Starting phenix.real_space_refine on Mon Apr 6 13:39:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wsq_66203/04_2026/9wsq_66203.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wsq_66203/04_2026/9wsq_66203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wsq_66203/04_2026/9wsq_66203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wsq_66203/04_2026/9wsq_66203.map" model { file = "/net/cci-nas-00/data/ceres_data/9wsq_66203/04_2026/9wsq_66203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wsq_66203/04_2026/9wsq_66203.cif" } resolution = 3.35 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= 0.003 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 159 5.16 5 C 11866 2.51 5 N 3276 2.21 5 O 3504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18805 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2184 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 263} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1274 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 152} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 5942 Classifications: {'peptide': 756} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 18, 'TRANS': 737} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'GLU:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "E" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2187 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain: "F" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1274 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 152} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 5944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 5944 Classifications: {'peptide': 756} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 737} Chain breaks: 2 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'GLU:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Time building chain proxies: 4.14, per 1000 atoms: 0.22 Number of scatterers: 18805 At special positions: 0 Unit cell: (133.45, 126.65, 163.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 159 16.00 O 3504 8.00 N 3276 7.00 C 11866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.58 Conformation dependent library (CDL) restraints added in 843.9 milliseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 12 sheets defined 53.4% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 890 through 902 removed outlier: 4.281A pdb=" N ARG B 894 " --> pdb=" O SER B 890 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 895 " --> pdb=" O TRP B 891 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 902 " --> pdb=" O MET B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 913 Processing helix chain 'B' and resid 916 through 924 removed outlier: 3.779A pdb=" N CYS B 924 " --> pdb=" O TYR B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 952 Processing helix chain 'B' and resid 964 through 973 Processing helix chain 'B' and resid 987 through 992 Processing helix chain 'B' and resid 993 through 996 removed outlier: 4.067A pdb=" N THR B 996 " --> pdb=" O ALA B 993 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 993 through 996' Processing helix chain 'B' and resid 1014 through 1023 Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 4.124A pdb=" N LEU B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B1056 " --> pdb=" O ASP B1052 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B1057 " --> pdb=" O ALA B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1085 removed outlier: 4.091A pdb=" N SER B1081 " --> pdb=" O THR B1077 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B1085 " --> pdb=" O SER B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1095 removed outlier: 3.578A pdb=" N SER B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1114 Processing helix chain 'B' and resid 1115 through 1117 No H-bonds generated for 'chain 'B' and resid 1115 through 1117' Processing helix chain 'B' and resid 1132 through 1144 removed outlier: 3.567A pdb=" N CYS B1136 " --> pdb=" O THR B1132 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.506A pdb=" N GLU C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.613A pdb=" N GLU C 79 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 75 through 80' Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 96 through 110 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.582A pdb=" N MET C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 157 through 163 removed outlier: 3.702A pdb=" N GLU C 161 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU C 162 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS C 163 " --> pdb=" O TRP C 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 163' Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 262 through 268 Processing helix chain 'A' and resid 271 through 289 removed outlier: 3.565A pdb=" N CYS A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.567A pdb=" N LEU A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 341 Processing helix chain 'A' and resid 347 through 353 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 383 through 398 removed outlier: 3.879A pdb=" N TYR A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.714A pdb=" N LEU A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 475 through 491 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.814A pdb=" N LYS A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 removed outlier: 3.757A pdb=" N GLU A 554 " --> pdb=" O MET A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 removed outlier: 4.254A pdb=" N GLN A 559 " --> pdb=" O GLY A 555 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 572 removed outlier: 3.561A pdb=" N HIS A 572 " --> pdb=" O SER A 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 569 through 572' Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 643 through 656 removed outlier: 3.776A pdb=" N CYS A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 684 Processing helix chain 'A' and resid 700 through 712 removed outlier: 3.680A pdb=" N VAL A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'A' and resid 732 through 743 Processing helix chain 'A' and resid 757 through 769 removed outlier: 3.756A pdb=" N HIS A 766 " --> pdb=" O LYS A 762 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 768 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 797 Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 814 through 826 removed outlier: 3.524A pdb=" N VAL A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 820 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'A' and resid 846 through 857 removed outlier: 3.603A pdb=" N LEU A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 883 removed outlier: 3.557A pdb=" N ASP A 880 " --> pdb=" O ASN A 876 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 881 " --> pdb=" O ILE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 903 through 914 removed outlier: 3.561A pdb=" N GLY A 909 " --> pdb=" O GLN A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 940 Processing helix chain 'A' and resid 952 through 957 Processing helix chain 'A' and resid 958 through 972 removed outlier: 3.952A pdb=" N LYS A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE A 964 " --> pdb=" O LYS A 960 " (cutoff:3.500A) Processing helix chain 'E' and resid 890 through 902 removed outlier: 4.280A pdb=" N ARG E 894 " --> pdb=" O SER E 890 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU E 895 " --> pdb=" O TRP E 891 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG E 902 " --> pdb=" O MET E 898 " (cutoff:3.500A) Processing helix chain 'E' and resid 905 through 913 Processing helix chain 'E' and resid 916 through 924 removed outlier: 3.778A pdb=" N CYS E 924 " --> pdb=" O TYR E 920 " (cutoff:3.500A) Processing helix chain 'E' and resid 941 through 952 Processing helix chain 'E' and resid 964 through 973 Processing helix chain 'E' and resid 987 through 992 Processing helix chain 'E' and resid 993 through 996 removed outlier: 4.068A pdb=" N THR E 996 " --> pdb=" O ALA E 993 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 993 through 996' Processing helix chain 'E' and resid 1014 through 1023 Processing helix chain 'E' and resid 1051 through 1062 removed outlier: 4.124A pdb=" N LEU E1055 " --> pdb=" O THR E1051 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG E1056 " --> pdb=" O ASP E1052 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU E1057 " --> pdb=" O ALA E1053 " (cutoff:3.500A) Processing helix chain 'E' and resid 1077 through 1085 removed outlier: 4.091A pdb=" N SER E1081 " --> pdb=" O THR E1077 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR E1085 " --> pdb=" O SER E1081 " (cutoff:3.500A) Processing helix chain 'E' and resid 1090 through 1095 removed outlier: 3.578A pdb=" N SER E1094 " --> pdb=" O SER E1090 " (cutoff:3.500A) Processing helix chain 'E' and resid 1109 through 1114 Processing helix chain 'E' and resid 1115 through 1117 No H-bonds generated for 'chain 'E' and resid 1115 through 1117' Processing helix chain 'E' and resid 1132 through 1144 removed outlier: 3.567A pdb=" N CYS E1136 " --> pdb=" O THR E1132 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 24 through 34 removed outlier: 3.507A pdb=" N GLU F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 65 Processing helix chain 'F' and resid 75 through 80 removed outlier: 3.612A pdb=" N GLU F 79 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 75 through 80' Processing helix chain 'F' and resid 86 through 93 Processing helix chain 'F' and resid 96 through 110 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.581A pdb=" N MET F 126 " --> pdb=" O THR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 140 Processing helix chain 'F' and resid 146 through 157 Processing helix chain 'F' and resid 157 through 163 removed outlier: 3.701A pdb=" N GLU F 161 " --> pdb=" O ASN F 157 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU F 162 " --> pdb=" O GLN F 158 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS F 163 " --> pdb=" O TRP F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 157 through 163' Processing helix chain 'D' and resid 235 through 246 Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 262 through 268 Processing helix chain 'D' and resid 271 through 289 removed outlier: 3.565A pdb=" N CYS D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.566A pdb=" N LEU D 310 " --> pdb=" O TYR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 341 Processing helix chain 'D' and resid 347 through 353 Processing helix chain 'D' and resid 356 through 366 Processing helix chain 'D' and resid 383 through 398 removed outlier: 3.879A pdb=" N TYR D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 removed outlier: 3.714A pdb=" N LEU D 417 " --> pdb=" O ASN D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 438 Processing helix chain 'D' and resid 440 through 452 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 475 through 491 Processing helix chain 'D' and resid 494 through 501 Processing helix chain 'D' and resid 515 through 526 removed outlier: 3.815A pdb=" N LYS D 526 " --> pdb=" O SER D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 554 removed outlier: 3.757A pdb=" N GLU D 554 " --> pdb=" O MET D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 568 removed outlier: 4.254A pdb=" N GLN D 559 " --> pdb=" O GLY D 555 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 572 removed outlier: 3.561A pdb=" N HIS D 572 " --> pdb=" O SER D 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 569 through 572' Processing helix chain 'D' and resid 588 through 600 Processing helix chain 'D' and resid 623 through 628 Processing helix chain 'D' and resid 643 through 656 removed outlier: 3.775A pdb=" N CYS D 656 " --> pdb=" O GLU D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 684 Processing helix chain 'D' and resid 700 through 712 removed outlier: 3.680A pdb=" N VAL D 710 " --> pdb=" O SER D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 732 through 743 Processing helix chain 'D' and resid 757 through 769 removed outlier: 3.756A pdb=" N HIS D 766 " --> pdb=" O LYS D 762 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU D 768 " --> pdb=" O LEU D 764 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS D 769 " --> pdb=" O SER D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 797 Processing helix chain 'D' and resid 798 through 800 No H-bonds generated for 'chain 'D' and resid 798 through 800' Processing helix chain 'D' and resid 814 through 826 removed outlier: 3.524A pdb=" N VAL D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 820 " --> pdb=" O ASN D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 843 through 845 No H-bonds generated for 'chain 'D' and resid 843 through 845' Processing helix chain 'D' and resid 846 through 857 removed outlier: 3.603A pdb=" N LEU D 850 " --> pdb=" O ALA D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 883 removed outlier: 3.558A pdb=" N ASP D 880 " --> pdb=" O ASN D 876 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D 881 " --> pdb=" O ILE D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 902 No H-bonds generated for 'chain 'D' and resid 900 through 902' Processing helix chain 'D' and resid 903 through 914 removed outlier: 3.560A pdb=" N GLY D 909 " --> pdb=" O GLN D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 940 Processing helix chain 'D' and resid 952 through 957 Processing helix chain 'D' and resid 958 through 972 removed outlier: 3.952A pdb=" N LYS D 963 " --> pdb=" O LYS D 959 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE D 964 " --> pdb=" O LYS D 960 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 931 through 933 removed outlier: 3.511A pdb=" N ARG B1044 " --> pdb=" O LEU B1005 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU B1068 " --> pdb=" O ASN B1099 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346 removed outlier: 3.514A pdb=" N MET A 380 " --> pdb=" O GLN A 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 514 removed outlier: 6.555A pdb=" N GLU A 514 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N ASP A 541 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALA A 538 " --> pdb=" O TYR A 583 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 721 " --> pdb=" O CYS A 750 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU A 749 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU A 778 " --> pdb=" O ASP A 807 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 806 " --> pdb=" O GLU A 836 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 586 through 587 Processing sheet with id=AA6, first strand: chain 'A' and resid 891 through 893 removed outlier: 7.105A pdb=" N LEU A 892 " --> pdb=" O ASN A 921 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 931 through 933 removed outlier: 3.510A pdb=" N ARG E1044 " --> pdb=" O LEU E1005 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU E1068 " --> pdb=" O ASN E1099 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'D' and resid 345 through 346 removed outlier: 3.514A pdb=" N MET D 380 " --> pdb=" O GLN D 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 507 through 514 removed outlier: 6.555A pdb=" N GLU D 514 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N ASP D 541 " --> pdb=" O GLU D 514 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALA D 538 " --> pdb=" O TYR D 583 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU D 721 " --> pdb=" O CYS D 750 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU D 749 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU D 778 " --> pdb=" O ASP D 807 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU D 806 " --> pdb=" O GLU D 836 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 586 through 587 Processing sheet with id=AB3, first strand: chain 'D' and resid 891 through 893 removed outlier: 7.106A pdb=" N LEU D 892 " --> pdb=" O ASN D 921 " (cutoff:3.500A) 814 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6242 1.34 - 1.46: 3819 1.46 - 1.58: 8860 1.58 - 1.69: 0 1.69 - 1.81: 208 Bond restraints: 19129 Sorted by residual: bond pdb=" CG LYS A 959 " pdb=" CD LYS A 959 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.44e+00 bond pdb=" CG LYS D 959 " pdb=" CD LYS D 959 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.36e+00 bond pdb=" CE LYS A 959 " pdb=" NZ LYS A 959 " ideal model delta sigma weight residual 1.489 1.455 0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CE LYS D 959 " pdb=" NZ LYS D 959 " ideal model delta sigma weight residual 1.489 1.455 0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C LYS D 958 " pdb=" N LYS D 959 " ideal model delta sigma weight residual 1.335 1.320 0.015 1.36e-02 5.41e+03 1.15e+00 ... (remaining 19124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 25170 1.03 - 2.06: 593 2.06 - 3.09: 102 3.09 - 4.12: 11 4.12 - 5.15: 10 Bond angle restraints: 25886 Sorted by residual: angle pdb=" C HIS D 353 " pdb=" N GLU D 354 " pdb=" CA GLU D 354 " ideal model delta sigma weight residual 121.54 126.69 -5.15 1.91e+00 2.74e-01 7.26e+00 angle pdb=" C HIS A 353 " pdb=" N GLU A 354 " pdb=" CA GLU A 354 " ideal model delta sigma weight residual 121.54 126.66 -5.12 1.91e+00 2.74e-01 7.18e+00 angle pdb=" N LYS B 979 " pdb=" CA LYS B 979 " pdb=" C LYS B 979 " ideal model delta sigma weight residual 114.56 111.55 3.01 1.27e+00 6.20e-01 5.61e+00 angle pdb=" N LYS E 979 " pdb=" CA LYS E 979 " pdb=" C LYS E 979 " ideal model delta sigma weight residual 114.56 111.60 2.96 1.27e+00 6.20e-01 5.43e+00 angle pdb=" N SER D 916 " pdb=" CA SER D 916 " pdb=" C SER D 916 " ideal model delta sigma weight residual 114.04 111.50 2.54 1.24e+00 6.50e-01 4.20e+00 ... (remaining 25881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 10854 14.40 - 28.80: 641 28.80 - 43.20: 179 43.20 - 57.60: 57 57.60 - 72.00: 15 Dihedral angle restraints: 11746 sinusoidal: 4734 harmonic: 7012 Sorted by residual: dihedral pdb=" N LEU A 696 " pdb=" CA LEU A 696 " pdb=" CB LEU A 696 " pdb=" CG LEU A 696 " ideal model delta sinusoidal sigma weight residual -60.00 -119.90 59.90 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU D 875 " pdb=" CB LEU D 875 " pdb=" CG LEU D 875 " pdb=" CD1 LEU D 875 " ideal model delta sinusoidal sigma weight residual 180.00 122.76 57.24 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA LEU A 875 " pdb=" CB LEU A 875 " pdb=" CG LEU A 875 " pdb=" CD1 LEU A 875 " ideal model delta sinusoidal sigma weight residual 180.00 122.79 57.21 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 11743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1942 0.028 - 0.057: 724 0.057 - 0.085: 242 0.085 - 0.113: 108 0.113 - 0.141: 15 Chirality restraints: 3031 Sorted by residual: chirality pdb=" CA ILE D 314 " pdb=" N ILE D 314 " pdb=" C ILE D 314 " pdb=" CB ILE D 314 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE A 314 " pdb=" N ILE A 314 " pdb=" C ILE A 314 " pdb=" CB ILE A 314 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA PRO A 787 " pdb=" N PRO A 787 " pdb=" C PRO A 787 " pdb=" CB PRO A 787 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 3028 not shown) Planarity restraints: 3288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 786 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 787 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 787 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 787 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 786 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO D 787 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 787 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 787 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 131 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO C 132 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " -0.018 5.00e-02 4.00e+02 ... (remaining 3285 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 8 2.35 - 2.99: 9065 2.99 - 3.63: 26462 3.63 - 4.26: 40247 4.26 - 4.90: 68607 Nonbonded interactions: 144389 Sorted by model distance: nonbonded pdb=" CD1 ILE E 949 " pdb=" CZ3 TRP E 970 " model vdw 1.715 3.760 nonbonded pdb=" OG1 THR F 26 " pdb=" OD2 ASP F 111 " model vdw 2.176 3.040 nonbonded pdb=" OG1 THR C 26 " pdb=" OD2 ASP C 111 " model vdw 2.176 3.040 nonbonded pdb=" OD1 ASP B1052 " pdb=" OG SER B1080 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP E1052 " pdb=" OG SER E1080 " model vdw 2.234 3.040 ... (remaining 144384 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'D' and (resid 234 through 315 or (resid 319 and (name N or name CA or na \ me C or name O or name CB )) or resid 320 through 993)) } ncs_group { reference = chain 'B' selection = (chain 'E' and (resid 889 through 897 or (resid 898 and (name N or name CA or na \ me C or name O or name CB )) or resid 899 through 1161)) } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.530 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 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 : 0.002 0.047 19129 Z= 0.089 Angle : 0.415 5.145 25886 Z= 0.233 Chirality : 0.036 0.141 3031 Planarity : 0.003 0.047 3288 Dihedral : 11.049 71.998 7146 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.38 % Allowed : 4.06 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.18), residues: 2364 helix: 1.38 (0.16), residues: 1128 sheet: -1.37 (0.36), residues: 228 loop : 0.44 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 675 TYR 0.006 0.001 TYR D 305 PHE 0.011 0.001 PHE D 411 TRP 0.006 0.001 TRP A 251 HIS 0.004 0.001 HIS D 270 Details of bonding type rmsd covalent geometry : bond 0.00173 (19129) covalent geometry : angle 0.41475 (25886) hydrogen bonds : bond 0.19113 ( 814) hydrogen bonds : angle 5.31672 ( 2412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 307 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 696 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8232 (tt) REVERT: F 37 ASP cc_start: 0.4151 (p0) cc_final: 0.3807 (m-30) outliers start: 8 outliers final: 2 residues processed: 315 average time/residue: 0.1789 time to fit residues: 80.1778 Evaluate side-chains 159 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain D residue 330 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0060 chunk 235 optimal weight: 5.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 962 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN A 285 GLN A 349 ASN A 559 GLN A 805 HIS ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN D 349 ASN D 559 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.075750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.058132 restraints weight = 89088.165| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.78 r_work: 0.2972 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19129 Z= 0.209 Angle : 0.624 8.805 25886 Z= 0.329 Chirality : 0.042 0.190 3031 Planarity : 0.004 0.054 3288 Dihedral : 4.878 70.841 2532 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.37 % Allowed : 8.25 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.85 (0.18), residues: 2364 helix: 1.19 (0.16), residues: 1174 sheet: -1.17 (0.34), residues: 248 loop : 0.46 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 914 TYR 0.012 0.001 TYR E 920 PHE 0.019 0.002 PHE D 611 TRP 0.021 0.002 TRP A 251 HIS 0.008 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00471 (19129) covalent geometry : angle 0.62351 (25886) hydrogen bonds : bond 0.05176 ( 814) hydrogen bonds : angle 4.48101 ( 2412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.751 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: B 893 GLN cc_start: 0.7437 (mt0) cc_final: 0.7017 (mp10) REVERT: B 897 TRP cc_start: 0.8631 (m100) cc_final: 0.8391 (m100) REVERT: B 913 MET cc_start: 0.8339 (mtp) cc_final: 0.8053 (mtm) REVERT: C 113 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8424 (pptt) REVERT: C 139 PHE cc_start: 0.8645 (m-80) cc_final: 0.8355 (m-10) REVERT: C 158 GLN cc_start: 0.9371 (pt0) cc_final: 0.8938 (pm20) REVERT: A 239 MET cc_start: 0.9107 (mtm) cc_final: 0.8813 (mtm) REVERT: A 431 MET cc_start: 0.9118 (ttp) cc_final: 0.8864 (ttm) REVERT: E 906 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8358 (ttm-80) REVERT: E 908 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8132 (tm-30) REVERT: E 1097 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8070 (tm-30) REVERT: D 274 MET cc_start: 0.8161 (mmm) cc_final: 0.7944 (mmm) REVERT: D 415 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.8057 (m-80) outliers start: 29 outliers final: 11 residues processed: 194 average time/residue: 0.1475 time to fit residues: 43.4564 Evaluate side-chains 157 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 894 ARG Chi-restraints excluded: chain B residue 903 TYR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain E residue 906 ARG Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 486 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 158 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 962 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 962 ASN E1033 ASN F 23 GLN F 152 GLN D 273 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.075352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057988 restraints weight = 87633.626| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.87 r_work: 0.2965 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19129 Z= 0.145 Angle : 0.501 7.444 25886 Z= 0.270 Chirality : 0.039 0.160 3031 Planarity : 0.004 0.053 3288 Dihedral : 4.422 67.644 2526 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.32 % Allowed : 9.10 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.18), residues: 2364 helix: 1.34 (0.16), residues: 1188 sheet: -1.17 (0.34), residues: 252 loop : 0.57 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 154 TYR 0.015 0.001 TYR C 109 PHE 0.014 0.001 PHE D 611 TRP 0.028 0.001 TRP A 251 HIS 0.007 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00327 (19129) covalent geometry : angle 0.50111 (25886) hydrogen bonds : bond 0.04609 ( 814) hydrogen bonds : angle 4.25478 ( 2412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.668 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: B 893 GLN cc_start: 0.7582 (mt0) cc_final: 0.7231 (mp10) REVERT: B 897 TRP cc_start: 0.8681 (m100) cc_final: 0.8236 (m100) REVERT: B 908 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9000 (pt0) REVERT: E 906 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8388 (ttm-80) REVERT: E 913 MET cc_start: 0.8139 (ptt) cc_final: 0.7570 (ptm) REVERT: E 1097 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8093 (tm-30) REVERT: F 152 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8207 (pp30) REVERT: D 274 MET cc_start: 0.8118 (mmm) cc_final: 0.7562 (mmm) REVERT: D 415 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: D 544 ASN cc_start: 0.8921 (m-40) cc_final: 0.8658 (m110) REVERT: D 579 GLU cc_start: 0.8881 (tt0) cc_final: 0.8623 (tm-30) outliers start: 28 outliers final: 7 residues processed: 182 average time/residue: 0.1387 time to fit residues: 39.3981 Evaluate side-chains 156 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 351 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain E residue 906 ARG Chi-restraints excluded: chain E residue 941 VAL Chi-restraints excluded: chain F residue 152 GLN Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 486 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 22 optimal weight: 0.0870 chunk 44 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 162 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 962 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 962 ASN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 HIS D 424 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.069990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.050381 restraints weight = 89973.155| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.32 r_work: 0.2981 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19129 Z= 0.118 Angle : 0.486 9.048 25886 Z= 0.258 Chirality : 0.038 0.164 3031 Planarity : 0.003 0.055 3288 Dihedral : 4.285 65.894 2526 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.37 % Allowed : 9.81 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.11 (0.18), residues: 2364 helix: 1.43 (0.16), residues: 1188 sheet: -1.06 (0.34), residues: 248 loop : 0.53 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 154 TYR 0.012 0.001 TYR C 109 PHE 0.016 0.001 PHE F 101 TRP 0.020 0.001 TRP A 251 HIS 0.005 0.001 HIS A 974 Details of bonding type rmsd covalent geometry : bond 0.00266 (19129) covalent geometry : angle 0.48564 (25886) hydrogen bonds : bond 0.03965 ( 814) hydrogen bonds : angle 4.15066 ( 2412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 893 GLN cc_start: 0.7582 (mt0) cc_final: 0.7274 (mp10) REVERT: B 897 TRP cc_start: 0.8635 (m100) cc_final: 0.8227 (m100) REVERT: B 911 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9163 (mt-10) REVERT: C 154 ARG cc_start: 0.9051 (tpt170) cc_final: 0.8429 (tpm170) REVERT: C 158 GLN cc_start: 0.9399 (pt0) cc_final: 0.8827 (pm20) REVERT: A 923 MET cc_start: 0.8914 (mtm) cc_final: 0.8610 (mtt) REVERT: E 906 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7919 (ttm-80) REVERT: E 908 GLU cc_start: 0.8669 (mt-10) cc_final: 0.7977 (tm-30) REVERT: E 913 MET cc_start: 0.7954 (ptt) cc_final: 0.7229 (ptm) REVERT: E 1097 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8122 (tm-30) REVERT: F 154 ARG cc_start: 0.9100 (ptm-80) cc_final: 0.8710 (mmm160) REVERT: D 251 TRP cc_start: 0.8173 (OUTLIER) cc_final: 0.7883 (p90) REVERT: D 274 MET cc_start: 0.7971 (mmm) cc_final: 0.7512 (mmm) REVERT: D 380 MET cc_start: 0.8234 (pmm) cc_final: 0.7963 (pmm) REVERT: D 415 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: D 544 ASN cc_start: 0.8956 (m-40) cc_final: 0.8691 (m110) REVERT: D 579 GLU cc_start: 0.8829 (tt0) cc_final: 0.8619 (tm-30) outliers start: 29 outliers final: 9 residues processed: 176 average time/residue: 0.1285 time to fit residues: 35.8390 Evaluate side-chains 154 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain E residue 906 ARG Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 424 HIS Chi-restraints excluded: chain D residue 486 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 233 optimal weight: 0.8980 chunk 27 optimal weight: 40.0000 chunk 172 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 962 ASN B1033 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN E 962 ASN E1075 HIS ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN D 559 GLN D 805 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.071532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.054332 restraints weight = 88386.835| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.72 r_work: 0.2843 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 19129 Z= 0.349 Angle : 0.717 9.520 25886 Z= 0.372 Chirality : 0.045 0.171 3031 Planarity : 0.004 0.058 3288 Dihedral : 4.837 64.194 2526 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.03 % Allowed : 10.09 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2364 helix: 1.08 (0.15), residues: 1164 sheet: -1.38 (0.32), residues: 244 loop : 0.15 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 969 TYR 0.014 0.002 TYR A 346 PHE 0.025 0.002 PHE A 411 TRP 0.041 0.002 TRP A 251 HIS 0.024 0.002 HIS D 424 Details of bonding type rmsd covalent geometry : bond 0.00799 (19129) covalent geometry : angle 0.71684 (25886) hydrogen bonds : bond 0.06488 ( 814) hydrogen bonds : angle 4.84594 ( 2412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 897 TRP cc_start: 0.8722 (m100) cc_final: 0.8214 (m100) REVERT: B 911 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9124 (mt-10) REVERT: B 1143 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8532 (tt) REVERT: C 99 THR cc_start: 0.7270 (p) cc_final: 0.7062 (t) REVERT: C 154 ARG cc_start: 0.9043 (tpt170) cc_final: 0.8616 (tpt90) REVERT: C 158 GLN cc_start: 0.9453 (pt0) cc_final: 0.8855 (pm20) REVERT: A 946 MET cc_start: 0.9053 (mmm) cc_final: 0.8596 (mmm) REVERT: E 908 GLU cc_start: 0.8694 (mt-10) cc_final: 0.7657 (tm-30) REVERT: E 913 MET cc_start: 0.8102 (ptt) cc_final: 0.7704 (ptm) REVERT: E 1097 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7964 (tm-30) REVERT: D 251 TRP cc_start: 0.8476 (OUTLIER) cc_final: 0.8239 (p90) REVERT: D 274 MET cc_start: 0.8102 (mmm) cc_final: 0.7717 (mmm) REVERT: D 345 LEU cc_start: 0.9173 (mp) cc_final: 0.8739 (pp) REVERT: D 396 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9048 (mp) REVERT: D 415 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: D 579 GLU cc_start: 0.8861 (tt0) cc_final: 0.8427 (tm-30) outliers start: 43 outliers final: 20 residues processed: 184 average time/residue: 0.1315 time to fit residues: 38.1105 Evaluate side-chains 165 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 894 ARG Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain E residue 941 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 243 HIS Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 832 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 144 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 31 optimal weight: 40.0000 chunk 133 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 164 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN C 157 ASN A 972 ASN E 962 ASN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN F 152 GLN D 559 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.068318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048918 restraints weight = 88904.955| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 4.23 r_work: 0.2955 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19129 Z= 0.108 Angle : 0.507 9.973 25886 Z= 0.269 Chirality : 0.038 0.176 3031 Planarity : 0.003 0.055 3288 Dihedral : 4.304 61.350 2526 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.89 % Allowed : 11.18 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.18), residues: 2364 helix: 1.49 (0.16), residues: 1164 sheet: -1.33 (0.35), residues: 222 loop : 0.25 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 902 TYR 0.010 0.001 TYR C 109 PHE 0.010 0.001 PHE A 411 TRP 0.062 0.001 TRP F 61 HIS 0.007 0.001 HIS D 424 Details of bonding type rmsd covalent geometry : bond 0.00238 (19129) covalent geometry : angle 0.50685 (25886) hydrogen bonds : bond 0.03935 ( 814) hydrogen bonds : angle 4.23604 ( 2412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 897 TRP cc_start: 0.8728 (m100) cc_final: 0.8142 (m100) REVERT: B 911 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9139 (mt-10) REVERT: C 154 ARG cc_start: 0.9042 (tpt170) cc_final: 0.8748 (tpt90) REVERT: C 158 GLN cc_start: 0.9447 (pt0) cc_final: 0.8933 (pm20) REVERT: A 946 MET cc_start: 0.8971 (mmm) cc_final: 0.8509 (mmm) REVERT: E 906 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7859 (ttm-80) REVERT: E 908 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7375 (tm-30) REVERT: E 913 MET cc_start: 0.8341 (ptt) cc_final: 0.7499 (ppp) REVERT: E 1097 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8034 (tm-30) REVERT: F 157 ASN cc_start: 0.9032 (m-40) cc_final: 0.8811 (m-40) REVERT: D 251 TRP cc_start: 0.8622 (OUTLIER) cc_final: 0.8329 (p90) REVERT: D 274 MET cc_start: 0.8029 (mmm) cc_final: 0.7687 (mmm) REVERT: D 415 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8162 (m-80) REVERT: D 544 ASN cc_start: 0.8969 (m-40) cc_final: 0.8766 (m110) REVERT: D 579 GLU cc_start: 0.8825 (tt0) cc_final: 0.8404 (tm-30) REVERT: D 584 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8574 (tm-30) outliers start: 40 outliers final: 16 residues processed: 179 average time/residue: 0.1295 time to fit residues: 36.7922 Evaluate side-chains 161 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 894 ARG Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain E residue 895 GLU Chi-restraints excluded: chain E residue 906 ARG Chi-restraints excluded: chain E residue 941 VAL Chi-restraints excluded: chain F residue 152 GLN Chi-restraints excluded: chain D residue 243 HIS Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 832 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 129 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 chunk 69 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 227 optimal weight: 0.3980 chunk 169 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 962 ASN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.068428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.048976 restraints weight = 89613.640| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.28 r_work: 0.2943 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19129 Z= 0.105 Angle : 0.499 9.981 25886 Z= 0.262 Chirality : 0.038 0.195 3031 Planarity : 0.003 0.057 3288 Dihedral : 4.084 60.914 2526 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.65 % Allowed : 11.56 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.18), residues: 2364 helix: 1.59 (0.16), residues: 1168 sheet: -1.23 (0.35), residues: 222 loop : 0.26 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 902 TYR 0.013 0.001 TYR E 920 PHE 0.009 0.001 PHE D 611 TRP 0.052 0.001 TRP F 61 HIS 0.005 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00229 (19129) covalent geometry : angle 0.49850 (25886) hydrogen bonds : bond 0.03715 ( 814) hydrogen bonds : angle 4.13736 ( 2412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 897 TRP cc_start: 0.8634 (m100) cc_final: 0.8180 (m100) REVERT: B 911 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9140 (mt-10) REVERT: B 1143 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8308 (tt) REVERT: C 154 ARG cc_start: 0.8994 (tpt170) cc_final: 0.8672 (tpt90) REVERT: C 158 GLN cc_start: 0.9444 (pt0) cc_final: 0.8918 (pm20) REVERT: E 906 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7895 (ttm-80) REVERT: E 908 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7390 (tm-30) REVERT: E 913 MET cc_start: 0.8409 (ptt) cc_final: 0.8011 (ptt) REVERT: E 1097 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8060 (tm-30) REVERT: F 157 ASN cc_start: 0.9052 (m-40) cc_final: 0.8704 (m-40) REVERT: F 160 CYS cc_start: 0.8013 (p) cc_final: 0.7732 (p) REVERT: D 251 TRP cc_start: 0.8497 (OUTLIER) cc_final: 0.8213 (p90) REVERT: D 274 MET cc_start: 0.8118 (mmm) cc_final: 0.7764 (mmm) REVERT: D 415 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: D 579 GLU cc_start: 0.8837 (tt0) cc_final: 0.8417 (tm-30) REVERT: D 970 ILE cc_start: 0.9427 (tp) cc_final: 0.9211 (mm) outliers start: 35 outliers final: 19 residues processed: 175 average time/residue: 0.1264 time to fit residues: 35.3483 Evaluate side-chains 163 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 894 ARG Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain E residue 895 GLU Chi-restraints excluded: chain E residue 906 ARG Chi-restraints excluded: chain E residue 941 VAL Chi-restraints excluded: chain D residue 243 HIS Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 875 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 182 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 962 ASN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.071628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054513 restraints weight = 88104.721| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.73 r_work: 0.2854 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 19129 Z= 0.248 Angle : 0.602 10.414 25886 Z= 0.316 Chirality : 0.042 0.183 3031 Planarity : 0.004 0.057 3288 Dihedral : 4.369 62.344 2526 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.89 % Allowed : 11.65 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.18), residues: 2364 helix: 1.45 (0.16), residues: 1166 sheet: -1.44 (0.34), residues: 226 loop : 0.19 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 154 TYR 0.024 0.001 TYR C 109 PHE 0.016 0.002 PHE A 411 TRP 0.054 0.002 TRP F 61 HIS 0.004 0.001 HIS E1061 Details of bonding type rmsd covalent geometry : bond 0.00567 (19129) covalent geometry : angle 0.60207 (25886) hydrogen bonds : bond 0.05291 ( 814) hydrogen bonds : angle 4.51267 ( 2412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 897 TRP cc_start: 0.8751 (m100) cc_final: 0.8221 (m100) REVERT: B 911 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9129 (mt-10) REVERT: B 1062 MET cc_start: 0.9127 (mmm) cc_final: 0.8850 (mtp) REVERT: B 1143 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8488 (tt) REVERT: C 158 GLN cc_start: 0.9475 (pt0) cc_final: 0.8958 (pm20) REVERT: A 946 MET cc_start: 0.9074 (mmm) cc_final: 0.8737 (mmm) REVERT: E 906 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8349 (ttm-80) REVERT: E 908 GLU cc_start: 0.8556 (mt-10) cc_final: 0.7462 (tm-30) REVERT: E 913 MET cc_start: 0.8544 (ptt) cc_final: 0.8074 (ptt) REVERT: E 1040 MET cc_start: 0.8754 (ttm) cc_final: 0.8542 (ttm) REVERT: E 1097 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8001 (tm-30) REVERT: F 10 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7305 (p0) REVERT: F 157 ASN cc_start: 0.9134 (m-40) cc_final: 0.8834 (m-40) REVERT: F 160 CYS cc_start: 0.7992 (p) cc_final: 0.7755 (p) REVERT: D 251 TRP cc_start: 0.8476 (OUTLIER) cc_final: 0.8251 (p90) REVERT: D 274 MET cc_start: 0.8197 (mmm) cc_final: 0.7826 (mmm) REVERT: D 415 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: D 579 GLU cc_start: 0.8871 (tt0) cc_final: 0.8488 (tm-30) REVERT: D 970 ILE cc_start: 0.9467 (tp) cc_final: 0.9266 (pt) outliers start: 40 outliers final: 20 residues processed: 170 average time/residue: 0.1251 time to fit residues: 34.9158 Evaluate side-chains 160 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 894 ARG Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain E residue 895 GLU Chi-restraints excluded: chain E residue 906 ARG Chi-restraints excluded: chain E residue 941 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain D residue 243 HIS Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 832 LEU Chi-restraints excluded: chain D residue 875 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 14 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 224 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 962 ASN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.068063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048778 restraints weight = 89107.332| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.23 r_work: 0.2957 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19129 Z= 0.104 Angle : 0.523 16.567 25886 Z= 0.272 Chirality : 0.038 0.185 3031 Planarity : 0.003 0.056 3288 Dihedral : 4.017 60.448 2526 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.27 % Allowed : 12.26 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.18), residues: 2364 helix: 1.58 (0.16), residues: 1170 sheet: -1.32 (0.35), residues: 222 loop : 0.26 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 481 TYR 0.009 0.001 TYR E 920 PHE 0.009 0.001 PHE A 611 TRP 0.045 0.001 TRP F 61 HIS 0.006 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00228 (19129) covalent geometry : angle 0.52271 (25886) hydrogen bonds : bond 0.03659 ( 814) hydrogen bonds : angle 4.14000 ( 2412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 897 TRP cc_start: 0.8704 (m100) cc_final: 0.8175 (m100) REVERT: B 911 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9157 (mt-10) REVERT: B 1143 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8367 (tt) REVERT: C 158 GLN cc_start: 0.9461 (pt0) cc_final: 0.8968 (pm20) REVERT: A 946 MET cc_start: 0.8989 (mmm) cc_final: 0.8710 (mmm) REVERT: E 906 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7759 (ttm-80) REVERT: E 1097 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8032 (tm-30) REVERT: F 23 GLN cc_start: 0.3702 (tm-30) cc_final: 0.3378 (tm-30) REVERT: F 36 MET cc_start: 0.1410 (mmp) cc_final: 0.0722 (tpt) REVERT: D 251 TRP cc_start: 0.8630 (OUTLIER) cc_final: 0.8342 (p90) REVERT: D 274 MET cc_start: 0.8095 (mmm) cc_final: 0.7751 (mmm) REVERT: D 415 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: D 579 GLU cc_start: 0.8851 (tt0) cc_final: 0.8447 (tm-30) REVERT: D 970 ILE cc_start: 0.9461 (tp) cc_final: 0.9259 (pt) outliers start: 27 outliers final: 16 residues processed: 167 average time/residue: 0.1268 time to fit residues: 34.4379 Evaluate side-chains 157 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 894 ARG Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain E residue 906 ARG Chi-restraints excluded: chain E residue 941 VAL Chi-restraints excluded: chain E residue 1100 MET Chi-restraints excluded: chain D residue 243 HIS Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 832 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 6 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 962 ASN ** F 23 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 = 0.3664 r_free = 0.3664 target = 0.068095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.048897 restraints weight = 89174.501| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.09 r_work: 0.2949 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19129 Z= 0.107 Angle : 0.520 15.483 25886 Z= 0.269 Chirality : 0.038 0.183 3031 Planarity : 0.003 0.057 3288 Dihedral : 3.873 59.378 2526 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.94 % Allowed : 12.74 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.18), residues: 2364 helix: 1.63 (0.16), residues: 1170 sheet: -1.28 (0.35), residues: 222 loop : 0.26 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.015 0.001 TYR E 920 PHE 0.009 0.001 PHE D 625 TRP 0.046 0.001 TRP F 61 HIS 0.005 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00240 (19129) covalent geometry : angle 0.51988 (25886) hydrogen bonds : bond 0.03585 ( 814) hydrogen bonds : angle 4.09110 ( 2412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 897 TRP cc_start: 0.8721 (m100) cc_final: 0.8193 (m100) REVERT: B 911 GLU cc_start: 0.9453 (mt-10) cc_final: 0.9143 (mt-10) REVERT: B 1143 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8305 (tt) REVERT: C 36 MET cc_start: -0.1903 (ptt) cc_final: -0.2212 (ptt) REVERT: C 158 GLN cc_start: 0.9469 (pt0) cc_final: 0.8968 (pm20) REVERT: A 946 MET cc_start: 0.8987 (mmm) cc_final: 0.8719 (mmm) REVERT: E 906 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8039 (ttm-80) REVERT: E 908 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8144 (pt0) REVERT: E 913 MET cc_start: 0.8386 (ptp) cc_final: 0.7536 (ppp) REVERT: E 1097 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8055 (tm-30) REVERT: F 23 GLN cc_start: 0.3573 (tm-30) cc_final: 0.3251 (tm-30) REVERT: F 36 MET cc_start: 0.1309 (mmp) cc_final: 0.0717 (tpt) REVERT: F 154 ARG cc_start: 0.8509 (mmp80) cc_final: 0.7973 (mmp80) REVERT: D 251 TRP cc_start: 0.8440 (OUTLIER) cc_final: 0.8213 (p90) REVERT: D 274 MET cc_start: 0.8104 (mmm) cc_final: 0.7749 (mmm) REVERT: D 415 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.8155 (m-80) REVERT: D 579 GLU cc_start: 0.8822 (tt0) cc_final: 0.8431 (tm-30) outliers start: 20 outliers final: 11 residues processed: 155 average time/residue: 0.1331 time to fit residues: 33.4008 Evaluate side-chains 151 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain E residue 906 ARG Chi-restraints excluded: chain E residue 941 VAL Chi-restraints excluded: chain D residue 243 HIS Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 415 TYR Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 832 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 92 optimal weight: 0.0070 chunk 68 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 0.0770 chunk 120 optimal weight: 10.0000 overall best weight: 0.9158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 962 ASN ** F 23 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 = 0.3668 r_free = 0.3668 target = 0.068218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.048989 restraints weight = 89540.460| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.12 r_work: 0.2962 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19129 Z= 0.104 Angle : 0.526 15.002 25886 Z= 0.275 Chirality : 0.039 0.223 3031 Planarity : 0.003 0.057 3288 Dihedral : 3.760 57.692 2526 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.94 % Allowed : 12.74 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.18), residues: 2364 helix: 1.67 (0.16), residues: 1174 sheet: -1.22 (0.35), residues: 222 loop : 0.26 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 154 TYR 0.012 0.001 TYR E 920 PHE 0.010 0.001 PHE E1043 TRP 0.045 0.001 TRP F 61 HIS 0.005 0.001 HIS D 974 Details of bonding type rmsd covalent geometry : bond 0.00233 (19129) covalent geometry : angle 0.52637 (25886) hydrogen bonds : bond 0.03456 ( 814) hydrogen bonds : angle 4.06133 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5506.26 seconds wall clock time: 94 minutes 47.37 seconds (5687.37 seconds total)