Starting phenix.real_space_refine on Sat Nov 18 05:46:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwo_34318/11_2023/8gwo_34318_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwo_34318/11_2023/8gwo_34318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwo_34318/11_2023/8gwo_34318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwo_34318/11_2023/8gwo_34318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwo_34318/11_2023/8gwo_34318_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwo_34318/11_2023/8gwo_34318_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 56 5.49 5 S 157 5.16 5 C 13689 2.51 5 N 3682 2.21 5 O 4288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 893": "OD1" <-> "OD2" Residue "A GLU 919": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 328": "OD1" <-> "OD2" Residue "F PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 369": "OD1" <-> "OD2" Residue "E ASP 458": "OD1" <-> "OD2" Residue "E TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 583": "OD1" <-> "OD2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 68": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 21880 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7458 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 888 Classifications: {'RNA': 1, 'peptide': 113} Modifications used: {'rna2p_pyr': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106, None: 1} Not linked: pdbres=" U G 0 " pdbres="ASN G 1 " Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GNP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 82.675 50.470 64.055 1.00 64.63 S ATOM 2487 SG CYS A 306 82.697 51.796 60.462 1.00 64.60 S ATOM 2519 SG CYS A 310 81.174 48.347 61.284 1.00 63.72 S ATOM 3927 SG CYS A 487 81.031 65.168 79.302 1.00 84.90 S ATOM 5180 SG CYS A 645 82.124 66.659 75.944 1.00102.92 S ATOM 5186 SG CYS A 646 83.731 63.408 77.227 1.00 97.68 S ATOM 12035 SG CYS F 16 52.929 63.017 134.833 1.00191.23 S ATOM 12050 SG CYS F 19 51.962 59.704 136.711 1.00207.65 S ATOM 11953 SG CYS F 5 40.570 66.188 132.135 1.00172.78 S ATOM 11974 SG CYS F 8 39.911 68.612 134.884 1.00193.87 S ATOM 12112 SG CYS F 26 41.858 69.862 132.030 1.00177.26 S ATOM 12129 SG CYS F 29 43.657 67.586 134.176 1.00184.44 S ATOM 12294 SG CYS F 50 66.174 72.667 121.669 1.00225.07 S ATOM 12324 SG CYS F 55 68.111 70.331 123.915 1.00221.22 S ATOM 12457 SG CYS F 72 67.786 74.162 124.908 1.00223.77 S ATOM 16548 SG CYS E 16 97.549 68.183 120.864 1.00141.25 S ATOM 16563 SG CYS E 19 99.383 65.136 122.370 1.00152.92 S ATOM 16466 SG CYS E 5 87.046 64.410 128.196 1.00145.34 S ATOM 16487 SG CYS E 8 87.101 66.377 131.444 1.00162.65 S ATOM 16625 SG CYS E 26 85.394 67.908 128.423 1.00163.75 S ATOM 16642 SG CYS E 29 89.242 67.644 128.841 1.00171.71 S ATOM 16807 SG CYS E 50 93.717 82.204 106.944 1.00209.10 S ATOM 16837 SG CYS E 55 97.251 83.057 105.932 1.00236.60 S ATOM 16970 SG CYS E 72 95.613 84.985 108.798 1.00208.87 S Time building chain proxies: 15.91, per 1000 atoms: 0.73 Number of scatterers: 21880 At special positions: 0 Unit cell: (154.16, 134.48, 186.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 157 16.00 P 56 15.00 O 4288 8.00 N 3682 7.00 C 13689 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: 9.97 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " Number of angles added : 27 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 21 sheets defined 34.7% alpha, 8.2% beta 17 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 11.27 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 169 through 177 removed outlier: 3.552A pdb=" N ASN A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 199 Processing helix chain 'A' and resid 236 through 244 Proline residue: A 243 - end of helix Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.631A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 449 through 458 removed outlier: 4.619A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 removed outlier: 4.815A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 579 removed outlier: 4.076A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 648 through 662 removed outlier: 3.838A pdb=" N PHE A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 708 removed outlier: 4.077A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 720 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 removed outlier: 4.114A pdb=" N GLN A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 789 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 857 through 866 removed outlier: 3.555A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 876 through 901 removed outlier: 4.178A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.959A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 4.226A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 98 removed outlier: 3.699A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.651A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.944A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.706A pdb=" N LEU C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 41 removed outlier: 3.785A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 61 removed outlier: 3.862A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 70 No H-bonds generated for 'chain 'C' and resid 67 through 70' Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 32 through 40 removed outlier: 4.267A pdb=" N LEU D 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 81 removed outlier: 3.926A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 98 removed outlier: 4.393A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'F' and resid 27 through 35 Processing helix chain 'F' and resid 60 through 62 No H-bonds generated for 'chain 'F' and resid 60 through 62' Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 117 through 123 Processing helix chain 'F' and resid 128 through 146 Processing helix chain 'F' and resid 266 through 273 removed outlier: 4.376A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 298 removed outlier: 3.808A pdb=" N ALA F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU F 297 " --> pdb=" O ILE F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 324 removed outlier: 4.421A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 390 removed outlier: 4.425A pdb=" N VAL F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 422 Processing helix chain 'F' and resid 424 through 431 removed outlier: 3.879A pdb=" N LEU F 428 " --> pdb=" O SER F 424 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS F 430 " --> pdb=" O CYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 455 removed outlier: 3.752A pdb=" N LEU F 455 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 502 Processing helix chain 'F' and resid 504 through 506 No H-bonds generated for 'chain 'F' and resid 504 through 506' Processing helix chain 'F' and resid 516 through 522 Processing helix chain 'F' and resid 561 through 567 removed outlier: 3.941A pdb=" N ILE F 565 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR F 566 " --> pdb=" O VAL F 563 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG F 567 " --> pdb=" O ALA F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 583 No H-bonds generated for 'chain 'F' and resid 581 through 583' Processing helix chain 'E' and resid 27 through 35 Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 128 through 146 Processing helix chain 'E' and resid 263 through 274 removed outlier: 4.819A pdb=" N ALA E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASN E 268 " --> pdb=" O SER E 264 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET E 274 " --> pdb=" O GLN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.958A pdb=" N PHE E 291 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA E 292 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 322 removed outlier: 4.195A pdb=" N ALA E 316 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU E 319 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS E 320 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA E 321 " --> pdb=" O CYS E 318 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU E 322 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 424 through 428 Processing helix chain 'E' and resid 446 through 455 Processing helix chain 'E' and resid 490 through 493 No H-bonds generated for 'chain 'E' and resid 490 through 493' Processing helix chain 'E' and resid 495 through 502 removed outlier: 5.933A pdb=" N ARG E 502 " --> pdb=" O GLU E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 523 Processing helix chain 'E' and resid 562 through 567 removed outlier: 4.230A pdb=" N THR E 566 " --> pdb=" O ASN E 562 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 562 through 567' Processing helix chain 'G' and resid 96 through 109 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.828A pdb=" N GLN A 57 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 102 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.611A pdb=" N ALA A 46 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 37 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.551A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 330 through 335 removed outlier: 3.592A pdb=" N VAL A 342 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 345 through 348 removed outlier: 3.564A pdb=" N GLY A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 666 through 668 removed outlier: 3.524A pdb=" N THR A 540 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET A 542 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 753 through 757 removed outlier: 3.749A pdb=" N SER A 754 " --> pdb=" O CYS A 765 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= I, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.739A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 146 through 149 removed outlier: 3.573A pdb=" N GLU D 155 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 63 through 65 Processing sheet with id= L, first strand: chain 'F' and resid 304 through 307 removed outlier: 6.825A pdb=" N ILE F 370 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR F 307 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL F 372 " --> pdb=" O THR F 307 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS F 395 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE F 373 " --> pdb=" O HIS F 395 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL F 397 " --> pdb=" O PHE F 373 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.764A pdb=" N TYR F 355 " --> pdb=" O SER F 331 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 472 through 474 removed outlier: 7.377A pdb=" N VAL F 544 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ILE F 575 " --> pdb=" O VAL F 544 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE F 546 " --> pdb=" O ILE F 575 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 153 through 157 removed outlier: 6.870A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 182 through 187 removed outlier: 3.500A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 63 through 66 Processing sheet with id= R, first strand: chain 'E' and resid 185 through 187 Processing sheet with id= S, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.905A pdb=" N TYR E 396 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU E 280 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N TYR E 398 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 15 through 17 removed outlier: 4.509A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 73 through 79 removed outlier: 6.142A pdb=" N TYR G 31 " --> pdb=" O LEU G 42 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 7.28 Time building geometry restraints manager: 10.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 16 1.22 - 1.37: 7276 1.37 - 1.52: 10601 1.52 - 1.67: 4336 1.67 - 1.82: 226 Bond restraints: 22455 Sorted by residual: bond pdb=" O5' U G 0 " pdb=" C5' U G 0 " ideal model delta sigma weight residual 1.424 1.075 0.349 1.50e-02 4.44e+03 5.43e+02 bond pdb=" P U G 0 " pdb=" OP1 U G 0 " ideal model delta sigma weight residual 1.485 1.813 -0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" P U G 0 " pdb=" OP2 U G 0 " ideal model delta sigma weight residual 1.485 1.781 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C4 U I 13 " pdb=" O4 U I 13 " ideal model delta sigma weight residual 1.232 1.426 -0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C4 U I 16 " pdb=" O4 U I 16 " ideal model delta sigma weight residual 1.232 1.426 -0.194 2.00e-02 2.50e+03 9.37e+01 ... (remaining 22450 not shown) Histogram of bond angle deviations from ideal: 84.94 - 94.78: 2 94.78 - 104.61: 578 104.61 - 114.44: 13451 114.44 - 124.27: 16184 124.27 - 134.10: 569 Bond angle restraints: 30784 Sorted by residual: angle pdb=" N PRO F 254 " pdb=" CD PRO F 254 " pdb=" CG PRO F 254 " ideal model delta sigma weight residual 103.20 84.94 18.26 1.50e+00 4.44e-01 1.48e+02 angle pdb=" CA PRO F 254 " pdb=" N PRO F 254 " pdb=" CD PRO F 254 " ideal model delta sigma weight residual 112.00 99.64 12.36 1.40e+00 5.10e-01 7.79e+01 angle pdb=" CA PRO F 254 " pdb=" CB PRO F 254 " pdb=" CG PRO F 254 " ideal model delta sigma weight residual 104.50 91.88 12.62 1.90e+00 2.77e-01 4.41e+01 angle pdb=" C HIS A 898 " pdb=" N MET A 899 " pdb=" CA MET A 899 " ideal model delta sigma weight residual 122.73 113.56 9.17 1.61e+00 3.86e-01 3.25e+01 angle pdb=" P U G 0 " pdb=" O5' U G 0 " pdb=" C5' U G 0 " ideal model delta sigma weight residual 120.90 128.54 -7.64 1.50e+00 4.44e-01 2.59e+01 ... (remaining 30779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.26: 12463 25.26 - 50.51: 778 50.51 - 75.77: 57 75.77 - 101.02: 11 101.02 - 126.28: 1 Dihedral angle restraints: 13310 sinusoidal: 5454 harmonic: 7856 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA VAL A 848 " pdb=" C VAL A 848 " pdb=" N LYS A 849 " pdb=" CA LYS A 849 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ARG E 502 " pdb=" C ARG E 502 " pdb=" N ASN E 503 " pdb=" CA ASN E 503 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 13307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.263: 3569 0.263 - 0.527: 0 0.527 - 0.790: 0 0.790 - 1.054: 0 1.054 - 1.317: 1 Chirality restraints: 3570 Sorted by residual: chirality pdb=" P U G 0 " pdb=" OP1 U G 0 " pdb=" OP2 U G 0 " pdb=" O5' U G 0 " both_signs ideal model delta sigma weight residual True 2.41 -3.73 -1.32 2.00e-01 2.50e+01 4.34e+01 chirality pdb=" CB ILE F 592 " pdb=" CA ILE F 592 " pdb=" CG1 ILE F 592 " pdb=" CG2 ILE F 592 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CB VAL E 449 " pdb=" CA VAL E 449 " pdb=" CG1 VAL E 449 " pdb=" CG2 VAL E 449 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 3567 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR F 253 " 0.090 5.00e-02 4.00e+02 1.27e-01 2.56e+01 pdb=" N PRO F 254 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO F 254 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO F 254 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 71 " 0.063 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO G 72 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO G 72 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO G 72 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 22 " -0.013 2.00e-02 2.50e+03 2.09e-02 8.77e+00 pdb=" CG TYR D 22 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR D 22 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 22 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR D 22 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D 22 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 22 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 22 " 0.004 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 94 2.38 - 3.01: 12581 3.01 - 3.64: 33104 3.64 - 4.27: 47929 4.27 - 4.90: 77363 Nonbonded interactions: 171071 Sorted by model distance: nonbonded pdb=" P U G 0 " pdb=" N ASN G 1 " model vdw 1.755 3.480 nonbonded pdb=" NE2 HIS A 295 " pdb="ZN ZN A1001 " model vdw 2.075 1.848 nonbonded pdb=" OP2 U G 0 " pdb=" O3G GNP A1003 " model vdw 2.092 3.040 nonbonded pdb=" OD1 ASP B 50 " pdb=" O2' A I 14 " model vdw 2.132 2.440 nonbonded pdb=" N ASN E 116 " pdb=" OD2 ASP E 119 " model vdw 2.138 2.520 ... (remaining 171066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 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: 0.020 Extract box with map and model: 28.310 Check model and map are aligned: 0.330 Set scattering table: 0.180 Process input model: 78.030 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.349 22455 Z= 0.445 Angle : 0.825 18.255 30784 Z= 0.461 Chirality : 0.048 1.317 3570 Planarity : 0.005 0.127 3732 Dihedral : 15.177 126.279 8242 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.81 % Favored : 91.11 % Rotamer: Outliers : 0.66 % Allowed : 18.26 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.16), residues: 2639 helix: -0.52 (0.17), residues: 934 sheet: -2.15 (0.33), residues: 224 loop : -2.50 (0.15), residues: 1481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 176 average time/residue: 0.3602 time to fit residues: 99.1551 Evaluate side-chains 163 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 2.490 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2168 time to fit residues: 7.0455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 111 optimal weight: 0.0070 chunk 68 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 0.0470 chunk 208 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 241 optimal weight: 20.0000 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22455 Z= 0.278 Angle : 0.633 7.829 30784 Z= 0.330 Chirality : 0.042 0.185 3570 Planarity : 0.005 0.081 3732 Dihedral : 7.148 126.955 3525 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.84 % Favored : 90.09 % Rotamer: Outliers : 3.97 % Allowed : 17.29 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.16), residues: 2639 helix: -0.39 (0.17), residues: 940 sheet: -2.01 (0.32), residues: 243 loop : -2.50 (0.16), residues: 1456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 163 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 42 residues processed: 236 average time/residue: 0.3321 time to fit residues: 124.5835 Evaluate side-chains 198 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 2.365 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 42 outliers final: 1 residues processed: 42 average time/residue: 0.1982 time to fit residues: 18.6689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 82 optimal weight: 0.4980 chunk 194 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN F 492 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22455 Z= 0.310 Angle : 0.644 10.615 30784 Z= 0.332 Chirality : 0.043 0.228 3570 Planarity : 0.005 0.053 3732 Dihedral : 6.991 125.840 3525 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.95 % Favored : 89.94 % Rotamer: Outliers : 3.04 % Allowed : 20.03 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.16), residues: 2639 helix: -0.34 (0.17), residues: 935 sheet: -1.98 (0.32), residues: 240 loop : -2.54 (0.15), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 163 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 37 residues processed: 222 average time/residue: 0.3398 time to fit residues: 119.6310 Evaluate side-chains 188 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 2.551 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.2167 time to fit residues: 18.0262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 0.0870 chunk 181 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 115 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 242 optimal weight: 4.9990 chunk 257 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 230 optimal weight: 0.0040 chunk 69 optimal weight: 0.6980 overall best weight: 0.3570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN D 140 ASN F 275 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22455 Z= 0.145 Angle : 0.570 8.759 30784 Z= 0.292 Chirality : 0.041 0.242 3570 Planarity : 0.004 0.054 3732 Dihedral : 6.395 123.973 3525 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.52 % Favored : 92.44 % Rotamer: Outliers : 1.24 % Allowed : 21.17 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.16), residues: 2639 helix: -0.08 (0.18), residues: 928 sheet: -2.03 (0.32), residues: 229 loop : -2.33 (0.15), residues: 1482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 209 average time/residue: 0.3474 time to fit residues: 114.8066 Evaluate side-chains 169 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 2.438 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2033 time to fit residues: 7.4092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 191 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 219 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 22455 Z= 0.368 Angle : 0.661 13.547 30784 Z= 0.337 Chirality : 0.043 0.248 3570 Planarity : 0.004 0.054 3732 Dihedral : 6.648 125.656 3525 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.91 % Favored : 90.01 % Rotamer: Outliers : 1.94 % Allowed : 22.45 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.16), residues: 2639 helix: -0.17 (0.17), residues: 918 sheet: -2.05 (0.30), residues: 260 loop : -2.40 (0.16), residues: 1461 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 199 average time/residue: 0.3638 time to fit residues: 112.5520 Evaluate side-chains 175 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 2.289 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.2208 time to fit residues: 12.4409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 0.7980 chunk 231 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 chunk 213 optimal weight: 0.0470 chunk 119 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN B 88 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22455 Z= 0.212 Angle : 0.595 8.971 30784 Z= 0.303 Chirality : 0.041 0.224 3570 Planarity : 0.004 0.055 3732 Dihedral : 6.450 124.773 3525 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.17 % Favored : 91.80 % Rotamer: Outliers : 1.46 % Allowed : 23.51 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.16), residues: 2639 helix: -0.07 (0.18), residues: 924 sheet: -1.88 (0.31), residues: 253 loop : -2.33 (0.16), residues: 1462 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 192 average time/residue: 0.3543 time to fit residues: 107.0009 Evaluate side-chains 170 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 2.395 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.2155 time to fit residues: 11.0137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 146 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 216 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 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 168 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN B 88 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22455 Z= 0.172 Angle : 0.580 16.287 30784 Z= 0.291 Chirality : 0.040 0.179 3570 Planarity : 0.004 0.054 3732 Dihedral : 6.217 124.282 3525 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.01 % Favored : 91.95 % Rotamer: Outliers : 0.84 % Allowed : 24.57 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.99 (0.16), residues: 2639 helix: 0.07 (0.18), residues: 921 sheet: -1.77 (0.31), residues: 241 loop : -2.25 (0.16), residues: 1477 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 179 average time/residue: 0.3606 time to fit residues: 101.7525 Evaluate side-chains 156 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 2.449 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2216 time to fit residues: 5.2956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 201 optimal weight: 0.0770 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22455 Z= 0.170 Angle : 0.580 13.611 30784 Z= 0.290 Chirality : 0.040 0.179 3570 Planarity : 0.004 0.054 3732 Dihedral : 6.134 124.069 3525 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.52 % Favored : 92.44 % Rotamer: Outliers : 0.75 % Allowed : 24.53 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -1.91 (0.16), residues: 2639 helix: 0.14 (0.18), residues: 919 sheet: -1.57 (0.33), residues: 232 loop : -2.22 (0.15), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 170 average time/residue: 0.3635 time to fit residues: 98.3413 Evaluate side-chains 164 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 2.426 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2084 time to fit residues: 6.5266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 238 optimal weight: 0.3980 chunk 143 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 73 optimal weight: 0.0570 chunk 215 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22455 Z= 0.307 Angle : 0.641 12.841 30784 Z= 0.324 Chirality : 0.042 0.185 3570 Planarity : 0.004 0.054 3732 Dihedral : 6.440 125.162 3525 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.27 % Favored : 90.62 % Rotamer: Outliers : 0.57 % Allowed : 24.57 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.16), residues: 2639 helix: -0.01 (0.18), residues: 923 sheet: -1.66 (0.31), residues: 258 loop : -2.24 (0.16), residues: 1458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 159 average time/residue: 0.3802 time to fit residues: 95.2094 Evaluate side-chains 156 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 2.416 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2118 time to fit residues: 6.7154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 265 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 163 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22455 Z= 0.245 Angle : 0.616 13.893 30784 Z= 0.311 Chirality : 0.041 0.182 3570 Planarity : 0.004 0.054 3732 Dihedral : 6.345 124.628 3525 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.28 % Favored : 91.68 % Rotamer: Outliers : 0.35 % Allowed : 24.92 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.16), residues: 2639 helix: 0.06 (0.18), residues: 919 sheet: -1.40 (0.33), residues: 242 loop : -2.27 (0.15), residues: 1478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 159 average time/residue: 0.3716 time to fit residues: 93.5619 Evaluate side-chains 152 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 2.637 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.3595 time to fit residues: 5.5447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 211 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.127197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.082465 restraints weight = 91391.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.082620 restraints weight = 51141.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.081931 restraints weight = 42801.296| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22455 Z= 0.257 Angle : 0.626 13.732 30784 Z= 0.316 Chirality : 0.041 0.181 3570 Planarity : 0.004 0.054 3732 Dihedral : 6.364 124.659 3525 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.12 % Favored : 90.85 % Rotamer: Outliers : 0.49 % Allowed : 25.32 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.16), residues: 2639 helix: 0.07 (0.18), residues: 921 sheet: -1.52 (0.33), residues: 252 loop : -2.22 (0.16), residues: 1466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4538.95 seconds wall clock time: 84 minutes 11.94 seconds (5051.94 seconds total)