp) REVERT: G 114 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6837 (pmm) REVERT: G 167 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5638 (mp0) REVERT: H 55 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7499 (pp) REVERT: M 154 GLU cc_start: 0.7064 (tp30) cc_final: 0.6693 (tp30) REVERT: M 261 LYS cc_start: 0.7595 (tmmt) cc_final: 0.7264 (tppt) REVERT: M 282 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7367 (t) REVERT: N 312 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6704 (ttp-170) REVERT: O 183 MET cc_start: 0.7314 (tpp) cc_final: 0.6927 (mmp) REVERT: O 317 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7209 (mpt-90) REVERT: O 343 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7063 (mppt) REVERT: O 484 MET cc_start: 0.7440 (mmm) cc_final: 0.6935 (mmp) REVERT: O 542 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.6925 (mmm160) REVERT: O 629 MET cc_start: 0.6783 (mmp) cc_final: 0.6479 (mpp) REVERT: O 653 MET cc_start: 0.7046 (mmt) cc_final: 0.6550 (mtt) REVERT: P 314 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6546 (mt-10) REVERT: Q 65 VAL cc_start: 0.8137 (t) cc_final: 0.7907 (t) outliers start: 99 outliers final: 62 residues processed: 552 average time/residue: 1.6207 time to fit residues: 1092.4322 Evaluate side-chains 567 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 487 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1373 ARG Chi-restraints excluded: chain A residue 1381 ASP Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 722 ASP Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 151 GLU Chi-restraints excluded: chain O residue 172 GLU Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 362 ASN Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain O residue 596 LYS Chi-restraints excluded: chain P residue 216 SER Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 314 GLU Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Q residue 105 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 302 optimal weight: 0.6980 chunk 487 optimal weight: 7.9990 chunk 297 optimal weight: 1.9990 chunk 231 optimal weight: 0.4980 chunk 338 optimal weight: 0.0970 chunk 511 optimal weight: 4.9990 chunk 470 optimal weight: 2.9990 chunk 406 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 314 optimal weight: 0.0970 chunk 249 optimal weight: 0.6980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN C 234 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Q 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.133 43278 Z= 0.158 Angle : 0.486 13.688 58733 Z= 0.250 Chirality : 0.041 0.184 6636 Planarity : 0.004 0.059 7320 Dihedral : 11.268 139.459 6489 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.74 % Allowed : 15.65 % Favored : 82.62 % 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: 0.85 (0.12), residues: 5092 helix: 1.66 (0.12), residues: 1888 sheet: 0.25 (0.20), residues: 705 loop : -0.13 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 197 HIS 0.003 0.001 HIS A 427 PHE 0.021 0.001 PHE O 217 TYR 0.013 0.001 TYR B 416 ARG 0.013 0.000 ARG A 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 504 time to evaluate : 4.535 Fit side-chains REVERT: A 361 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7641 (mm-40) REVERT: A 714 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7976 (tp) REVERT: A 774 ARG cc_start: 0.6992 (ttt180) cc_final: 0.6690 (ttt180) REVERT: A 784 GLU cc_start: 0.7060 (tp30) cc_final: 0.6674 (tp30) REVERT: A 819 SER cc_start: 0.8448 (t) cc_final: 0.8175 (m) REVERT: A 1058 GLN cc_start: 0.7895 (mt0) cc_final: 0.7645 (mt0) REVERT: A 1118 ASN cc_start: 0.7535 (t0) cc_final: 0.7323 (t0) REVERT: A 1168 ASP cc_start: 0.7291 (m-30) cc_final: 0.6983 (t70) REVERT: A 1173 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7500 (t) REVERT: A 1210 THR cc_start: 0.8120 (m) cc_final: 0.7903 (m) REVERT: A 1294 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7593 (pp) REVERT: A 1337 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7547 (mtm180) REVERT: A 1373 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7347 (ptp-170) REVERT: B 239 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7839 (mtpt) REVERT: B 250 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: B 281 ASP cc_start: 0.7238 (m-30) cc_final: 0.6823 (m-30) REVERT: B 639 ASP cc_start: 0.6955 (t70) cc_final: 0.6723 (t0) REVERT: B 743 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B 882 ASP cc_start: 0.7109 (t0) cc_final: 0.6829 (t0) REVERT: C 9 TYR cc_start: 0.8675 (p90) cc_final: 0.8271 (p90) REVERT: C 154 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7702 (mmpt) REVERT: D 92 LYS cc_start: 0.6791 (mmpt) cc_final: 0.6579 (mmtm) REVERT: E 69 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7803 (tp) REVERT: G 75 VAL cc_start: 0.7435 (t) cc_final: 0.7214 (m) REVERT: G 84 ILE cc_start: 0.8504 (pt) cc_final: 0.8285 (pp) REVERT: G 114 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6700 (pmm) REVERT: G 167 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5669 (mp0) REVERT: H 55 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7497 (pp) REVERT: M 154 GLU cc_start: 0.7064 (tp30) cc_final: 0.6692 (tp30) REVERT: M 261 LYS cc_start: 0.7535 (tmmt) cc_final: 0.7197 (tppt) REVERT: M 282 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7392 (t) REVERT: N 312 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6742 (ttp-170) REVERT: O 172 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6777 (pt0) REVERT: O 343 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7031 (mppt) REVERT: O 542 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6851 (mmm160) REVERT: O 629 MET cc_start: 0.6760 (mmp) cc_final: 0.6463 (mpp) REVERT: P 314 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6460 (mt-10) REVERT: Q 65 VAL cc_start: 0.8009 (t) cc_final: 0.7796 (t) outliers start: 79 outliers final: 47 residues processed: 551 average time/residue: 1.5977 time to fit residues: 1077.2306 Evaluate side-chains 564 residues out of total 4557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 499 time to evaluate : 5.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1373 ARG Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 172 GLU Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 314 GLU Chi-restraints excluded: chain Q residue 105 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 323 optimal weight: 1.9990 chunk 433 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 375 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 407 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 418 optimal weight: 0.0470 chunk 51 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Q 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.136796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105522 restraints weight = 56623.770| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.95 r_work: 0.3305 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 43278 Z= 0.285 Angle : 0.528 13.838 58733 Z= 0.271 Chirality : 0.043 0.187 6636 Planarity : 0.004 0.062 7320 Dihedral : 11.310 139.587 6489 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.69 % Allowed : 15.89 % Favored : 82.42 % 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: 0.74 (0.12), residues: 5092 helix: 1.55 (0.12), residues: 1889 sheet: 0.23 (0.19), residues: 717 loop : -0.19 (0.12), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 201 HIS 0.008 0.001 HIS A 427 PHE 0.022 0.001 PHE O 217 TYR 0.016 0.001 TYR B 92 ARG 0.014 0.000 ARG O 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16652.92 seconds wall clock time: 296 minutes 1.32 seconds (17761.32 seconds total)