Starting phenix.real_space_refine on Fri Feb 16 03:19:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2024/7bg9_12174_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2024/7bg9_12174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2024/7bg9_12174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2024/7bg9_12174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2024/7bg9_12174_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bg9_12174/02_2024/7bg9_12174_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 262 5.49 5 S 37 5.16 5 C 8028 2.51 5 N 2586 2.21 5 O 3320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A PHE 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "M TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 77": "OE1" <-> "OE2" Residue "L PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14233 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7333 Classifications: {'peptide': 913} Link IDs: {'PTRANS': 51, 'TRANS': 861} Chain breaks: 4 Chain: "N" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 127 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "M" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "L" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 643 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "B" Number of atoms: 5431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 5431 Classifications: {'RNA': 256} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 10, 'rna3p_pur': 103, 'rna3p_pyr': 130} Link IDs: {'rna2p': 23, 'rna3p': 232} Chain breaks: 3 Time building chain proxies: 8.39, per 1000 atoms: 0.59 Number of scatterers: 14233 At special positions: 0 Unit cell: (134.31, 139.86, 135.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 262 15.00 O 3320 8.00 N 2586 7.00 C 8028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 54.7% alpha, 6.5% beta 70 base pairs and 128 stacking pairs defined. Time for finding SS restraints: 5.42 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.727A pdb=" N ARG A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 21 " --> pdb=" O HIS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 78 through 88 removed outlier: 4.297A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 removed outlier: 4.322A pdb=" N PHE A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 100' Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.543A pdb=" N LEU A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.113A pdb=" N ALA A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.630A pdb=" N LYS A 329 " --> pdb=" O TYR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 removed outlier: 3.523A pdb=" N LEU A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 366 removed outlier: 4.184A pdb=" N ARG A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 389 through 402 removed outlier: 4.044A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.593A pdb=" N VAL A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 470 removed outlier: 4.117A pdb=" N GLY A 463 " --> pdb=" O TRP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 4.012A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 479' Processing helix chain 'A' and resid 480 through 496 removed outlier: 4.259A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 558 removed outlier: 3.599A pdb=" N ILE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 595 removed outlier: 3.574A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 610 removed outlier: 3.839A pdb=" N GLN A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 672 removed outlier: 3.509A pdb=" N VAL A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 Processing helix chain 'A' and resid 683 through 697 removed outlier: 3.587A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 removed outlier: 4.204A pdb=" N LEU A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 731 " --> pdb=" O GLU A 727 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 781 Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 801 through 815 removed outlier: 3.706A pdb=" N PHE A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 854 removed outlier: 3.541A pdb=" N CYS A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 846 " --> pdb=" O CYS A 842 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A 851 " --> pdb=" O GLY A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 889 removed outlier: 3.843A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.854A pdb=" N SER A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 953 through 958' Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.810A pdb=" N ARG A 972 " --> pdb=" O ARG A 968 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 removed outlier: 3.725A pdb=" N LEU A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1017 removed outlier: 4.017A pdb=" N THR A 999 " --> pdb=" O GLN A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1027 removed outlier: 3.531A pdb=" N LYS A1027 " --> pdb=" O GLN A1024 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1024 through 1027' Processing helix chain 'A' and resid 1028 through 1052 removed outlier: 4.230A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1033 " --> pdb=" O PRO A1029 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A1038 " --> pdb=" O ARG A1034 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A1042 " --> pdb=" O ASP A1038 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A1051 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 removed outlier: 4.412A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS A1075 " --> pdb=" O GLN A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1090 removed outlier: 3.903A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1106 removed outlier: 3.901A pdb=" N ALA A1099 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 removed outlier: 3.510A pdb=" N THR A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A1118 " --> pdb=" O ALA A1114 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 50 removed outlier: 3.801A pdb=" N TYR M 43 " --> pdb=" O SER M 39 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 86 removed outlier: 4.108A pdb=" N SER M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL M 67 " --> pdb=" O MET M 63 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN M 68 " --> pdb=" O ASN M 64 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE M 74 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 103 removed outlier: 4.193A pdb=" N ILE M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN M 96 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR M 97 " --> pdb=" O ARG M 93 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU M 101 " --> pdb=" O THR M 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 124 removed outlier: 3.550A pdb=" N LYS M 109 " --> pdb=" O GLY M 105 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS M 121 " --> pdb=" O LYS M 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 27 through 35 removed outlier: 3.517A pdb=" N LEU L 35 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 74 removed outlier: 4.561A pdb=" N VAL L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL L 55 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR L 58 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU L 64 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA L 67 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP L 73 " --> pdb=" O ASN L 69 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN L 74 " --> pdb=" O ALA L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 91 removed outlier: 3.810A pdb=" N ALA L 87 " --> pdb=" O HIS L 83 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG L 89 " --> pdb=" O GLN L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.596A pdb=" N LEU L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 4.151A pdb=" N LEU A 24 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 58 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 600 Processing sheet with id=AA4, first strand: chain 'A' and resid 619 through 625 Processing sheet with id=AA5, first strand: chain 'A' and resid 862 through 866 removed outlier: 3.722A pdb=" N LEU A 866 " --> pdb=" O ASP A 869 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 711 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 905 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 755 through 761 removed outlier: 3.598A pdb=" N TYR A 744 " --> pdb=" O LYS A 757 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 928 through 930 Processing sheet with id=AA8, first strand: chain 'M' and resid 89 through 90 removed outlier: 3.757A pdb=" N ILE M 90 " --> pdb=" O ARG L 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 339 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 182 hydrogen bonds 350 hydrogen bond angles 0 basepair planarities 70 basepair parallelities 128 stacking parallelities Total time for adding SS restraints: 7.05 Time building geometry restraints manager: 6.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1592 1.29 - 1.43: 5038 1.43 - 1.56: 7769 1.56 - 1.70: 613 1.70 - 1.84: 51 Bond restraints: 15063 Sorted by residual: bond pdb=" CA VAL A 529 " pdb=" C VAL A 529 " ideal model delta sigma weight residual 1.524 1.622 -0.097 1.05e-02 9.07e+03 8.57e+01 bond pdb=" C VAL A 529 " pdb=" N PRO A 530 " ideal model delta sigma weight residual 1.328 1.441 -0.113 1.25e-02 6.40e+03 8.22e+01 bond pdb=" C PHE A 560 " pdb=" O PHE A 560 " ideal model delta sigma weight residual 1.235 1.148 0.088 1.02e-02 9.61e+03 7.37e+01 bond pdb=" C GLN A1023 " pdb=" O GLN A1023 " ideal model delta sigma weight residual 1.235 1.327 -0.092 1.14e-02 7.69e+03 6.49e+01 bond pdb=" CA ILE A1004 " pdb=" C ILE A1004 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.22e-02 6.72e+03 4.84e+01 ... (remaining 15058 not shown) Histogram of bond angle deviations from ideal: 97.72 - 106.00: 1668 106.00 - 114.29: 8480 114.29 - 122.57: 8542 122.57 - 130.86: 2867 130.86 - 139.14: 85 Bond angle restraints: 21642 Sorted by residual: angle pdb=" N LYS A 410 " pdb=" CA LYS A 410 " pdb=" C LYS A 410 " ideal model delta sigma weight residual 112.68 99.30 13.38 1.33e+00 5.65e-01 1.01e+02 angle pdb=" N ASP A 337 " pdb=" CA ASP A 337 " pdb=" C ASP A 337 " ideal model delta sigma weight residual 111.02 123.23 -12.21 1.22e+00 6.72e-01 1.00e+02 angle pdb=" N PHE A 561 " pdb=" CA PHE A 561 " pdb=" C PHE A 561 " ideal model delta sigma weight residual 108.76 125.23 -16.47 1.69e+00 3.50e-01 9.50e+01 angle pdb=" C VAL A 529 " pdb=" N PRO A 530 " pdb=" CA PRO A 530 " ideal model delta sigma weight residual 120.85 110.36 10.49 1.08e+00 8.57e-01 9.44e+01 angle pdb=" N LYS A 338 " pdb=" CA LYS A 338 " pdb=" C LYS A 338 " ideal model delta sigma weight residual 111.71 122.61 -10.90 1.15e+00 7.56e-01 8.99e+01 ... (remaining 21637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 8712 35.65 - 71.29: 690 71.29 - 106.94: 111 106.94 - 142.59: 6 142.59 - 178.24: 7 Dihedral angle restraints: 9526 sinusoidal: 6373 harmonic: 3153 Sorted by residual: dihedral pdb=" C5' A B 176 " pdb=" C4' A B 176 " pdb=" C3' A B 176 " pdb=" O3' A B 176 " ideal model delta sinusoidal sigma weight residual 147.00 73.18 73.82 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" O4' U B 316 " pdb=" C1' U B 316 " pdb=" N1 U B 316 " pdb=" C2 U B 316 " ideal model delta sinusoidal sigma weight residual -160.00 16.07 -176.07 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" C4' U B 307 " pdb=" C3' U B 307 " pdb=" C2' U B 307 " pdb=" C1' U B 307 " ideal model delta sinusoidal sigma weight residual -35.00 23.52 -58.52 1 8.00e+00 1.56e-02 7.17e+01 ... (remaining 9523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2269 0.156 - 0.313: 356 0.313 - 0.469: 28 0.469 - 0.625: 2 0.625 - 0.782: 3 Chirality restraints: 2658 Sorted by residual: chirality pdb=" C3' U B 312 " pdb=" C4' U B 312 " pdb=" O3' U B 312 " pdb=" C2' U B 312 " both_signs ideal model delta sigma weight residual False -2.48 -1.70 -0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" C3' G B 300 " pdb=" C4' G B 300 " pdb=" O3' G B 300 " pdb=" C2' G B 300 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C3' A B 176 " pdb=" C4' A B 176 " pdb=" O3' A B 176 " pdb=" C2' A B 176 " both_signs ideal model delta sigma weight residual False -2.74 -2.11 -0.63 2.00e-01 2.50e+01 9.94e+00 ... (remaining 2655 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA N 15 " 0.077 2.00e-02 2.50e+03 3.25e-02 2.90e+01 pdb=" N9 DA N 15 " -0.034 2.00e-02 2.50e+03 pdb=" C8 DA N 15 " -0.015 2.00e-02 2.50e+03 pdb=" N7 DA N 15 " -0.018 2.00e-02 2.50e+03 pdb=" C5 DA N 15 " -0.018 2.00e-02 2.50e+03 pdb=" C6 DA N 15 " 0.028 2.00e-02 2.50e+03 pdb=" N6 DA N 15 " 0.039 2.00e-02 2.50e+03 pdb=" N1 DA N 15 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DA N 15 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA N 15 " -0.017 2.00e-02 2.50e+03 pdb=" C4 DA N 15 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 177 " -0.073 2.00e-02 2.50e+03 3.57e-02 2.86e+01 pdb=" N1 U B 177 " 0.034 2.00e-02 2.50e+03 pdb=" C2 U B 177 " 0.023 2.00e-02 2.50e+03 pdb=" O2 U B 177 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U B 177 " 0.021 2.00e-02 2.50e+03 pdb=" C4 U B 177 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U B 177 " -0.051 2.00e-02 2.50e+03 pdb=" C5 U B 177 " 0.018 2.00e-02 2.50e+03 pdb=" C6 U B 177 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 547 " 0.043 2.00e-02 2.50e+03 3.25e-02 2.64e+01 pdb=" CG TRP A 547 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 547 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 547 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 547 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 547 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 547 " -0.067 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 547 " 0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 547 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 547 " 0.016 2.00e-02 2.50e+03 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 6 2.19 - 2.87: 4325 2.87 - 3.55: 19210 3.55 - 4.22: 34638 4.22 - 4.90: 50134 Nonbonded interactions: 108313 Sorted by model distance: nonbonded pdb=" NE1 TRP A 510 " pdb=" CE1 HIS A1022 " model vdw 1.518 3.340 nonbonded pdb=" CB PRO A 23 " pdb=" CZ3 TRP A 60 " model vdw 1.745 3.740 nonbonded pdb=" CE2 TRP A 510 " pdb=" CE1 HIS A1022 " model vdw 1.921 3.480 nonbonded pdb=" ND1 HIS A1022 " pdb=" O2' U B 312 " model vdw 1.946 2.520 nonbonded pdb=" NE1 TRP A 510 " pdb=" NE2 HIS A1022 " model vdw 2.130 3.200 ... (remaining 108308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.010 Extract box with map and model: 3.700 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 43.970 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.013 0.143 15063 Z= 0.854 Angle : 1.642 16.474 21642 Z= 1.041 Chirality : 0.110 0.782 2658 Planarity : 0.009 0.101 1784 Dihedral : 22.530 178.236 7486 Min Nonbonded Distance : 1.518 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 1.59 % Allowed : 11.95 % Favored : 86.46 % Rotamer: Outliers : 0.75 % Allowed : 10.39 % Favored : 88.87 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -5.05 (0.20), residues: 1071 helix: -3.42 (0.15), residues: 461 sheet: -3.45 (0.47), residues: 66 loop : -3.29 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.009 TRP A 547 HIS 0.023 0.004 HIS A 412 PHE 0.067 0.009 PHE A 575 TYR 0.050 0.008 TYR A 325 ARG 0.026 0.002 ARG A1011 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8887 (tp30) cc_final: 0.8649 (tm-30) REVERT: A 60 TRP cc_start: 0.5856 (p90) cc_final: 0.5107 (p-90) REVERT: A 91 ARG cc_start: 0.4298 (tpt170) cc_final: 0.3908 (mmm-85) REVERT: A 152 LEU cc_start: 0.8796 (mp) cc_final: 0.8445 (tt) REVERT: A 347 LEU cc_start: 0.9199 (mp) cc_final: 0.8925 (tt) REVERT: A 450 GLN cc_start: 0.8956 (mm110) cc_final: 0.8438 (tp40) REVERT: A 491 THR cc_start: 0.8828 (m) cc_final: 0.8529 (m) REVERT: A 502 LYS cc_start: 0.8544 (mttp) cc_final: 0.8329 (ptmm) REVERT: A 511 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8545 (ttmt) REVERT: A 553 VAL cc_start: 0.8552 (t) cc_final: 0.8334 (p) REVERT: A 559 SER cc_start: 0.8315 (t) cc_final: 0.7861 (t) REVERT: A 560 PHE cc_start: 0.8958 (m-80) cc_final: 0.8712 (m-10) REVERT: A 607 ARG cc_start: 0.8953 (mmt-90) cc_final: 0.8602 (mpt180) REVERT: A 608 GLN cc_start: 0.9012 (mp10) cc_final: 0.8445 (pp30) REVERT: A 610 ARG cc_start: 0.8892 (mtt180) cc_final: 0.8629 (mtt180) REVERT: A 766 LEU cc_start: 0.8398 (mm) cc_final: 0.7832 (tt) REVERT: A 770 GLN cc_start: 0.9170 (mt0) cc_final: 0.8477 (mm110) REVERT: A 813 MET cc_start: 0.9261 (ptm) cc_final: 0.9031 (ppp) REVERT: A 854 PHE cc_start: 0.7242 (m-80) cc_final: 0.6997 (m-10) REVERT: A 893 GLU cc_start: 0.9557 (mt-10) cc_final: 0.9328 (tm-30) REVERT: A 899 ASN cc_start: 0.9187 (m-40) cc_final: 0.8828 (p0) REVERT: A 922 MET cc_start: 0.7376 (ptp) cc_final: 0.6949 (mpp) REVERT: A 941 GLU cc_start: 0.8450 (tt0) cc_final: 0.7884 (tm-30) REVERT: M 41 TYR cc_start: 0.9139 (m-80) cc_final: 0.8698 (m-10) REVERT: M 44 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8192 (mttp) REVERT: M 55 ILE cc_start: 0.8213 (tp) cc_final: 0.7880 (tt) REVERT: M 63 MET cc_start: 0.9586 (ptt) cc_final: 0.9065 (mmt) REVERT: M 122 TYR cc_start: 0.8569 (t80) cc_final: 0.7785 (t80) REVERT: L 18 ARG cc_start: 0.7398 (mtm110) cc_final: 0.6946 (mtm-85) REVERT: L 40 TYR cc_start: 0.7600 (m-80) cc_final: 0.7323 (m-80) REVERT: L 62 GLU cc_start: 0.8939 (tp30) cc_final: 0.8653 (tt0) REVERT: L 69 ASN cc_start: 0.8027 (m-40) cc_final: 0.7778 (m110) REVERT: L 72 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7947 (mtp-110) REVERT: L 75 LYS cc_start: 0.7682 (tppt) cc_final: 0.7369 (ttpp) REVERT: L 91 ASP cc_start: 0.8345 (t70) cc_final: 0.7936 (t70) outliers start: 7 outliers final: 1 residues processed: 190 average time/residue: 0.3758 time to fit residues: 94.2091 Evaluate side-chains 125 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 511 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 120 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 40 GLN A 412 HIS A 454 GLN A 546 HIS ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN A 990 GLN A 995 GLN A1024 GLN A1100 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15063 Z= 0.221 Angle : 0.734 9.344 21642 Z= 0.374 Chirality : 0.039 0.299 2658 Planarity : 0.006 0.072 1784 Dihedral : 23.555 179.209 5384 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 3.43 % Allowed : 13.17 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.23), residues: 1071 helix: -1.34 (0.20), residues: 518 sheet: -2.67 (0.49), residues: 80 loop : -2.75 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 60 HIS 0.014 0.002 HIS A 412 PHE 0.024 0.002 PHE A 708 TYR 0.017 0.002 TYR A 552 ARG 0.005 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.4478 (tpt170) cc_final: 0.3989 (mmm160) REVERT: A 152 LEU cc_start: 0.8700 (mp) cc_final: 0.8414 (tt) REVERT: A 450 GLN cc_start: 0.9006 (mm110) cc_final: 0.8502 (tp40) REVERT: A 556 LEU cc_start: 0.8076 (pp) cc_final: 0.7679 (pt) REVERT: A 608 GLN cc_start: 0.8973 (mp10) cc_final: 0.8760 (pp30) REVERT: A 636 MET cc_start: 0.8828 (mmt) cc_final: 0.8148 (ppp) REVERT: A 650 ARG cc_start: 0.7667 (mmt180) cc_final: 0.7426 (mmp-170) REVERT: A 762 HIS cc_start: 0.8258 (t-90) cc_final: 0.7859 (t-90) REVERT: A 770 GLN cc_start: 0.9147 (mt0) cc_final: 0.8449 (mm110) REVERT: A 772 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: A 902 LYS cc_start: 0.9383 (mmtt) cc_final: 0.9161 (ptpp) REVERT: M 44 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7933 (mttp) REVERT: M 63 MET cc_start: 0.9372 (ptt) cc_final: 0.9091 (mmt) REVERT: M 73 ARG cc_start: 0.9231 (mmt-90) cc_final: 0.8885 (mtm180) REVERT: M 122 TYR cc_start: 0.8255 (t80) cc_final: 0.7449 (t80) REVERT: L 18 ARG cc_start: 0.7262 (mtm110) cc_final: 0.6923 (mtm-85) REVERT: L 40 TYR cc_start: 0.7628 (m-80) cc_final: 0.7280 (m-80) REVERT: L 62 GLU cc_start: 0.8925 (tp30) cc_final: 0.8621 (tt0) REVERT: L 72 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7716 (mtp-110) REVERT: L 75 LYS cc_start: 0.7610 (tppt) cc_final: 0.7335 (tttp) outliers start: 32 outliers final: 11 residues processed: 150 average time/residue: 0.3176 time to fit residues: 66.6131 Evaluate side-chains 120 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15063 Z= 0.283 Angle : 0.724 9.037 21642 Z= 0.369 Chirality : 0.040 0.294 2658 Planarity : 0.006 0.060 1784 Dihedral : 23.585 177.128 5380 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.85 % Allowed : 17.34 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.29 (0.25), residues: 1071 helix: -0.47 (0.22), residues: 523 sheet: -2.64 (0.48), residues: 87 loop : -2.52 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 60 HIS 0.015 0.002 HIS A 412 PHE 0.028 0.002 PHE A 345 TYR 0.015 0.002 TYR A 18 ARG 0.007 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 105 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.4564 (tpt170) cc_final: 0.3892 (mmm160) REVERT: A 152 LEU cc_start: 0.8643 (mp) cc_final: 0.8359 (tt) REVERT: A 450 GLN cc_start: 0.9001 (mm110) cc_final: 0.8686 (tp40) REVERT: A 631 ARG cc_start: 0.8702 (ttp-170) cc_final: 0.8349 (ptp-110) REVERT: A 770 GLN cc_start: 0.9108 (mt0) cc_final: 0.8437 (mm110) REVERT: A 772 TYR cc_start: 0.8803 (t80) cc_final: 0.8007 (m-80) REVERT: A 774 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7823 (ptt-90) REVERT: M 73 ARG cc_start: 0.9212 (mmt-90) cc_final: 0.8913 (mtm180) REVERT: M 122 TYR cc_start: 0.8145 (t80) cc_final: 0.7375 (t80) REVERT: L 18 ARG cc_start: 0.7199 (mtm110) cc_final: 0.6900 (mtm-85) REVERT: L 40 TYR cc_start: 0.7501 (m-80) cc_final: 0.7058 (m-80) REVERT: L 62 GLU cc_start: 0.8927 (tp30) cc_final: 0.8664 (tt0) REVERT: L 75 LYS cc_start: 0.7507 (tppt) cc_final: 0.7280 (ttpp) outliers start: 36 outliers final: 21 residues processed: 127 average time/residue: 0.3020 time to fit residues: 54.5676 Evaluate side-chains 117 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 HIS M 50 HIS M 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15063 Z= 0.176 Angle : 0.623 10.786 21642 Z= 0.314 Chirality : 0.035 0.256 2658 Planarity : 0.005 0.058 1784 Dihedral : 23.454 178.056 5378 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.18 % Allowed : 19.38 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.26), residues: 1071 helix: 0.27 (0.23), residues: 519 sheet: -2.08 (0.54), residues: 81 loop : -2.39 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 60 HIS 0.011 0.001 HIS A 412 PHE 0.022 0.002 PHE A 345 TYR 0.016 0.001 TYR M 41 ARG 0.005 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 104 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.4617 (tpt170) cc_final: 0.3991 (mmm160) REVERT: A 152 LEU cc_start: 0.8585 (mp) cc_final: 0.8319 (tt) REVERT: A 450 GLN cc_start: 0.8993 (mm110) cc_final: 0.8664 (tp40) REVERT: A 631 ARG cc_start: 0.8590 (ttp-170) cc_final: 0.8184 (ptp-110) REVERT: A 636 MET cc_start: 0.8551 (mmt) cc_final: 0.8097 (ppp) REVERT: A 685 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8365 (p0) REVERT: A 770 GLN cc_start: 0.9067 (mt0) cc_final: 0.8624 (tp-100) REVERT: A 772 TYR cc_start: 0.8597 (t80) cc_final: 0.7818 (m-80) REVERT: A 972 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8140 (ttp-110) REVERT: M 73 ARG cc_start: 0.9209 (mmt-90) cc_final: 0.8937 (mtm180) REVERT: M 122 TYR cc_start: 0.8051 (t80) cc_final: 0.7217 (t80) REVERT: L 18 ARG cc_start: 0.7168 (mtm110) cc_final: 0.6813 (mtm-85) REVERT: L 40 TYR cc_start: 0.7517 (m-80) cc_final: 0.7276 (m-80) REVERT: L 62 GLU cc_start: 0.8922 (tp30) cc_final: 0.8669 (tt0) REVERT: L 75 LYS cc_start: 0.7533 (tppt) cc_final: 0.7293 (ttpp) REVERT: L 85 GLN cc_start: 0.8869 (mm110) cc_final: 0.8296 (pt0) outliers start: 39 outliers final: 19 residues processed: 131 average time/residue: 0.2829 time to fit residues: 53.3636 Evaluate side-chains 118 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 96 GLN Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 506 GLN A 592 HIS ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 HIS A1100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15063 Z= 0.416 Angle : 0.833 10.718 21642 Z= 0.420 Chirality : 0.043 0.310 2658 Planarity : 0.007 0.059 1784 Dihedral : 23.972 175.923 5378 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.15 % Favored : 90.76 % Rotamer: Outliers : 5.03 % Allowed : 19.59 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.25), residues: 1071 helix: -0.28 (0.22), residues: 530 sheet: -1.99 (0.55), residues: 75 loop : -2.86 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 60 HIS 0.018 0.002 HIS A 412 PHE 0.026 0.003 PHE A 708 TYR 0.034 0.003 TYR A 168 ARG 0.007 0.001 ARG A 521 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 89 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.5030 (tpt170) cc_final: 0.4262 (mmm160) REVERT: A 152 LEU cc_start: 0.8693 (mp) cc_final: 0.8441 (tt) REVERT: A 372 MET cc_start: 0.5569 (ppp) cc_final: 0.4640 (mmt) REVERT: A 450 GLN cc_start: 0.8954 (mm110) cc_final: 0.8717 (tp40) REVERT: A 631 ARG cc_start: 0.8727 (ttp-170) cc_final: 0.8275 (ptp-110) REVERT: A 636 MET cc_start: 0.8540 (mmt) cc_final: 0.8240 (ppp) REVERT: A 770 GLN cc_start: 0.9041 (mt0) cc_final: 0.8535 (tp-100) REVERT: A 772 TYR cc_start: 0.8693 (t80) cc_final: 0.7941 (m-80) REVERT: M 62 ILE cc_start: 0.8714 (tp) cc_final: 0.8439 (tt) REVERT: M 66 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7274 (t80) REVERT: M 73 ARG cc_start: 0.9162 (mmt-90) cc_final: 0.8919 (mtm180) REVERT: M 122 TYR cc_start: 0.8129 (t80) cc_final: 0.7365 (t80) REVERT: L 18 ARG cc_start: 0.7415 (mtm110) cc_final: 0.6924 (mpp-170) REVERT: L 40 TYR cc_start: 0.7534 (m-80) cc_final: 0.7326 (m-80) REVERT: L 62 GLU cc_start: 0.8877 (tp30) cc_final: 0.8660 (pt0) REVERT: L 75 LYS cc_start: 0.7524 (tppt) cc_final: 0.7297 (tttt) REVERT: L 85 GLN cc_start: 0.8917 (mm110) cc_final: 0.8183 (pt0) outliers start: 47 outliers final: 35 residues processed: 124 average time/residue: 0.2976 time to fit residues: 52.9510 Evaluate side-chains 120 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 66 PHE Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 42 optimal weight: 0.0050 chunk 67 optimal weight: 2.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 608 GLN ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15063 Z= 0.170 Angle : 0.624 8.848 21642 Z= 0.313 Chirality : 0.036 0.222 2658 Planarity : 0.005 0.062 1784 Dihedral : 23.666 177.819 5378 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.43 % Allowed : 21.52 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.26), residues: 1071 helix: 0.48 (0.23), residues: 525 sheet: -2.08 (0.51), residues: 87 loop : -2.47 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 60 HIS 0.010 0.001 HIS A 412 PHE 0.013 0.001 PHE A 575 TYR 0.029 0.001 TYR A 168 ARG 0.006 0.000 ARG M 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.5047 (tpt170) cc_final: 0.4438 (mmm-85) REVERT: A 152 LEU cc_start: 0.8614 (mp) cc_final: 0.8383 (tt) REVERT: A 372 MET cc_start: 0.5747 (ppp) cc_final: 0.4854 (mmt) REVERT: A 450 GLN cc_start: 0.8927 (mm110) cc_final: 0.8686 (tp40) REVERT: A 631 ARG cc_start: 0.8598 (ttp-170) cc_final: 0.8096 (ptp-110) REVERT: A 636 MET cc_start: 0.8518 (mmt) cc_final: 0.8158 (ppp) REVERT: A 685 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8352 (p0) REVERT: A 770 GLN cc_start: 0.8890 (mt0) cc_final: 0.8323 (tp-100) REVERT: A 772 TYR cc_start: 0.8704 (t80) cc_final: 0.7899 (m-80) REVERT: M 73 ARG cc_start: 0.9174 (mmt-90) cc_final: 0.8920 (mtm180) REVERT: M 122 TYR cc_start: 0.8058 (t80) cc_final: 0.7679 (t80) REVERT: L 18 ARG cc_start: 0.7438 (mtm110) cc_final: 0.6962 (mtm-85) REVERT: L 40 TYR cc_start: 0.7421 (m-80) cc_final: 0.7017 (m-80) REVERT: L 62 GLU cc_start: 0.8869 (tp30) cc_final: 0.8649 (pt0) REVERT: L 75 LYS cc_start: 0.7541 (tppt) cc_final: 0.7291 (tttt) REVERT: L 85 GLN cc_start: 0.8993 (mm110) cc_final: 0.8130 (pt0) outliers start: 32 outliers final: 23 residues processed: 121 average time/residue: 0.3110 time to fit residues: 54.2296 Evaluate side-chains 114 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 50.0000 chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 30.0000 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 80 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 608 GLN ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15063 Z= 0.197 Angle : 0.629 7.695 21642 Z= 0.318 Chirality : 0.036 0.206 2658 Planarity : 0.005 0.057 1784 Dihedral : 23.644 177.643 5378 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.32 % Allowed : 21.84 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.26), residues: 1071 helix: 0.55 (0.23), residues: 527 sheet: -1.98 (0.53), residues: 87 loop : -2.51 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 60 HIS 0.010 0.001 HIS A 412 PHE 0.016 0.002 PHE M 71 TYR 0.024 0.002 TYR A 168 ARG 0.011 0.000 ARG M 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.5209 (tpt170) cc_final: 0.4588 (mmm-85) REVERT: A 152 LEU cc_start: 0.8622 (mp) cc_final: 0.8403 (tt) REVERT: A 372 MET cc_start: 0.5360 (ppp) cc_final: 0.4830 (mmt) REVERT: A 450 GLN cc_start: 0.8956 (mm110) cc_final: 0.8742 (tp40) REVERT: A 502 LYS cc_start: 0.8849 (mttp) cc_final: 0.8588 (ptmt) REVERT: A 516 ASP cc_start: 0.8917 (m-30) cc_final: 0.8282 (p0) REVERT: A 631 ARG cc_start: 0.8700 (ttp-170) cc_final: 0.8209 (ptp-110) REVERT: A 685 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8377 (p0) REVERT: A 772 TYR cc_start: 0.8581 (t80) cc_final: 0.7872 (m-80) REVERT: M 73 ARG cc_start: 0.9119 (mmt-90) cc_final: 0.8853 (mtm180) REVERT: M 122 TYR cc_start: 0.8228 (t80) cc_final: 0.7569 (t80) REVERT: L 40 TYR cc_start: 0.7460 (m-80) cc_final: 0.7043 (m-80) REVERT: L 75 LYS cc_start: 0.7505 (tppt) cc_final: 0.7298 (tttt) REVERT: L 85 GLN cc_start: 0.8998 (mm110) cc_final: 0.8184 (pt0) outliers start: 31 outliers final: 24 residues processed: 113 average time/residue: 0.3057 time to fit residues: 49.4416 Evaluate side-chains 108 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 100 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15063 Z= 0.190 Angle : 0.632 8.600 21642 Z= 0.318 Chirality : 0.036 0.293 2658 Planarity : 0.005 0.059 1784 Dihedral : 23.616 177.157 5378 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.21 % Allowed : 22.59 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 1071 helix: 0.67 (0.23), residues: 527 sheet: -1.84 (0.54), residues: 87 loop : -2.49 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 60 HIS 0.010 0.001 HIS A 412 PHE 0.022 0.002 PHE A 560 TYR 0.029 0.002 TYR A 168 ARG 0.006 0.000 ARG M 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.5218 (tpt170) cc_final: 0.4634 (mmm-85) REVERT: A 152 LEU cc_start: 0.8576 (mp) cc_final: 0.8358 (tt) REVERT: A 372 MET cc_start: 0.5648 (ppp) cc_final: 0.4995 (mmm) REVERT: A 450 GLN cc_start: 0.8949 (mm110) cc_final: 0.8731 (tp40) REVERT: A 502 LYS cc_start: 0.8834 (mttp) cc_final: 0.8566 (ptmt) REVERT: A 631 ARG cc_start: 0.8661 (ttp-170) cc_final: 0.8183 (ptp-110) REVERT: A 685 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8359 (p0) REVERT: A 772 TYR cc_start: 0.8589 (t80) cc_final: 0.7914 (m-80) REVERT: M 73 ARG cc_start: 0.9154 (mmt-90) cc_final: 0.8928 (mtm180) REVERT: M 122 TYR cc_start: 0.8317 (t80) cc_final: 0.7685 (t80) REVERT: L 40 TYR cc_start: 0.7450 (m-80) cc_final: 0.7047 (m-80) REVERT: L 85 GLN cc_start: 0.9006 (mm110) cc_final: 0.8209 (pt0) outliers start: 30 outliers final: 27 residues processed: 110 average time/residue: 0.2686 time to fit residues: 43.6550 Evaluate side-chains 116 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 38 TYR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 71 optimal weight: 0.0020 chunk 52 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15063 Z= 0.317 Angle : 0.728 8.171 21642 Z= 0.367 Chirality : 0.040 0.266 2658 Planarity : 0.006 0.059 1784 Dihedral : 23.871 175.954 5378 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.53 % Allowed : 23.02 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.25), residues: 1071 helix: 0.30 (0.23), residues: 525 sheet: -1.90 (0.54), residues: 87 loop : -2.77 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 60 HIS 0.014 0.002 HIS A 412 PHE 0.026 0.002 PHE A 560 TYR 0.027 0.002 TYR A 168 ARG 0.014 0.001 ARG M 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 83 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.5471 (tpt170) cc_final: 0.4812 (mmm-85) REVERT: A 631 ARG cc_start: 0.8746 (ttp-170) cc_final: 0.8278 (ptp-110) REVERT: A 772 TYR cc_start: 0.8574 (t80) cc_final: 0.7890 (m-80) REVERT: A 774 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8781 (ptt-90) REVERT: M 73 ARG cc_start: 0.9071 (mmt-90) cc_final: 0.8849 (mtm180) REVERT: M 122 TYR cc_start: 0.8302 (t80) cc_final: 0.7690 (t80) REVERT: L 40 TYR cc_start: 0.7370 (m-80) cc_final: 0.7059 (m-80) REVERT: L 62 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8235 (pt0) REVERT: L 85 GLN cc_start: 0.9066 (mm110) cc_final: 0.8273 (pt0) outliers start: 33 outliers final: 29 residues processed: 107 average time/residue: 0.2877 time to fit residues: 44.5341 Evaluate side-chains 111 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 80 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 774 ARG Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 132 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 105 optimal weight: 0.0980 chunk 10 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 608 GLN ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15063 Z= 0.166 Angle : 0.622 10.467 21642 Z= 0.312 Chirality : 0.035 0.246 2658 Planarity : 0.005 0.061 1784 Dihedral : 23.725 176.217 5378 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.10 % Allowed : 23.88 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.26), residues: 1071 helix: 0.60 (0.23), residues: 538 sheet: -1.72 (0.55), residues: 87 loop : -2.65 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 60 HIS 0.009 0.001 HIS A 412 PHE 0.022 0.002 PHE A 560 TYR 0.027 0.001 TYR A 168 ARG 0.013 0.000 ARG M 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.5471 (tpt170) cc_final: 0.4829 (mmm-85) REVERT: A 372 MET cc_start: 0.4981 (ppp) cc_final: 0.4105 (mtt) REVERT: A 502 LYS cc_start: 0.8885 (mttp) cc_final: 0.8628 (ptmt) REVERT: A 631 ARG cc_start: 0.8675 (ttp-170) cc_final: 0.8176 (ptp-110) REVERT: A 685 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8371 (p0) REVERT: A 772 TYR cc_start: 0.8631 (t80) cc_final: 0.7951 (m-80) REVERT: M 73 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8870 (mtm180) REVERT: M 122 TYR cc_start: 0.8354 (t80) cc_final: 0.7973 (t80) REVERT: L 85 GLN cc_start: 0.8985 (mm110) cc_final: 0.8230 (pt0) outliers start: 29 outliers final: 26 residues processed: 110 average time/residue: 0.2835 time to fit residues: 45.0780 Evaluate side-chains 112 residues out of total 934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 15 optimal weight: 0.0060 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 108 optimal weight: 40.0000 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS ** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN A 925 HIS ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.114052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.078651 restraints weight = 50013.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.080612 restraints weight = 29468.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080680 restraints weight = 19733.881| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15063 Z= 0.157 Angle : 0.611 10.679 21642 Z= 0.305 Chirality : 0.034 0.232 2658 Planarity : 0.005 0.061 1784 Dihedral : 23.653 175.963 5378 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.89 % Allowed : 24.20 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.26), residues: 1071 helix: 0.92 (0.24), residues: 520 sheet: -1.70 (0.54), residues: 87 loop : -2.41 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 60 HIS 0.012 0.001 HIS A 609 PHE 0.018 0.001 PHE A 560 TYR 0.026 0.001 TYR A 168 ARG 0.008 0.000 ARG M 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2286.29 seconds wall clock time: 43 minutes 16.78 seconds (2596.78 seconds total)