Starting phenix.real_space_refine on Sun Feb 18 10:51:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xez_22160/02_2024/6xez_22160_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xez_22160/02_2024/6xez_22160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xez_22160/02_2024/6xez_22160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xez_22160/02_2024/6xez_22160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xez_22160/02_2024/6xez_22160_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xez_22160/02_2024/6xez_22160_updated.pdb" } resolution = 3.5 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= 0.002 sd= 0.058 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 76 5.49 5 Mg 3 5.21 5 S 148 5.16 5 C 13519 2.51 5 N 3671 2.21 5 O 4309 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A GLU 802": "OE1" <-> "OE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "E PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "E GLU 540": "OE1" <-> "OE2" Residue "E GLU 551": "OE1" <-> "OE2" Residue "E TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 591": "OE1" <-> "OE2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 341": "OE1" <-> "OE2" Residue "F ASP 401": "OD1" <-> "OD2" Residue "F GLU 418": "OE1" <-> "OE2" Residue "F GLU 551": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21742 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7459 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1383 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 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, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4618 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 4, 'PTRANS': 30, 'TRANS': 561} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 769 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 88.721 102.304 119.424 1.00 68.21 S ATOM 2487 SG CYS A 306 88.421 100.924 122.609 1.00 63.53 S ATOM 2519 SG CYS A 310 86.803 104.423 121.909 1.00 60.93 S ATOM 3927 SG CYS A 487 86.518 86.967 105.077 1.00 80.68 S ATOM 5180 SG CYS A 645 87.725 84.546 108.337 1.00 88.48 S ATOM 5186 SG CYS A 646 88.285 87.912 107.513 1.00 83.87 S ATOM 10836 SG CYS E 5 35.198 82.097 55.078 1.00166.51 S ATOM 10857 SG CYS E 8 31.322 80.782 54.935 1.00172.10 S ATOM 10995 SG CYS E 26 34.582 78.680 55.069 1.00168.19 S ATOM 11016 SG CYS E 29 33.664 79.940 52.226 1.00172.63 S ATOM 11181 SG CYS E 50 56.471 65.217 50.133 1.00219.44 S ATOM 11211 SG CYS E 55 56.897 64.867 46.869 1.00232.67 S ATOM 11344 SG CYS E 72 55.192 62.162 47.361 1.00223.45 S ATOM 10918 SG CYS E 16 44.259 80.491 46.350 1.00182.34 S ATOM 10933 SG CYS E 19 42.754 82.711 44.924 1.00184.86 S ATOM 15454 SG CYS F 5 88.579 86.061 55.194 1.00180.72 S ATOM 15475 SG CYS F 8 85.587 84.904 54.927 1.00185.31 S ATOM 15613 SG CYS F 26 87.698 81.703 54.852 1.00198.76 S ATOM 15634 SG CYS F 29 89.784 82.795 52.868 1.00206.02 S ATOM 15799 SG CYS F 50 98.078 68.991 74.102 1.00227.89 S ATOM 15829 SG CYS F 55 101.194 68.363 74.238 1.00239.77 S ATOM 15962 SG CYS F 72 100.061 65.848 72.923 1.00235.51 S ATOM 15536 SG CYS F 16 98.784 82.792 61.307 1.00188.21 S ATOM 15551 SG CYS F 19 100.099 86.280 59.520 1.00196.10 S Time building chain proxies: 11.99, per 1000 atoms: 0.55 Number of scatterers: 21742 At special positions: 0 Unit cell: (152.9, 149.6, 185.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 148 16.00 P 76 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4309 8.00 N 3671 7.00 C 13519 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.86 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " 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 ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " 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=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 33 " Number of angles added : 28 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 23 sheets defined 36.2% alpha, 6.6% beta 32 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 10.42 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.557A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) 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 removed outlier: 3.655A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 169 through 199 removed outlier: 3.819A pdb=" N ALA A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ARG A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 186 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS A 193 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 244 through 247 No H-bonds generated for 'chain 'A' and resid 244 through 247' 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 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 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 307 through 317 removed outlier: 4.060A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (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 368 through 376 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 446 through 458 removed outlier: 4.467A pdb=" N ALA A 449 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 450 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 480 removed outlier: 4.336A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (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 518 Processing helix chain 'A' and resid 521 through 531 removed outlier: 4.192A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 579 removed outlier: 4.511A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 720 through 732 removed outlier: 4.041A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 789 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 849 No H-bonds generated for 'chain 'A' and resid 847 through 849' Processing helix chain 'A' and resid 855 through 871 removed outlier: 4.624A pdb=" N VAL A 860 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 4.699A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 4.729A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 914 Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.668A pdb=" N GLU A 922 " --> pdb=" O PRO A 918 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.703A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 97 removed outlier: 3.670A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 8 through 20 removed outlier: 3.547A pdb=" N LEU C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.634A pdb=" N ALA C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 60 Processing helix chain 'C' and resid 69 through 72 No H-bonds generated for 'chain 'C' and resid 69 through 72' Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.955A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 81 removed outlier: 3.909A pdb=" N GLN D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 97 removed outlier: 4.094A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 174 through 179 Proline residue: D 178 - end of helix No H-bonds generated for 'chain 'D' and resid 174 through 179' Processing helix chain 'E' and resid 27 through 35 Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 128 through 147 removed outlier: 3.590A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 266 through 274 removed outlier: 3.835A pdb=" N LYS E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY E 273 " --> pdb=" O TYR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 298 Processing helix chain 'E' and resid 311 through 324 removed outlier: 3.551A pdb=" N TYR E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 419 through 422 Processing helix chain 'E' and resid 424 through 430 Processing helix chain 'E' and resid 446 through 454 Processing helix chain 'E' and resid 490 through 499 removed outlier: 3.546A pdb=" N VAL E 495 " --> pdb=" O PRO E 491 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL E 496 " --> pdb=" O GLN E 492 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU E 498 " --> pdb=" O GLY E 494 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE E 499 " --> pdb=" O VAL E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 522 removed outlier: 3.850A pdb=" N ALA E 522 " --> pdb=" O GLN E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 567 removed outlier: 4.671A pdb=" N ARG E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 584 No H-bonds generated for 'chain 'E' and resid 581 through 584' Processing helix chain 'F' and resid 27 through 36 removed outlier: 3.590A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) 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 103 through 111 Processing helix chain 'F' and resid 117 through 123 Processing helix chain 'F' and resid 128 through 148 Processing helix chain 'F' and resid 260 through 274 removed outlier: 4.376A pdb=" N SER F 264 " --> pdb=" O GLU F 261 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA F 267 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN F 270 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 298 Processing helix chain 'F' and resid 311 through 318 Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 381 through 390 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 431 Processing helix chain 'F' and resid 446 through 448 No H-bonds generated for 'chain 'F' and resid 446 through 448' Processing helix chain 'F' and resid 490 through 495 removed outlier: 3.851A pdb=" N VAL F 495 " --> pdb=" O PRO F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 524 removed outlier: 3.922A pdb=" N ALA F 522 " --> pdb=" O GLN F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 565 Processing helix chain 'F' and resid 581 through 584 No H-bonds generated for 'chain 'F' and resid 581 through 584' Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 Processing sheet with id= B, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 100 through 105 Processing sheet with id= D, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.558A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= F, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.500A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 755 through 758 Processing sheet with id= H, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.629A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 146 through 148 removed outlier: 4.061A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 159 through 161 Processing sheet with id= K, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.917A pdb=" N LEU D 128 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 146 through 148 removed outlier: 3.698A pdb=" N TRP D 154 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 182 through 186 Processing sheet with id= N, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.475A pdb=" N TYR E 396 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU E 280 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR E 398 " --> pdb=" O LEU E 280 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 355 through 359 removed outlier: 6.894A pdb=" N ILE E 304 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N CYS E 358 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR E 306 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE E 370 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N THR E 307 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL E 372 " --> pdb=" O THR E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 470 through 472 removed outlier: 6.473A pdb=" N ILE E 572 " --> pdb=" O CYS E 471 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 510 through 512 Processing sheet with id= R, first strand: chain 'E' and resid 152 through 157 removed outlier: 7.116A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 63 through 65 Processing sheet with id= T, first strand: chain 'F' and resid 224 through 227 removed outlier: 4.296A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.405A pdb=" N TYR F 396 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU F 280 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR F 398 " --> pdb=" O LEU F 280 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 511 through 513 removed outlier: 6.398A pdb=" N ILE F 545 " --> pdb=" O ILE F 512 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 152 through 156 removed outlier: 7.077A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 7.42 Time building geometry restraints manager: 10.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3784 1.32 - 1.44: 6140 1.44 - 1.57: 12017 1.57 - 1.69: 202 1.69 - 1.81: 212 Bond restraints: 22355 Sorted by residual: bond pdb=" F1 AF3 E 705 " pdb="AL AF3 E 705 " ideal model delta sigma weight residual 1.637 1.787 -0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" F1 AF3 F1004 " pdb="AL AF3 F1004 " ideal model delta sigma weight residual 1.637 1.787 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" F2 AF3 F1004 " pdb="AL AF3 F1004 " ideal model delta sigma weight residual 1.637 1.779 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" F2 AF3 E 705 " pdb="AL AF3 E 705 " ideal model delta sigma weight residual 1.637 1.779 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" F3 AF3 E 705 " pdb="AL AF3 E 705 " ideal model delta sigma weight residual 1.637 1.772 -0.135 2.00e-02 2.50e+03 4.54e+01 ... (remaining 22350 not shown) Histogram of bond angle deviations from ideal: 95.22 - 103.47: 467 103.47 - 111.73: 10917 111.73 - 119.98: 9567 119.98 - 128.23: 9559 128.23 - 136.48: 232 Bond angle restraints: 30742 Sorted by residual: angle pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta sigma weight residual 121.70 134.55 -12.85 1.80e+00 3.09e-01 5.10e+01 angle pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta sigma weight residual 121.70 132.81 -11.11 1.80e+00 3.09e-01 3.81e+01 angle pdb=" O1B ADP E 704 " pdb=" PB ADP E 704 " pdb=" O2B ADP E 704 " ideal model delta sigma weight residual 119.90 105.32 14.58 3.00e+00 1.11e-01 2.36e+01 angle pdb=" O1B ADP F1003 " pdb=" PB ADP F1003 " pdb=" O2B ADP F1003 " ideal model delta sigma weight residual 119.90 105.35 14.55 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C1' ADP F1003 " pdb=" C2' ADP F1003 " pdb=" C3' ADP F1003 " ideal model delta sigma weight residual 111.00 96.73 14.27 3.00e+00 1.11e-01 2.26e+01 ... (remaining 30737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 12946 34.01 - 68.01: 610 68.01 - 102.02: 55 102.02 - 136.03: 6 136.03 - 170.04: 8 Dihedral angle restraints: 13625 sinusoidal: 6039 harmonic: 7586 Sorted by residual: dihedral pdb=" C5' ADP A1004 " pdb=" O5' ADP A1004 " pdb=" PA ADP A1004 " pdb=" O2A ADP A1004 " ideal model delta sinusoidal sigma weight residual -60.00 110.04 -170.04 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP E 704 " pdb=" O3A ADP E 704 " pdb=" PB ADP E 704 " pdb=" PA ADP E 704 " ideal model delta sinusoidal sigma weight residual -60.00 87.69 -147.69 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O2A ADP A1004 " pdb=" O3A ADP A1004 " pdb=" PA ADP A1004 " pdb=" PB ADP A1004 " ideal model delta sinusoidal sigma weight residual 300.00 157.79 142.21 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 13622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 3488 0.123 - 0.247: 60 0.247 - 0.370: 19 0.370 - 0.493: 6 0.493 - 0.617: 1 Chirality restraints: 3574 Sorted by residual: chirality pdb=" CG LEU E 455 " pdb=" CB LEU E 455 " pdb=" CD1 LEU E 455 " pdb=" CD2 LEU E 455 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.51e+00 chirality pdb=" C6 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" C5 1N7 A1006 " pdb=" C7 1N7 A1006 " both_signs ideal model delta sigma weight residual False -2.43 -2.86 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" C2 1N7 A1005 " pdb=" C1 1N7 A1005 " pdb=" C15 1N7 A1005 " pdb=" C19 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.81 -2.40 -0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 3571 not shown) Planarity restraints: 3641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 824 " 0.039 2.00e-02 2.50e+03 7.84e-02 6.14e+01 pdb=" CG ASP A 824 " -0.136 2.00e-02 2.50e+03 pdb=" OD1 ASP A 824 " 0.050 2.00e-02 2.50e+03 pdb=" OD2 ASP A 824 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 289 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C SER F 289 " 0.060 2.00e-02 2.50e+03 pdb=" O SER F 289 " -0.023 2.00e-02 2.50e+03 pdb=" N HIS F 290 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 582 " 0.028 2.00e-02 2.50e+03 2.15e-02 9.23e+00 pdb=" CG TYR F 582 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR F 582 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR F 582 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 582 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR F 582 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR F 582 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 582 " 0.006 2.00e-02 2.50e+03 ... (remaining 3638 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 5 1.90 - 2.65: 697 2.65 - 3.40: 31652 3.40 - 4.15: 52012 4.15 - 4.90: 88322 Nonbonded interactions: 172688 Sorted by model distance: nonbonded pdb=" O LEU E 65 " pdb=" OG SER E 80 " model vdw 1.146 2.440 nonbonded pdb=" O1B ADP E 704 " pdb=" F3 AF3 E 705 " model vdw 1.813 2.390 nonbonded pdb=" O2B ADP F1003 " pdb=" F3 AF3 F1004 " model vdw 1.813 2.390 nonbonded pdb=" O1B ADP F1003 " pdb=" F1 AF3 F1004 " model vdw 1.820 2.390 nonbonded pdb=" O2B ADP E 704 " pdb=" F1 AF3 E 705 " model vdw 1.820 2.390 ... (remaining 172683 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 41 or (resid 42 through 4 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 44 through 1 \ 91)) 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 50 or (resid 51 and (name N or name CA or name C or na \ me O or name CB )) or resid 52 through 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 226 or (resid 227 and (name N or name CA or name \ C or name O or name CB )) or resid 228 through 596 or resid 701 through 706)) selection = (chain 'F' and (resid 1 through 247 or (resid 248 and (name N or name CA or name \ C or name O or name CB )) or resid 249 through 331 or (resid 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 377 or (resid 37 \ 8 through 379 and (name N or name CA or name C or name O or name CB )) or resid \ 380 through 596 or resid 1000 through 1005)) } 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: 1.820 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: 8.220 Check model and map are aligned: 0.300 Set scattering table: 0.210 Process input model: 69.480 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.011 0.150 22355 Z= 0.676 Angle : 0.965 14.580 30742 Z= 0.485 Chirality : 0.057 0.617 3574 Planarity : 0.005 0.078 3641 Dihedral : 19.277 170.035 8731 Min Nonbonded Distance : 1.146 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.01 % Favored : 86.91 % Rotamer: Outliers : 10.77 % Allowed : 22.63 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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: -4.50 (0.14), residues: 2551 helix: -2.11 (0.13), residues: 946 sheet: -3.54 (0.25), residues: 312 loop : -3.60 (0.14), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 916 HIS 0.016 0.002 HIS F 39 PHE 0.020 0.002 PHE A 471 TYR 0.051 0.002 TYR F 582 ARG 0.011 0.001 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 131 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: A 261 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8770 (tt) REVERT: A 331 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7992 (ttm-80) REVERT: A 431 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7432 (mm-30) REVERT: A 553 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7272 (ptt180) REVERT: A 668 MET cc_start: 0.8593 (ttp) cc_final: 0.8353 (ttt) REVERT: B 55 MET cc_start: 0.9535 (mmm) cc_final: 0.9279 (mmm) REVERT: B 165 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8340 (pttt) REVERT: B 174 MET cc_start: 0.9046 (tpt) cc_final: 0.8801 (tpp) REVERT: B 189 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8121 (mt) REVERT: C 38 ASP cc_start: 0.8737 (t0) cc_final: 0.8483 (t0) REVERT: E 274 MET cc_start: 0.8360 (mmm) cc_final: 0.8115 (mmp) REVERT: E 448 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8064 (pt) REVERT: F 62 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: F 502 ARG cc_start: 0.7972 (mmt180) cc_final: 0.7649 (ptm160) REVERT: F 585 LEU cc_start: 0.3740 (OUTLIER) cc_final: 0.3531 (pt) outliers start: 237 outliers final: 178 residues processed: 356 average time/residue: 0.3096 time to fit residues: 174.1115 Evaluate side-chains 303 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 117 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 354 GLN Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 40.0000 chunk 196 optimal weight: 3.9990 chunk 108 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 203 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 overall best weight: 1.2360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 81 GLN A 99 HIS A 117 GLN ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN A 224 GLN A 360 ASN A 404 ASN A 439 HIS A 489 ASN A 492 GLN A 568 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 810 HIS A 816 HIS A 911 ASN B 108 ASN B 157 GLN B 168 GLN C 34 GLN D 104 ASN D 109 ASN E 46 ASN E 257 ASN E 275 GLN E 311 HIS E 388 ASN E 464 HIS E 470 GLN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 559 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN F 51 ASN F 164 HIS F 177 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 503 ASN ** F 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22355 Z= 0.195 Angle : 0.638 12.882 30742 Z= 0.323 Chirality : 0.041 0.269 3574 Planarity : 0.004 0.046 3641 Dihedral : 15.547 160.251 4444 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.58 % Favored : 91.38 % Rotamer: Outliers : 6.82 % Allowed : 25.81 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.16), residues: 2551 helix: -0.30 (0.17), residues: 936 sheet: -3.09 (0.25), residues: 322 loop : -2.86 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 916 HIS 0.008 0.001 HIS E 290 PHE 0.015 0.001 PHE F 422 TYR 0.017 0.001 TYR A 788 ARG 0.003 0.000 ARG F 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 133 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8785 (tt) REVERT: A 340 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: A 370 GLU cc_start: 0.8657 (tp30) cc_final: 0.8387 (tp30) REVERT: A 431 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7289 (mm-30) REVERT: A 786 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8830 (mp) REVERT: A 891 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8805 (tt) REVERT: B 56 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: B 77 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8286 (mm-30) REVERT: C 38 ASP cc_start: 0.8593 (t0) cc_final: 0.8183 (t0) REVERT: F 41 LEU cc_start: 0.7463 (tt) cc_final: 0.7048 (pp) REVERT: F 399 ILE cc_start: 0.8726 (mp) cc_final: 0.8476 (pt) REVERT: F 429 MET cc_start: 0.6053 (mmm) cc_final: 0.5846 (mmt) REVERT: F 502 ARG cc_start: 0.8016 (mmt180) cc_final: 0.7775 (ptm160) outliers start: 150 outliers final: 107 residues processed: 277 average time/residue: 0.3041 time to fit residues: 135.1176 Evaluate side-chains 232 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 120 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 306 TYR Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 575 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 160 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 254 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 233 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 503 ASN ** F 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 22355 Z= 0.363 Angle : 0.676 12.867 30742 Z= 0.343 Chirality : 0.042 0.200 3574 Planarity : 0.004 0.046 3641 Dihedral : 14.691 159.313 4279 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.05 % Favored : 88.91 % Rotamer: Outliers : 8.13 % Allowed : 25.58 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.16), residues: 2551 helix: -0.09 (0.17), residues: 955 sheet: -2.76 (0.26), residues: 313 loop : -2.75 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 916 HIS 0.009 0.001 HIS F 164 PHE 0.015 0.001 PHE A 471 TYR 0.022 0.002 TYR A 748 ARG 0.003 0.000 ARG F 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 124 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8819 (tt) REVERT: A 340 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: A 370 GLU cc_start: 0.8687 (tp30) cc_final: 0.8406 (tp30) REVERT: A 431 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7388 (mm-30) REVERT: A 661 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8818 (mt0) REVERT: A 786 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8868 (mp) REVERT: A 891 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8772 (tt) REVERT: B 56 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: B 62 MET cc_start: 0.8932 (tpp) cc_final: 0.8708 (tpp) REVERT: B 70 MET cc_start: 0.7859 (mmt) cc_final: 0.7531 (mmp) REVERT: B 77 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8437 (mm-30) REVERT: B 155 GLU cc_start: 0.8123 (pm20) cc_final: 0.7892 (pm20) REVERT: B 165 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8245 (pttt) REVERT: C 38 ASP cc_start: 0.8662 (t0) cc_final: 0.8257 (t0) REVERT: D 62 MET cc_start: 0.8873 (tpt) cc_final: 0.8638 (tpp) REVERT: E 274 MET cc_start: 0.8512 (mmp) cc_final: 0.7904 (mmm) REVERT: F 41 LEU cc_start: 0.7357 (tt) cc_final: 0.7052 (pp) REVERT: F 333 ILE cc_start: 0.6393 (OUTLIER) cc_final: 0.6144 (mt) REVERT: F 353 GLU cc_start: 0.5453 (OUTLIER) cc_final: 0.5130 (tm-30) REVERT: F 474 MET cc_start: 0.6171 (mmm) cc_final: 0.5944 (mmm) REVERT: F 502 ARG cc_start: 0.8050 (mmt180) cc_final: 0.7821 (ptm160) REVERT: F 576 MET cc_start: 0.4420 (tpt) cc_final: 0.4175 (tpt) outliers start: 179 outliers final: 131 residues processed: 291 average time/residue: 0.3105 time to fit residues: 145.3938 Evaluate side-chains 256 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 117 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 661 GLN Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 306 TYR Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 575 ILE Chi-restraints excluded: chain F residue 585 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 236 optimal weight: 0.5980 chunk 250 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 224 optimal weight: 50.0000 chunk 67 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN D 109 ASN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 503 ASN F 586 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22355 Z= 0.188 Angle : 0.604 12.864 30742 Z= 0.305 Chirality : 0.040 0.200 3574 Planarity : 0.004 0.043 3641 Dihedral : 14.321 153.904 4268 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.51 % Favored : 91.45 % Rotamer: Outliers : 7.31 % Allowed : 26.72 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.17), residues: 2551 helix: 0.42 (0.18), residues: 935 sheet: -2.60 (0.26), residues: 320 loop : -2.45 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 916 HIS 0.008 0.001 HIS E 290 PHE 0.015 0.001 PHE F 422 TYR 0.018 0.001 TYR F 582 ARG 0.003 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 121 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8802 (tt) REVERT: A 340 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: A 370 GLU cc_start: 0.8645 (tp30) cc_final: 0.8395 (tp30) REVERT: A 431 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7335 (mm-30) REVERT: A 786 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8843 (mp) REVERT: A 891 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 56 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: B 70 MET cc_start: 0.7805 (mmt) cc_final: 0.7505 (mmp) REVERT: B 77 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8388 (mm-30) REVERT: B 80 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8395 (ttt-90) REVERT: B 165 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8267 (pttt) REVERT: C 38 ASP cc_start: 0.8573 (t0) cc_final: 0.8087 (t0) REVERT: D 62 MET cc_start: 0.8868 (tpt) cc_final: 0.8637 (tpp) REVERT: E 274 MET cc_start: 0.8522 (mmp) cc_final: 0.8208 (mmm) REVERT: F 333 ILE cc_start: 0.6538 (OUTLIER) cc_final: 0.6291 (mt) REVERT: F 353 GLU cc_start: 0.5477 (OUTLIER) cc_final: 0.5150 (tm-30) REVERT: F 502 ARG cc_start: 0.8024 (mmt180) cc_final: 0.7771 (ptm160) REVERT: F 506 TRP cc_start: 0.2414 (OUTLIER) cc_final: 0.1879 (m100) outliers start: 161 outliers final: 120 residues processed: 271 average time/residue: 0.3128 time to fit residues: 135.4511 Evaluate side-chains 244 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 115 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 306 TYR Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 213 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 224 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN D 109 ASN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 503 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22355 Z= 0.304 Angle : 0.638 12.866 30742 Z= 0.323 Chirality : 0.041 0.197 3574 Planarity : 0.004 0.043 3641 Dihedral : 14.138 147.348 4256 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.23 % Favored : 89.73 % Rotamer: Outliers : 7.86 % Allowed : 26.08 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.16), residues: 2551 helix: 0.35 (0.17), residues: 942 sheet: -2.53 (0.26), residues: 318 loop : -2.39 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 916 HIS 0.005 0.001 HIS E 290 PHE 0.014 0.001 PHE A 471 TYR 0.021 0.001 TYR A 748 ARG 0.003 0.000 ARG A 735 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 116 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8349 (m-80) cc_final: 0.7798 (m-80) REVERT: A 261 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8802 (tt) REVERT: A 340 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: A 370 GLU cc_start: 0.8679 (tp30) cc_final: 0.8427 (tp30) REVERT: A 431 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7386 (mm-30) REVERT: A 786 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8842 (mp) REVERT: A 891 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8706 (tt) REVERT: B 56 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: B 60 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8947 (mp0) REVERT: B 65 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: B 70 MET cc_start: 0.7875 (mmt) cc_final: 0.7571 (mmp) REVERT: B 77 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8400 (mm-30) REVERT: B 80 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8423 (ttt-90) REVERT: B 165 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8271 (pttt) REVERT: C 38 ASP cc_start: 0.8642 (t0) cc_final: 0.8162 (t0) REVERT: D 22 TYR cc_start: 0.7140 (t80) cc_final: 0.6904 (t80) REVERT: E 161 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7017 (mmp-170) REVERT: E 235 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6907 (mm) REVERT: E 274 MET cc_start: 0.8511 (mmp) cc_final: 0.8201 (mmm) REVERT: F 41 LEU cc_start: 0.7362 (tt) cc_final: 0.7086 (pp) REVERT: F 63 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7924 (tp) REVERT: F 333 ILE cc_start: 0.6506 (OUTLIER) cc_final: 0.6252 (mt) REVERT: F 353 GLU cc_start: 0.5523 (OUTLIER) cc_final: 0.5168 (tm-30) REVERT: F 474 MET cc_start: 0.6061 (mmm) cc_final: 0.5840 (mmm) REVERT: F 502 ARG cc_start: 0.8069 (mmt180) cc_final: 0.7812 (ptm160) REVERT: F 506 TRP cc_start: 0.2665 (OUTLIER) cc_final: 0.1984 (m100) outliers start: 173 outliers final: 135 residues processed: 278 average time/residue: 0.3124 time to fit residues: 137.9760 Evaluate side-chains 265 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 117 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 306 TYR Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 250 optimal weight: 20.0000 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN D 109 ASN E 51 ASN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22355 Z= 0.178 Angle : 0.583 12.874 30742 Z= 0.294 Chirality : 0.039 0.200 3574 Planarity : 0.003 0.042 3641 Dihedral : 13.834 130.458 4249 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 6.63 % Allowed : 27.35 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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: -1.69 (0.17), residues: 2551 helix: 0.66 (0.18), residues: 935 sheet: -2.30 (0.28), residues: 296 loop : -2.24 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 916 HIS 0.005 0.001 HIS A 82 PHE 0.015 0.001 PHE E 291 TYR 0.015 0.001 TYR F 582 ARG 0.006 0.000 ARG F 502 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 120 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8363 (m-80) cc_final: 0.8022 (m-80) REVERT: A 261 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8777 (tt) REVERT: A 340 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: A 370 GLU cc_start: 0.8600 (tp30) cc_final: 0.8330 (tp30) REVERT: A 431 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7314 (mm-30) REVERT: A 477 ASP cc_start: 0.8838 (t70) cc_final: 0.8587 (t0) REVERT: A 542 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8296 (mtt) REVERT: A 629 MET cc_start: 0.8200 (mmm) cc_final: 0.7917 (tpp) REVERT: A 786 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8673 (mp) REVERT: A 891 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8615 (tt) REVERT: B 56 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: B 70 MET cc_start: 0.7815 (mmt) cc_final: 0.7505 (mmp) REVERT: B 77 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8345 (mm-30) REVERT: B 80 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8345 (ttt-90) REVERT: E 161 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7048 (mmp-170) REVERT: E 235 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6848 (mm) REVERT: E 274 MET cc_start: 0.8465 (mmp) cc_final: 0.8120 (mmm) REVERT: F 41 LEU cc_start: 0.7310 (tt) cc_final: 0.7054 (pp) REVERT: F 63 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7921 (tp) REVERT: F 333 ILE cc_start: 0.6562 (OUTLIER) cc_final: 0.6294 (mt) REVERT: F 339 ARG cc_start: 0.2084 (OUTLIER) cc_final: 0.0857 (ptp90) REVERT: F 353 GLU cc_start: 0.5497 (OUTLIER) cc_final: 0.5155 (tm-30) REVERT: F 474 MET cc_start: 0.6055 (mmm) cc_final: 0.5770 (mmm) REVERT: F 506 TRP cc_start: 0.2565 (OUTLIER) cc_final: 0.1927 (m100) REVERT: F 576 MET cc_start: 0.4110 (tpt) cc_final: 0.3544 (tpt) outliers start: 146 outliers final: 109 residues processed: 257 average time/residue: 0.3418 time to fit residues: 138.4018 Evaluate side-chains 239 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 116 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 542 ASP Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 306 TYR Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 554 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 141 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 A 611 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN B 140 ASN D 109 ASN E 51 ASN E 354 GLN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 22355 Z= 0.435 Angle : 0.706 12.833 30742 Z= 0.356 Chirality : 0.044 0.197 3574 Planarity : 0.004 0.045 3641 Dihedral : 13.939 124.302 4226 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 8.36 % Allowed : 26.31 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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: -1.96 (0.16), residues: 2551 helix: 0.34 (0.17), residues: 942 sheet: -2.35 (0.27), residues: 300 loop : -2.35 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 290 HIS 0.006 0.001 HIS A 810 PHE 0.025 0.002 PHE F 422 TYR 0.030 0.002 TYR A 748 ARG 0.005 0.000 ARG F 502 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 117 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.8517 (mtt) cc_final: 0.8265 (mtt) REVERT: A 261 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8784 (tt) REVERT: A 340 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: A 370 GLU cc_start: 0.8704 (tp30) cc_final: 0.8443 (tp30) REVERT: A 431 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7435 (mm-30) REVERT: A 629 MET cc_start: 0.8574 (mmm) cc_final: 0.8303 (tpp) REVERT: A 786 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8876 (mp) REVERT: A 891 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8739 (tt) REVERT: B 56 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: B 65 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: B 77 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8422 (mm-30) REVERT: B 80 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8471 (ttt-90) REVERT: B 165 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8309 (pttt) REVERT: D 22 TYR cc_start: 0.7142 (t80) cc_final: 0.6896 (t80) REVERT: D 168 GLN cc_start: 0.9294 (mp10) cc_final: 0.8980 (pm20) REVERT: E 161 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7166 (mmp-170) REVERT: E 235 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6995 (mm) REVERT: F 41 LEU cc_start: 0.7392 (tt) cc_final: 0.7074 (pp) REVERT: F 97 CYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6923 (t) REVERT: F 333 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6318 (mt) REVERT: F 339 ARG cc_start: 0.2123 (OUTLIER) cc_final: 0.0843 (ptp90) REVERT: F 353 GLU cc_start: 0.5631 (OUTLIER) cc_final: 0.5204 (tm-30) REVERT: F 461 LEU cc_start: 0.3241 (OUTLIER) cc_final: 0.2741 (tp) REVERT: F 576 MET cc_start: 0.4094 (tpt) cc_final: 0.3894 (tpp) outliers start: 184 outliers final: 142 residues processed: 290 average time/residue: 0.3133 time to fit residues: 146.8531 Evaluate side-chains 273 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 117 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 542 ASP Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 306 TYR Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 519 ASN Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN D 109 ASN E 164 HIS ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22355 Z= 0.182 Angle : 0.598 12.882 30742 Z= 0.299 Chirality : 0.040 0.201 3574 Planarity : 0.003 0.043 3641 Dihedral : 13.698 124.284 4224 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 6.22 % Allowed : 28.44 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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: -1.60 (0.17), residues: 2551 helix: 0.69 (0.18), residues: 932 sheet: -2.13 (0.29), residues: 284 loop : -2.18 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 916 HIS 0.009 0.001 HIS A 295 PHE 0.013 0.001 PHE F 422 TYR 0.021 0.001 TYR F 582 ARG 0.004 0.000 ARG F 502 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 123 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8237 (m-80) cc_final: 0.7934 (m-80) REVERT: A 261 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8729 (tt) REVERT: A 300 ASN cc_start: 0.9387 (OUTLIER) cc_final: 0.8886 (p0) REVERT: A 340 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: A 370 GLU cc_start: 0.8631 (tp30) cc_final: 0.8372 (tp30) REVERT: A 431 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7344 (mm-30) REVERT: A 477 ASP cc_start: 0.8844 (t70) cc_final: 0.8607 (t0) REVERT: A 542 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8305 (mtt) REVERT: A 786 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8802 (mp) REVERT: A 891 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8593 (tt) REVERT: B 56 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7960 (mp10) REVERT: B 77 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8356 (mm-30) REVERT: B 80 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8361 (ttt-90) REVERT: D 168 GLN cc_start: 0.9056 (mp10) cc_final: 0.8782 (pm20) REVERT: E 161 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7134 (mmp-170) REVERT: E 235 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7043 (mm) REVERT: E 274 MET cc_start: 0.8352 (mmp) cc_final: 0.8040 (mmm) REVERT: F 41 LEU cc_start: 0.7329 (tt) cc_final: 0.7050 (pp) REVERT: F 63 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7933 (tp) REVERT: F 97 CYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6972 (t) REVERT: F 333 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6294 (mt) REVERT: F 339 ARG cc_start: 0.2024 (OUTLIER) cc_final: 0.0763 (ptp90) REVERT: F 353 GLU cc_start: 0.5663 (OUTLIER) cc_final: 0.5234 (tm-30) REVERT: F 422 PHE cc_start: 0.7561 (m-10) cc_final: 0.7312 (m-10) REVERT: F 461 LEU cc_start: 0.3181 (OUTLIER) cc_final: 0.2734 (tp) REVERT: F 576 MET cc_start: 0.4039 (tpt) cc_final: 0.3739 (tpp) outliers start: 137 outliers final: 112 residues processed: 252 average time/residue: 0.3289 time to fit residues: 132.0146 Evaluate side-chains 246 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 118 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.1980 chunk 239 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 chunk 231 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN B 140 ASN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22355 Z= 0.213 Angle : 0.602 12.860 30742 Z= 0.300 Chirality : 0.040 0.199 3574 Planarity : 0.003 0.041 3641 Dihedral : 13.591 123.579 4224 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 6.63 % Allowed : 28.31 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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: -1.52 (0.17), residues: 2551 helix: 0.78 (0.18), residues: 928 sheet: -2.07 (0.29), residues: 285 loop : -2.15 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.004 0.001 HIS F 290 PHE 0.012 0.001 PHE E 291 TYR 0.020 0.001 TYR F 582 ARG 0.003 0.000 ARG F 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 123 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: A 261 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8731 (tt) REVERT: A 340 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: A 370 GLU cc_start: 0.8657 (tp30) cc_final: 0.8396 (tp30) REVERT: A 431 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7373 (mm-30) REVERT: A 477 ASP cc_start: 0.8831 (t70) cc_final: 0.8593 (t0) REVERT: A 542 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8316 (mtt) REVERT: A 629 MET cc_start: 0.8258 (mmm) cc_final: 0.7980 (tpp) REVERT: A 786 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8813 (mp) REVERT: A 891 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8605 (tt) REVERT: B 56 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: B 65 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: B 80 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8392 (ttt-90) REVERT: B 165 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8252 (pttt) REVERT: D 60 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8601 (mt-10) REVERT: D 168 GLN cc_start: 0.9065 (mp10) cc_final: 0.8795 (pm20) REVERT: E 161 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7169 (mmp-170) REVERT: E 235 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7024 (mm) REVERT: E 274 MET cc_start: 0.8282 (mmp) cc_final: 0.7962 (mmm) REVERT: F 63 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7939 (tp) REVERT: F 97 CYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6913 (t) REVERT: F 333 ILE cc_start: 0.6565 (OUTLIER) cc_final: 0.6300 (mt) REVERT: F 339 ARG cc_start: 0.2091 (OUTLIER) cc_final: 0.0847 (ptp90) REVERT: F 353 GLU cc_start: 0.5586 (OUTLIER) cc_final: 0.5182 (tm-30) REVERT: F 422 PHE cc_start: 0.7467 (m-10) cc_final: 0.7266 (m-10) REVERT: F 461 LEU cc_start: 0.3358 (OUTLIER) cc_final: 0.2645 (tt) outliers start: 146 outliers final: 126 residues processed: 260 average time/residue: 0.3239 time to fit residues: 135.0399 Evaluate side-chains 258 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 115 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 258 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN D 109 ASN E 245 HIS ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 22355 Z= 0.451 Angle : 0.717 13.749 30742 Z= 0.360 Chirality : 0.044 0.197 3574 Planarity : 0.004 0.047 3641 Dihedral : 13.822 124.334 4224 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 6.91 % Allowed : 28.26 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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: -1.79 (0.17), residues: 2551 helix: 0.45 (0.17), residues: 930 sheet: -2.14 (0.29), residues: 292 loop : -2.24 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 290 HIS 0.006 0.001 HIS A 810 PHE 0.018 0.002 PHE A 471 TYR 0.031 0.002 TYR A 748 ARG 0.003 0.000 ARG F 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 117 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: A 261 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8724 (tt) REVERT: A 340 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7142 (m-10) REVERT: A 370 GLU cc_start: 0.8703 (tp30) cc_final: 0.8440 (tp30) REVERT: A 431 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7441 (mm-30) REVERT: A 629 MET cc_start: 0.8568 (mmm) cc_final: 0.8326 (tpp) REVERT: A 786 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8864 (mp) REVERT: A 891 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8729 (tt) REVERT: B 56 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: B 65 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8236 (tm-30) REVERT: B 80 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8499 (ttt-90) REVERT: B 165 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8231 (pttt) REVERT: D 22 TYR cc_start: 0.7133 (t80) cc_final: 0.6891 (t80) REVERT: D 168 GLN cc_start: 0.9142 (mp10) cc_final: 0.8848 (pm20) REVERT: E 161 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7247 (mmp-170) REVERT: E 233 MET cc_start: 0.8235 (tpp) cc_final: 0.7828 (tpp) REVERT: E 235 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7144 (mm) REVERT: E 274 MET cc_start: 0.8350 (mmp) cc_final: 0.8008 (mmm) REVERT: F 41 LEU cc_start: 0.7336 (tt) cc_final: 0.6995 (pp) REVERT: F 97 CYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6896 (t) REVERT: F 333 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6320 (mt) REVERT: F 353 GLU cc_start: 0.5722 (OUTLIER) cc_final: 0.5252 (tm-30) REVERT: F 461 LEU cc_start: 0.3301 (OUTLIER) cc_final: 0.2857 (tp) REVERT: F 474 MET cc_start: 0.5783 (mmm) cc_final: 0.3455 (ttp) outliers start: 152 outliers final: 130 residues processed: 260 average time/residue: 0.3254 time to fit residues: 135.3846 Evaluate side-chains 258 residues out of total 2240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 114 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 508 LYS Chi-restraints excluded: chain E residue 516 ASN Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 476 TYR Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 528 LEU Chi-restraints excluded: chain F residue 549 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 585 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 6.9990 chunk 218 optimal weight: 0.0870 chunk 62 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 211 optimal weight: 30.0000 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 468 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 882 HIS D 109 ASN ** E 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.122338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.069593 restraints weight = 56158.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.071708 restraints weight = 24044.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.073108 restraints weight = 14409.086| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22355 Z= 0.154 Angle : 0.594 12.898 30742 Z= 0.294 Chirality : 0.039 0.201 3574 Planarity : 0.003 0.042 3641 Dihedral : 13.525 123.727 4224 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.54 % Allowed : 29.90 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.37 % 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: -1.37 (0.17), residues: 2551 helix: 0.88 (0.18), residues: 925 sheet: -1.95 (0.28), residues: 300 loop : -2.03 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 114 HIS 0.005 0.001 HIS A 82 PHE 0.030 0.001 PHE F 422 TYR 0.019 0.001 TYR F 582 ARG 0.003 0.000 ARG A 735 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4218.37 seconds wall clock time: 78 minutes 15.79 seconds (4695.79 seconds total)