Starting phenix.real_space_refine on Sat Jul 4 00:46:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qxb_14197/07_2026/7qxb_14197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qxb_14197/07_2026/7qxb_14197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qxb_14197/07_2026/7qxb_14197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qxb_14197/07_2026/7qxb_14197.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7qxb_14197/07_2026/7qxb_14197.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qxb_14197/07_2026/7qxb_14197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qxb_14197/07_2026/7qxb_14197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qxb_14197/07_2026/7qxb_14197.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 277 5.49 5 S 42 5.16 5 C 9714 2.51 5 N 3124 2.21 5 O 3896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17053 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7626 Classifications: {'peptide': 951} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 54, 'TRANS': 893} Chain breaks: 3 Chain: "B" Number of atoms: 5431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 5431 Classifications: {'RNA': 256} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 16, 'rna3p_pur': 99, 'rna3p_pyr': 124} Link IDs: {'rna2p': 33, 'rna3p': 222} Chain breaks: 3 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: "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: "N" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 461 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "O" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 955 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 3 Chain: "P" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1238 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PTRANS': 9, 'TRANS': 241} Chain breaks: 3 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 814 Unresolved non-hydrogen angles: 1054 Unresolved non-hydrogen dihedrals: 678 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'ASN:plan1': 11, 'TYR:plan': 13, 'GLN:plan1': 10, 'PHE:plan': 13, 'ASP:plan': 14, 'GLU:plan': 7, 'ARG:plan': 10, 'HIS:plan': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 420 Time building chain proxies: 3.19, per 1000 atoms: 0.19 Number of scatterers: 17053 At special positions: 0 Unit cell: (166.77, 128.62, 143.88, 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 42 16.00 P 277 15.00 O 3896 8.00 N 3124 7.00 C 9714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 982 " - pdb=" SG CYS A1043 " distance=2.57 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.73 Conformation dependent library (CDL) restraints added in 649.3 milliseconds 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2806 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 50.9% alpha, 19.5% beta 70 base pairs and 135 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.742A pdb=" N ARG A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.559A pdb=" N LEU A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.904A pdb=" N TRP A 387 " --> pdb=" O PRO A 383 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 390 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 445 through 454 removed outlier: 3.554A pdb=" N GLN A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.666A pdb=" N VAL A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.852A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.882A pdb=" N GLU A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 530 through 551 Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.786A pdb=" N LYS A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 653 through 672 removed outlier: 3.792A pdb=" N ARG A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.742A pdb=" N ILE A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 721 through 734 removed outlier: 3.529A pdb=" N LEU A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 802 through 815 Processing helix chain 'A' and resid 835 through 854 removed outlier: 3.719A pdb=" N THR A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU A 840 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 853 " --> pdb=" O MET A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 861 removed outlier: 4.271A pdb=" N ASP A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 890 Processing helix chain 'A' and resid 899 through 902 removed outlier: 3.699A pdb=" N LYS A 902 " --> pdb=" O ASN A 899 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 899 through 902' Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.521A pdb=" N ASN A 969 " --> pdb=" O LYS A 965 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 removed outlier: 3.704A pdb=" N LEU A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1018 removed outlier: 3.516A pdb=" N TYR A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1028 removed outlier: 3.504A pdb=" N LYS A1027 " --> pdb=" O GLN A1024 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A1028 " --> pdb=" O VAL A1025 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1024 through 1028' Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 4.271A pdb=" N CYS A1043 " --> pdb=" O THR A1039 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1085 removed outlier: 3.758A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.618A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.150A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1119 Processing helix chain 'A' and resid 1124 through 1129 removed outlier: 3.899A pdb=" N LYS A1128 " --> pdb=" O PRO A1124 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR A1129 " --> pdb=" O SER A1125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1124 through 1129' Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 27 through 38 removed outlier: 3.826A pdb=" N ARG L 32 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG L 33 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU L 35 " --> pdb=" O VAL L 31 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG L 36 " --> pdb=" O ARG L 32 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS L 37 " --> pdb=" O ARG L 33 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 73 removed outlier: 4.571A pdb=" N VAL L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL L 55 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR L 58 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU L 64 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA L 67 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP L 73 " --> pdb=" O ASN L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 90 removed outlier: 3.816A pdb=" N LEU L 84 " --> pdb=" O ILE L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.590A pdb=" N LEU L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 50 removed outlier: 3.843A pdb=" N TYR M 43 " --> pdb=" O SER M 39 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL M 45 " --> pdb=" O TYR M 41 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL M 49 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 86 removed outlier: 4.111A pdb=" N SER M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL M 67 " --> pdb=" O MET M 63 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN M 68 " --> pdb=" O ASN M 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE M 74 " --> pdb=" O ILE M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 103 removed outlier: 4.149A pdb=" N ILE M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN M 96 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR M 97 " --> pdb=" O ARG M 93 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL M 99 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU M 101 " --> pdb=" O THR M 97 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 124 removed outlier: 3.593A pdb=" N LYS M 109 " --> pdb=" O GLY M 105 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS M 121 " --> pdb=" O LYS M 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 104 Processing helix chain 'O' and resid 158 through 165 Processing helix chain 'O' and resid 169 through 173 Processing helix chain 'O' and resid 223 through 226 Processing helix chain 'O' and resid 227 through 238 Processing helix chain 'P' and resid 65 through 69 removed outlier: 3.525A pdb=" N LEU P 69 " --> pdb=" O TYR P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 156 Processing helix chain 'P' and resid 206 through 214 removed outlier: 3.529A pdb=" N GLN P 214 " --> pdb=" O ILE P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 217 No H-bonds generated for 'chain 'P' and resid 215 through 217' Processing helix chain 'P' and resid 225 through 232 removed outlier: 4.198A pdb=" N VAL P 229 " --> pdb=" O ASN P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 273 Processing helix chain 'P' and resid 282 through 299 removed outlier: 3.697A pdb=" N THR P 298 " --> pdb=" O SER P 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 4.110A pdb=" N ALA A 167 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU A 793 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 790 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU A 798 " --> pdb=" O TYR A 739 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR A 739 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA5, first strand: chain 'A' and resid 599 through 600 removed outlier: 7.101A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 633 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 624 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 629 " --> pdb=" O LYS A 626 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 863 through 865 Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 930 Processing sheet with id=AA8, first strand: chain 'L' and resid 43 through 44 removed outlier: 7.850A pdb=" N ARG L 43 " --> pdb=" O ILE M 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'O' and resid 113 through 122 removed outlier: 6.832A pdb=" N LEU O 145 " --> pdb=" O LEU O 118 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL O 120 " --> pdb=" O THR O 143 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR O 143 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL O 206 " --> pdb=" O CYS O 187 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS O 187 " --> pdb=" O VAL O 206 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG O 208 " --> pdb=" O GLN O 185 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU O 181 " --> pdb=" O LEU O 212 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG O 180 " --> pdb=" O LEU O 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 21 through 37 removed outlier: 6.728A pdb=" N THR P 48 " --> pdb=" O LYS P 30 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE P 32 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL P 46 " --> pdb=" O PHE P 32 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS P 44 " --> pdb=" O PRO P 34 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N THR P 93 " --> pdb=" O LYS P 56 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR P 58 " --> pdb=" O THR P 93 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE P 62 " --> pdb=" O THR P 97 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N SER P 99 " --> pdb=" O PHE P 62 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG P 83 " --> pdb=" O SER P 98 " (cutoff:3.500A) removed outlier: 11.364A pdb=" N GLY P 100 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N PHE P 81 " --> pdb=" O GLY P 100 " (cutoff:3.500A) removed outlier: 11.031A pdb=" N ALA P 102 " --> pdb=" O VAL P 79 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N VAL P 79 " --> pdb=" O ALA P 102 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE P 78 " --> pdb=" O VAL P 29 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL P 29 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG P 80 " --> pdb=" O GLY P 27 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLY P 27 " --> pdb=" O ARG P 80 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N HIS P 82 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL P 25 " --> pdb=" O HIS P 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 204 through 205 removed outlier: 6.580A pdb=" N LYS P 182 " --> pdb=" O LEU P 169 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS P 171 " --> pdb=" O LEU P 180 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU P 180 " --> pdb=" O LYS P 171 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU P 173 " --> pdb=" O SER P 178 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N SER P 178 " --> pdb=" O GLU P 173 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE P 263 " --> pdb=" O ASP P 219 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE P 238 " --> pdb=" O LEU P 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 204 through 205 removed outlier: 5.081A pdb=" N PHE P 162 " --> pdb=" O SER P 243 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE P 238 " --> pdb=" O LEU P 278 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 186 hydrogen bonds 352 hydrogen bond angles 0 basepair planarities 70 basepair parallelities 135 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3290 1.33 - 1.46: 5953 1.46 - 1.59: 8201 1.59 - 1.73: 445 1.73 - 1.86: 55 Bond restraints: 17944 Sorted by residual: bond pdb=" N SER A 586 " pdb=" CA SER A 586 " ideal model delta sigma weight residual 1.459 1.529 -0.070 1.20e-02 6.94e+03 3.38e+01 bond pdb=" CE1 TYR A 638 " pdb=" CZ TYR A 638 " ideal model delta sigma weight residual 1.378 1.501 -0.123 2.40e-02 1.74e+03 2.64e+01 bond pdb=" N PHE A 544 " pdb=" CA PHE A 544 " ideal model delta sigma weight residual 1.459 1.402 0.057 1.17e-02 7.31e+03 2.40e+01 bond pdb=" CA VAL A1087 " pdb=" CB VAL A1087 " ideal model delta sigma weight residual 1.540 1.606 -0.066 1.36e-02 5.41e+03 2.38e+01 bond pdb=" N LEU A1082 " pdb=" CA LEU A1082 " ideal model delta sigma weight residual 1.458 1.518 -0.060 1.30e-02 5.92e+03 2.13e+01 ... (remaining 17939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 24342 2.98 - 5.97: 1207 5.97 - 8.95: 99 8.95 - 11.93: 8 11.93 - 14.91: 3 Bond angle restraints: 25659 Sorted by residual: angle pdb=" O3' C B 142 " pdb=" C3' C B 142 " pdb=" C2' C B 142 " ideal model delta sigma weight residual 113.70 128.61 -14.91 1.50e+00 4.44e-01 9.88e+01 angle pdb=" C4' G B 300 " pdb=" C3' G B 300 " pdb=" O3' G B 300 " ideal model delta sigma weight residual 109.40 122.48 -13.08 1.50e+00 4.44e-01 7.60e+01 angle pdb=" N ARG A1084 " pdb=" CA ARG A1084 " pdb=" C ARG A1084 " ideal model delta sigma weight residual 111.14 119.63 -8.49 1.08e+00 8.57e-01 6.17e+01 angle pdb=" C4' C B 321 " pdb=" C3' C B 321 " pdb=" O3' C B 321 " ideal model delta sigma weight residual 113.00 124.45 -11.45 1.50e+00 4.44e-01 5.83e+01 angle pdb=" N ASP A 516 " pdb=" CA ASP A 516 " pdb=" C ASP A 516 " ideal model delta sigma weight residual 111.82 120.52 -8.70 1.16e+00 7.43e-01 5.62e+01 ... (remaining 25654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.39: 9752 34.39 - 68.78: 343 68.78 - 103.17: 37 103.17 - 137.56: 9 137.56 - 171.95: 14 Dihedral angle restraints: 10155 sinusoidal: 5831 harmonic: 4324 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 71.59 75.41 1 8.00e+00 1.56e-02 1.12e+02 dihedral pdb=" O4' U B 194 " pdb=" C1' U B 194 " pdb=" N1 U B 194 " pdb=" C2 U B 194 " ideal model delta sinusoidal sigma weight residual 200.00 28.05 171.95 1 1.50e+01 4.44e-03 8.49e+01 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 200.00 40.96 159.04 1 1.50e+01 4.44e-03 8.25e+01 ... (remaining 10152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2527 0.118 - 0.236: 557 0.236 - 0.354: 54 0.354 - 0.472: 10 0.472 - 0.590: 5 Chirality restraints: 3153 Sorted by residual: 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 -2.15 -0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" C3' C B 142 " pdb=" C4' C B 142 " pdb=" O3' C B 142 " pdb=" C2' C B 142 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" C3' G B 292 " pdb=" C4' G B 292 " pdb=" O3' G B 292 " pdb=" C2' G B 292 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 3150 not shown) Planarity restraints: 2272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 75 " -0.220 2.00e-02 2.50e+03 1.00e-01 2.25e+02 pdb=" N1 C B 75 " 0.114 2.00e-02 2.50e+03 pdb=" C2 C B 75 " 0.058 2.00e-02 2.50e+03 pdb=" O2 C B 75 " 0.055 2.00e-02 2.50e+03 pdb=" N3 C B 75 " -0.012 2.00e-02 2.50e+03 pdb=" C4 C B 75 " -0.057 2.00e-02 2.50e+03 pdb=" N4 C B 75 " -0.081 2.00e-02 2.50e+03 pdb=" C5 C B 75 " 0.037 2.00e-02 2.50e+03 pdb=" C6 C B 75 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 292 " 0.196 2.00e-02 2.50e+03 8.08e-02 1.96e+02 pdb=" N9 G B 292 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G B 292 " -0.079 2.00e-02 2.50e+03 pdb=" N7 G B 292 " -0.076 2.00e-02 2.50e+03 pdb=" C5 G B 292 " -0.035 2.00e-02 2.50e+03 pdb=" C6 G B 292 " 0.046 2.00e-02 2.50e+03 pdb=" O6 G B 292 " 0.112 2.00e-02 2.50e+03 pdb=" N1 G B 292 " 0.036 2.00e-02 2.50e+03 pdb=" C2 G B 292 " -0.033 2.00e-02 2.50e+03 pdb=" N2 G B 292 " -0.020 2.00e-02 2.50e+03 pdb=" N3 G B 292 " -0.069 2.00e-02 2.50e+03 pdb=" C4 G B 292 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 27 " 0.193 2.00e-02 2.50e+03 7.96e-02 1.74e+02 pdb=" N9 DA N 27 " -0.041 2.00e-02 2.50e+03 pdb=" C8 DA N 27 " -0.067 2.00e-02 2.50e+03 pdb=" N7 DA N 27 " -0.051 2.00e-02 2.50e+03 pdb=" C5 DA N 27 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DA N 27 " 0.044 2.00e-02 2.50e+03 pdb=" N6 DA N 27 " 0.095 2.00e-02 2.50e+03 pdb=" N1 DA N 27 " 0.028 2.00e-02 2.50e+03 pdb=" C2 DA N 27 " -0.037 2.00e-02 2.50e+03 pdb=" N3 DA N 27 " -0.080 2.00e-02 2.50e+03 pdb=" C4 DA N 27 " -0.061 2.00e-02 2.50e+03 ... (remaining 2269 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1283 2.74 - 3.28: 16577 3.28 - 3.82: 28842 3.82 - 4.36: 35195 4.36 - 4.90: 52349 Nonbonded interactions: 134246 Sorted by model distance: nonbonded pdb=" OE1 GLN A 943 " pdb=" NZ LYS A1003 " model vdw 2.203 3.120 nonbonded pdb=" NZ LYS A1027 " pdb=" OP1 U B 312 " model vdw 2.209 3.120 nonbonded pdb=" OP2 C B 244 " pdb=" NH2 ARG L 43 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG A 481 " pdb=" OP2 C B 183 " model vdw 2.269 3.120 nonbonded pdb=" O TRP A 510 " pdb=" O2' C B 313 " model vdw 2.314 3.040 ... (remaining 134241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.620 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.210 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 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 0.535 17945 Z= 0.710 Angle : 1.486 36.960 25661 Z= 1.004 Chirality : 0.096 0.590 3153 Planarity : 0.011 0.118 2272 Dihedral : 17.710 171.949 7346 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.64 % Favored : 95.02 % Rotamer: Outliers : 0.47 % Allowed : 4.01 % Favored : 95.52 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.19), residues: 1466 helix: -0.97 (0.18), residues: 591 sheet: -1.19 (0.34), residues: 188 loop : -1.71 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 175 TYR 0.068 0.009 TYR A 949 PHE 0.063 0.006 PHE A 331 TRP 0.052 0.009 TRP A 510 HIS 0.014 0.004 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00987 / 0.68 (17944) covalent geometry : angle 1.46004 / 1.00 (25659) SS BOND : bond 0.53508 / 28.16 ( 1) SS BOND : angle 31.45145 / 17.92 ( 2) hydrogen bonds : bond 0.21906 / 15.01 ( 746) hydrogen bonds : angle 8.13514 / 5.91 ( 1948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 224 time to evaluate : 0.516 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: A 99 PHE cc_start: 0.8758 (m-10) cc_final: 0.8285 (m-80) REVERT: A 333 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.8768 (m-80) REVERT: A 536 LEU cc_start: 0.9115 (tp) cc_final: 0.8895 (tt) REVERT: A 656 SER cc_start: 0.8454 (t) cc_final: 0.7973 (m) REVERT: A 850 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8152 (mt-10) REVERT: A 899 ASN cc_start: 0.8334 (t0) cc_final: 0.8084 (t0) REVERT: A 902 LYS cc_start: 0.8765 (mttt) cc_final: 0.8536 (tptt) REVERT: L 89 ARG cc_start: 0.6555 (mmt-90) cc_final: 0.6194 (ptm-80) REVERT: M 49 VAL cc_start: 0.7324 (m) cc_final: 0.7120 (m) REVERT: M 117 LYS cc_start: 0.7704 (mttt) cc_final: 0.7326 (tppt) REVERT: O 103 ILE cc_start: 0.7819 (mm) cc_final: 0.7475 (mm) outliers start: 5 outliers final: 1 residues processed: 227 average time/residue: 0.1774 time to fit residues: 55.7268 Evaluate side-chains 127 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 1074 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN A 330 HIS A 388 GLN A 482 HIS A 585 GLN A 700 GLN A 969 ASN A1013 HIS M 50 HIS M 64 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.102803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.074316 restraints weight = 88021.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.076314 restraints weight = 42915.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.077315 restraints weight = 28308.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.078090 restraints weight = 23187.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.078441 restraints weight = 20594.103| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17945 Z= 0.211 Angle : 0.866 10.030 25661 Z= 0.456 Chirality : 0.048 0.397 3153 Planarity : 0.007 0.100 2272 Dihedral : 18.435 178.357 4937 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.61 % Allowed : 11.20 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.21), residues: 1466 helix: 0.68 (0.20), residues: 601 sheet: -0.79 (0.36), residues: 186 loop : -1.19 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 220 TYR 0.021 0.002 TYR A1002 PHE 0.027 0.002 PHE A 331 TRP 0.026 0.002 TRP A 547 HIS 0.006 0.001 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 (17944) covalent geometry : angle 0.86572 / 0.46 (25659) SS BOND : bond 0.00129 / 0.07 ( 1) SS BOND : angle 3.49492 / 2.04 ( 2) hydrogen bonds : bond 0.06742 / 4.59 ( 746) hydrogen bonds : angle 5.09932 / 3.72 ( 1948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.511 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: A 72 ARG cc_start: 0.7512 (mpt180) cc_final: 0.7293 (mmt180) REVERT: A 372 MET cc_start: -0.1542 (mmt) cc_final: -0.1763 (mmt) REVERT: A 605 GLU cc_start: 0.8828 (mp0) cc_final: 0.8568 (mp0) REVERT: A 718 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7982 (p0) REVERT: A 809 PHE cc_start: 0.8732 (t80) cc_final: 0.8490 (t80) REVERT: A 902 LYS cc_start: 0.8604 (mttt) cc_final: 0.8383 (tptt) REVERT: A 903 THR cc_start: 0.8906 (m) cc_final: 0.8595 (p) REVERT: A 930 TRP cc_start: 0.7808 (t60) cc_final: 0.7456 (t60) REVERT: M 52 ASP cc_start: 0.8575 (t0) cc_final: 0.8079 (p0) REVERT: M 69 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.8011 (p0) REVERT: M 117 LYS cc_start: 0.7308 (mttt) cc_final: 0.6999 (tppt) REVERT: O 103 ILE cc_start: 0.7917 (mm) cc_final: 0.7680 (mt) outliers start: 28 outliers final: 12 residues processed: 152 average time/residue: 0.1369 time to fit residues: 31.2428 Evaluate side-chains 115 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 183 LEU Chi-restraints excluded: chain O residue 238 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 152 optimal weight: 50.0000 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN O 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.100175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.072144 restraints weight = 89578.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.073873 restraints weight = 45899.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.074886 restraints weight = 31585.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.075481 restraints weight = 25950.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.075713 restraints weight = 23588.777| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 17945 Z= 0.231 Angle : 0.807 10.354 25661 Z= 0.422 Chirality : 0.046 0.301 3153 Planarity : 0.006 0.122 2272 Dihedral : 18.138 171.353 4935 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.16 % Favored : 95.77 % Rotamer: Outliers : 3.73 % Allowed : 13.45 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1466 helix: 0.78 (0.20), residues: 613 sheet: -0.69 (0.36), residues: 198 loop : -1.07 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 30 TYR 0.023 0.003 TYR A 462 PHE 0.026 0.003 PHE A 575 TRP 0.023 0.002 TRP A 547 HIS 0.006 0.002 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (17944) covalent geometry : angle 0.80667 / 0.42 (25659) SS BOND : bond 0.01229 / 0.65 ( 1) SS BOND : angle 4.10833 / 2.38 ( 2) hydrogen bonds : bond 0.06073 / 4.15 ( 746) hydrogen bonds : angle 4.88024 / 3.57 ( 1948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.607 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: A 55 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 123 LEU cc_start: 0.8210 (mt) cc_final: 0.7953 (pp) REVERT: A 366 LEU cc_start: 0.6866 (mt) cc_final: 0.6583 (mp) REVERT: A 412 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.6787 (m170) REVERT: L 85 GLN cc_start: 0.7505 (mm110) cc_final: 0.7179 (pp30) REVERT: M 52 ASP cc_start: 0.8615 (t0) cc_final: 0.8216 (p0) REVERT: O 231 GLN cc_start: 0.9069 (mt0) cc_final: 0.8609 (mp10) outliers start: 40 outliers final: 23 residues processed: 141 average time/residue: 0.1332 time to fit residues: 28.7199 Evaluate side-chains 115 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain O residue 155 CYS Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 238 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 74 optimal weight: 0.0870 chunk 91 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 chunk 169 optimal weight: 50.0000 chunk 103 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 GLN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN M 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.100149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.072118 restraints weight = 88678.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.073802 restraints weight = 45950.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.074810 restraints weight = 31843.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.075229 restraints weight = 26281.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.075603 restraints weight = 24140.488| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17945 Z= 0.203 Angle : 0.747 10.528 25661 Z= 0.387 Chirality : 0.043 0.290 3153 Planarity : 0.005 0.050 2272 Dihedral : 18.142 176.900 4935 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.82 % Favored : 96.11 % Rotamer: Outliers : 3.55 % Allowed : 15.50 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1466 helix: 0.97 (0.21), residues: 614 sheet: -0.60 (0.37), residues: 189 loop : -1.14 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 865 TYR 0.016 0.002 TYR A 462 PHE 0.025 0.002 PHE A 809 TRP 0.022 0.002 TRP A 581 HIS 0.005 0.002 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (17944) covalent geometry : angle 0.74654 / 0.39 (25659) SS BOND : bond 0.00568 / 0.30 ( 1) SS BOND : angle 2.41642 / 1.42 ( 2) hydrogen bonds : bond 0.05433 / 3.65 ( 746) hydrogen bonds : angle 4.70272 / 3.45 ( 1948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.505 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: A 123 LEU cc_start: 0.8251 (mt) cc_final: 0.8006 (pp) REVERT: A 176 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.7215 (t80) REVERT: L 52 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8068 (mt) REVERT: M 52 ASP cc_start: 0.8645 (t0) cc_final: 0.8234 (p0) REVERT: O 231 GLN cc_start: 0.8858 (mt0) cc_final: 0.8640 (mt0) outliers start: 38 outliers final: 26 residues processed: 126 average time/residue: 0.1222 time to fit residues: 23.1598 Evaluate side-chains 115 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 183 LEU Chi-restraints excluded: chain O residue 208 ARG Chi-restraints excluded: chain O residue 238 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 27 optimal weight: 0.4980 chunk 105 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 GLN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.103519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.075572 restraints weight = 87537.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.077389 restraints weight = 44074.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.078293 restraints weight = 29992.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.079043 restraints weight = 24850.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.079286 restraints weight = 22330.421| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17945 Z= 0.130 Angle : 0.655 9.830 25661 Z= 0.338 Chirality : 0.040 0.274 3153 Planarity : 0.005 0.052 2272 Dihedral : 17.922 179.371 4935 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 2.52 % Allowed : 16.71 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.22), residues: 1466 helix: 1.34 (0.21), residues: 620 sheet: -0.27 (0.37), residues: 194 loop : -0.95 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 979 TYR 0.026 0.002 TYR O 235 PHE 0.021 0.002 PHE M 71 TRP 0.019 0.001 TRP A 581 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (17944) covalent geometry : angle 0.65487 / 0.34 (25659) SS BOND : bond 0.00802 / 0.42 ( 1) SS BOND : angle 1.56107 / 0.89 ( 2) hydrogen bonds : bond 0.04391 / 3.00 ( 746) hydrogen bonds : angle 4.25897 / 3.13 ( 1948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.401 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: A 176 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.6859 (t80) REVERT: A 903 THR cc_start: 0.9080 (m) cc_final: 0.8789 (p) REVERT: A 930 TRP cc_start: 0.7600 (t60) cc_final: 0.7130 (t60) REVERT: A 970 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7050 (ptm) REVERT: L 75 LYS cc_start: 0.7105 (tppt) cc_final: 0.6634 (tptt) REVERT: M 52 ASP cc_start: 0.8665 (t0) cc_final: 0.8353 (p0) REVERT: M 64 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6670 (m110) outliers start: 27 outliers final: 14 residues processed: 132 average time/residue: 0.1252 time to fit residues: 25.1163 Evaluate side-chains 109 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 970 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 71 PHE Chi-restraints excluded: chain O residue 183 LEU Chi-restraints excluded: chain O residue 208 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.098829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.070821 restraints weight = 91938.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.072481 restraints weight = 47753.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.073471 restraints weight = 33211.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.073947 restraints weight = 27500.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.074281 restraints weight = 25129.120| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 17945 Z= 0.253 Angle : 0.787 10.521 25661 Z= 0.404 Chirality : 0.043 0.261 3153 Planarity : 0.006 0.047 2272 Dihedral : 18.018 174.104 4935 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 3.36 % Allowed : 17.83 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1466 helix: 0.79 (0.20), residues: 621 sheet: -0.58 (0.36), residues: 201 loop : -1.22 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 390 TYR 0.025 0.003 TYR A 462 PHE 0.029 0.003 PHE A 809 TRP 0.043 0.003 TRP A 387 HIS 0.009 0.002 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.25 (17944) covalent geometry : angle 0.78719 / 0.40 (25659) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 2.54494 / 1.49 ( 2) hydrogen bonds : bond 0.06002 / 4.08 ( 746) hydrogen bonds : angle 4.61066 / 3.38 ( 1948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6790 (t80) REVERT: A 362 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7489 (mt-10) REVERT: A 412 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6786 (m-70) REVERT: A 462 TYR cc_start: 0.8540 (t80) cc_final: 0.8318 (t80) REVERT: L 52 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8034 (mt) REVERT: L 75 LYS cc_start: 0.7168 (tppt) cc_final: 0.6726 (tptt) REVERT: M 52 ASP cc_start: 0.8717 (t0) cc_final: 0.8405 (p0) REVERT: M 64 ASN cc_start: 0.7216 (OUTLIER) cc_final: 0.6871 (m110) outliers start: 36 outliers final: 27 residues processed: 120 average time/residue: 0.1198 time to fit residues: 21.9025 Evaluate side-chains 117 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 208 ARG Chi-restraints excluded: chain O residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 116 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 82 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.099763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.071707 restraints weight = 91147.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.073398 restraints weight = 46805.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.074434 restraints weight = 32356.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.074999 restraints weight = 26685.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.075215 restraints weight = 24248.793| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17945 Z= 0.183 Angle : 0.689 10.987 25661 Z= 0.356 Chirality : 0.041 0.253 3153 Planarity : 0.005 0.064 2272 Dihedral : 18.034 170.234 4935 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.16 % Favored : 95.77 % Rotamer: Outliers : 3.83 % Allowed : 18.30 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1466 helix: 0.96 (0.21), residues: 622 sheet: -0.60 (0.36), residues: 200 loop : -1.16 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 865 TYR 0.027 0.002 TYR A 462 PHE 0.020 0.002 PHE M 71 TRP 0.018 0.002 TRP A 581 HIS 0.005 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (17944) covalent geometry : angle 0.68910 / 0.36 (25659) SS BOND : bond 0.00403 / 0.21 ( 1) SS BOND : angle 1.99213 / 1.16 ( 2) hydrogen bonds : bond 0.04938 / 3.36 ( 746) hydrogen bonds : angle 4.46218 / 3.25 ( 1948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 0.531 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: A 176 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6743 (t80) REVERT: A 362 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 390 ARG cc_start: 0.4853 (OUTLIER) cc_final: 0.4170 (ptt180) REVERT: A 412 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6798 (m-70) REVERT: A 459 TRP cc_start: 0.6999 (OUTLIER) cc_final: 0.6249 (t60) REVERT: A 462 TYR cc_start: 0.8540 (t80) cc_final: 0.8297 (t80) REVERT: L 52 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8029 (mt) REVERT: L 75 LYS cc_start: 0.7230 (tppt) cc_final: 0.6731 (tptt) REVERT: M 52 ASP cc_start: 0.8751 (t0) cc_final: 0.8434 (p0) REVERT: M 64 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6868 (m110) outliers start: 41 outliers final: 27 residues processed: 126 average time/residue: 0.1323 time to fit residues: 25.2905 Evaluate side-chains 122 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 208 ARG Chi-restraints excluded: chain O residue 235 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 107 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 156 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 30.0000 chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.096571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.068559 restraints weight = 92905.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.070048 restraints weight = 50414.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.070917 restraints weight = 36124.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.071432 restraints weight = 30550.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.071649 restraints weight = 27918.389| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 17945 Z= 0.308 Angle : 0.848 10.738 25661 Z= 0.435 Chirality : 0.047 0.502 3153 Planarity : 0.006 0.054 2272 Dihedral : 18.354 171.936 4935 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 4.30 % Allowed : 18.21 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.21), residues: 1466 helix: 0.11 (0.20), residues: 628 sheet: -0.84 (0.36), residues: 199 loop : -1.48 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 390 TYR 0.025 0.003 TYR A 462 PHE 0.038 0.003 PHE A 809 TRP 0.024 0.003 TRP A 387 HIS 0.011 0.003 HIS L 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.31 (17944) covalent geometry : angle 0.84757 / 0.43 (25659) SS BOND : bond 0.00389 / 0.20 ( 1) SS BOND : angle 3.02123 / 1.77 ( 2) hydrogen bonds : bond 0.06765 / 4.64 ( 746) hydrogen bonds : angle 4.98879 / 3.63 ( 1948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 91 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6944 (t80) REVERT: A 362 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 459 TRP cc_start: 0.7323 (OUTLIER) cc_final: 0.6542 (t60) REVERT: A 462 TYR cc_start: 0.8711 (t80) cc_final: 0.8341 (t80) REVERT: A 507 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6782 (mt-10) REVERT: L 25 GLN cc_start: 0.5779 (OUTLIER) cc_final: 0.5559 (tt0) REVERT: L 52 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8079 (mt) REVERT: L 75 LYS cc_start: 0.7186 (tppt) cc_final: 0.6917 (tmtt) REVERT: M 52 ASP cc_start: 0.8834 (t0) cc_final: 0.8462 (p0) REVERT: M 64 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.7075 (m110) REVERT: M 122 TYR cc_start: 0.9022 (t80) cc_final: 0.8617 (t80) outliers start: 46 outliers final: 36 residues processed: 130 average time/residue: 0.1171 time to fit residues: 23.3086 Evaluate side-chains 127 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain O residue 155 CYS Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 208 ARG Chi-restraints excluded: chain O residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 149 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 156 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 HIS ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.100176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.072136 restraints weight = 91174.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.073906 restraints weight = 46576.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.074962 restraints weight = 31802.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.075401 restraints weight = 26090.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.075785 restraints weight = 23881.849| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17945 Z= 0.142 Angle : 0.687 11.376 25661 Z= 0.351 Chirality : 0.040 0.243 3153 Planarity : 0.005 0.059 2272 Dihedral : 18.208 169.135 4935 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 2.61 % Allowed : 20.17 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.22), residues: 1466 helix: 0.95 (0.21), residues: 626 sheet: -0.52 (0.36), residues: 203 loop : -1.24 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 72 TYR 0.034 0.002 TYR A 894 PHE 0.023 0.002 PHE A 809 TRP 0.021 0.002 TRP A 581 HIS 0.010 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (17944) covalent geometry : angle 0.68684 / 0.35 (25659) SS BOND : bond 0.01156 / 0.61 ( 1) SS BOND : angle 2.30588 / 1.35 ( 2) hydrogen bonds : bond 0.04767 / 3.30 ( 746) hydrogen bonds : angle 4.41588 / 3.20 ( 1948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.6506 (t80) REVERT: A 362 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7856 (mt-10) REVERT: A 462 TYR cc_start: 0.8430 (t80) cc_final: 0.8213 (t80) REVERT: L 52 LEU cc_start: 0.8456 (tp) cc_final: 0.8049 (mt) REVERT: L 75 LYS cc_start: 0.7236 (tppt) cc_final: 0.6915 (tmtt) REVERT: M 64 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.7100 (m110) outliers start: 28 outliers final: 21 residues processed: 117 average time/residue: 0.1307 time to fit residues: 23.2259 Evaluate side-chains 113 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 208 ARG Chi-restraints excluded: chain O residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 124 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 152 optimal weight: 50.0000 chunk 166 optimal weight: 50.0000 chunk 44 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.100947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.074248 restraints weight = 90175.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.076604 restraints weight = 53146.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.076170 restraints weight = 31903.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.076383 restraints weight = 29309.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.076518 restraints weight = 26719.004| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17945 Z= 0.131 Angle : 0.655 10.709 25661 Z= 0.335 Chirality : 0.039 0.234 3153 Planarity : 0.005 0.056 2272 Dihedral : 18.032 168.788 4935 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.82 % Favored : 96.11 % Rotamer: Outliers : 2.15 % Allowed : 21.01 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1466 helix: 1.32 (0.21), residues: 610 sheet: -0.38 (0.36), residues: 204 loop : -1.02 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 390 TYR 0.034 0.002 TYR A 894 PHE 0.020 0.001 PHE M 71 TRP 0.020 0.002 TRP A 581 HIS 0.006 0.001 HIS L 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (17944) covalent geometry : angle 0.65505 / 0.33 (25659) SS BOND : bond 0.00910 / 0.48 ( 1) SS BOND : angle 2.28565 / 1.29 ( 2) hydrogen bonds : bond 0.04223 / 2.87 ( 746) hydrogen bonds : angle 4.20771 / 3.06 ( 1948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.417 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: A 176 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.6252 (t80) REVERT: A 362 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 462 TYR cc_start: 0.8411 (t80) cc_final: 0.8202 (t80) REVERT: A 512 MET cc_start: 0.7288 (mtp) cc_final: 0.7076 (mtt) REVERT: A 903 THR cc_start: 0.9137 (m) cc_final: 0.8813 (p) REVERT: L 52 LEU cc_start: 0.8438 (tp) cc_final: 0.8014 (mt) outliers start: 23 outliers final: 21 residues processed: 109 average time/residue: 0.1283 time to fit residues: 21.5007 Evaluate side-chains 109 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TYR Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1074 CYS Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain L residue 25 GLN Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 174 PHE Chi-restraints excluded: chain O residue 208 ARG Chi-restraints excluded: chain O residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 133 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 96 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 174 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.100677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.072839 restraints weight = 91477.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.074580 restraints weight = 47242.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.075612 restraints weight = 32641.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.076191 restraints weight = 26994.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.076409 restraints weight = 24492.739| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17945 Z= 0.135 Angle : 0.642 10.772 25661 Z= 0.326 Chirality : 0.039 0.262 3153 Planarity : 0.004 0.050 2272 Dihedral : 17.988 169.483 4935 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 2.43 % Allowed : 21.01 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.22), residues: 1466 helix: 1.37 (0.21), residues: 613 sheet: -0.31 (0.36), residues: 204 loop : -0.93 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 390 TYR 0.023 0.002 TYR A 462 PHE 0.021 0.002 PHE M 71 TRP 0.019 0.002 TRP A 581 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (17944) covalent geometry : angle 0.64171 / 0.33 (25659) SS BOND : bond 0.00779 / 0.41 ( 1) SS BOND : angle 2.10104 / 1.20 ( 2) hydrogen bonds : bond 0.04205 / 2.83 ( 746) hydrogen bonds : angle 4.17663 / 3.05 ( 1948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3958.56 seconds wall clock time: 68 minutes 28.93 seconds (4108.93 seconds total)