Starting phenix.real_space_refine on Thu Feb 15 12:00:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv9_34288/02_2024/8gv9_34288.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv9_34288/02_2024/8gv9_34288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv9_34288/02_2024/8gv9_34288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv9_34288/02_2024/8gv9_34288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv9_34288/02_2024/8gv9_34288.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gv9_34288/02_2024/8gv9_34288.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.152 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 Cl 2 4.86 5 C 7964 2.51 5 N 2046 2.21 5 O 2098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 375": "OE1" <-> "OE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 593": "OD1" <-> "OD2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 705": "OD1" <-> "OD2" Residue "A TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 788": "OE1" <-> "OE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 838": "OE1" <-> "OE2" Residue "A TYR 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 951": "OD1" <-> "OD2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1085": "OE1" <-> "OE2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 542": "OE1" <-> "OE2" Residue "B GLU 571": "OE1" <-> "OE2" Residue "B GLU 587": "OE1" <-> "OE2" Residue "B TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 702": "OD1" <-> "OD2" Residue "B TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 776": "OE1" <-> "OE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 838": "OE1" <-> "OE2" Residue "B TYR 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 849": "OE1" <-> "OE2" Residue "B PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1011": "OE1" <-> "OE2" Residue "B PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1210": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12170 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6084 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 727} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6084 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 727} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.59, per 1000 atoms: 0.54 Number of scatterers: 12170 At special positions: 0 Unit cell: (91.3, 127.6, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 60 16.00 O 2098 8.00 N 2046 7.00 C 7964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 2.2 seconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2892 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 7 sheets defined 60.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 415 through 424 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 568 through 580 Processing helix chain 'A' and resid 582 through 591 removed outlier: 3.944A pdb=" N TYR A 590 " --> pdb=" O HIS A 586 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.916A pdb=" N LEU A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 641 removed outlier: 4.088A pdb=" N SER A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 632 " --> pdb=" O HIS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 694 through 696 No H-bonds generated for 'chain 'A' and resid 694 through 696' Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.674A pdb=" N ASP A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 734 removed outlier: 4.234A pdb=" N LEU A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 710 " --> pdb=" O PRO A 706 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 739 through 758 Processing helix chain 'A' and resid 768 through 785 Processing helix chain 'A' and resid 788 through 810 removed outlier: 3.654A pdb=" N GLY A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A 793 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP A 795 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 802 " --> pdb=" O PHE A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 819 removed outlier: 4.296A pdb=" N PHE A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 819 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 850 removed outlier: 3.505A pdb=" N GLN A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 923 removed outlier: 3.960A pdb=" N LEU A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 923 " --> pdb=" O ARG A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 937 Processing helix chain 'A' and resid 938 through 954 removed outlier: 3.554A pdb=" N ILE A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 996 removed outlier: 3.722A pdb=" N MET A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1020 removed outlier: 3.791A pdb=" N LEU A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A1004 " --> pdb=" O PRO A1000 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1046 removed outlier: 4.203A pdb=" N LEU A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A1037 " --> pdb=" O HIS A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1067 Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1106 through 1111 Processing helix chain 'A' and resid 1114 through 1129 removed outlier: 3.941A pdb=" N LEU A1118 " --> pdb=" O PRO A1114 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A1129 " --> pdb=" O MET A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1141 Processing helix chain 'A' and resid 1142 through 1144 No H-bonds generated for 'chain 'A' and resid 1142 through 1144' Processing helix chain 'A' and resid 1145 through 1149 removed outlier: 3.570A pdb=" N HIS A1149 " --> pdb=" O PRO A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1157 removed outlier: 4.006A pdb=" N LYS A1157 " --> pdb=" O THR A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1183 removed outlier: 3.639A pdb=" N THR A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1188 through 1195 removed outlier: 3.549A pdb=" N ILE A1192 " --> pdb=" O ALA A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1208 removed outlier: 3.675A pdb=" N LEU A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A1204 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR A1205 " --> pdb=" O MET A1201 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A1207 " --> pdb=" O VAL A1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 381 removed outlier: 3.842A pdb=" N ALA B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 415 through 424 Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.636A pdb=" N GLU B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 580 Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.793A pdb=" N LEU B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 607 removed outlier: 3.536A pdb=" N THR B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 601 " --> pdb=" O ASP B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 641 removed outlier: 3.920A pdb=" N GLN B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 693 Processing helix chain 'B' and resid 695 through 700 removed outlier: 4.059A pdb=" N ASP B 699 " --> pdb=" O HIS B 695 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 700' Processing helix chain 'B' and resid 705 through 734 removed outlier: 3.580A pdb=" N LEU B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 712 " --> pdb=" O CYS B 708 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE B 713 " --> pdb=" O LEU B 709 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) Proline residue: B 722 - end of helix Processing helix chain 'B' and resid 739 through 758 removed outlier: 3.674A pdb=" N VAL B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 754 " --> pdb=" O GLN B 750 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 784 Processing helix chain 'B' and resid 788 through 810 removed outlier: 3.925A pdb=" N GLY B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG B 793 " --> pdb=" O TYR B 789 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B 794 " --> pdb=" O LEU B 790 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TRP B 795 " --> pdb=" O VAL B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 819 Processing helix chain 'B' and resid 820 through 850 removed outlier: 3.859A pdb=" N ILE B 826 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 848 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 923 removed outlier: 3.504A pdb=" N LEU B 903 " --> pdb=" O ASN B 899 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 915 " --> pdb=" O THR B 911 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 917 " --> pdb=" O PHE B 913 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 918 " --> pdb=" O ILE B 914 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 921 " --> pdb=" O PHE B 917 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 937 Processing helix chain 'B' and resid 938 through 954 removed outlier: 3.543A pdb=" N ILE B 942 " --> pdb=" O PHE B 938 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 954 " --> pdb=" O VAL B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1020 removed outlier: 3.557A pdb=" N ALA B1001 " --> pdb=" O SER B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1047 removed outlier: 3.574A pdb=" N LEU B1037 " --> pdb=" O HIS B1033 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B1047 " --> pdb=" O GLY B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1050 No H-bonds generated for 'chain 'B' and resid 1048 through 1050' Processing helix chain 'B' and resid 1057 through 1067 Processing helix chain 'B' and resid 1091 through 1102 Processing helix chain 'B' and resid 1109 through 1113 removed outlier: 3.767A pdb=" N GLN B1112 " --> pdb=" O LEU B1109 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B1113 " --> pdb=" O LEU B1110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1109 through 1113' Processing helix chain 'B' and resid 1114 through 1129 removed outlier: 3.913A pdb=" N LEU B1118 " --> pdb=" O PRO B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1141 Processing helix chain 'B' and resid 1145 through 1149 removed outlier: 3.654A pdb=" N HIS B1149 " --> pdb=" O PRO B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1157 removed outlier: 3.969A pdb=" N LYS B1157 " --> pdb=" O THR B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1159 through 1182 removed outlier: 3.660A pdb=" N SER B1182 " --> pdb=" O TRP B1178 " (cutoff:3.500A) Processing helix chain 'B' and resid 1188 through 1208 Proline residue: B1198 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 352 removed outlier: 5.293A pdb=" N GLU A 342 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU A 329 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 344 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N CYS A 523 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N ALA A 514 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N PHE A 555 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 516 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N PHE A 557 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 518 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU A 559 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 520 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLY A 561 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY A 522 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE A 555 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N GLU A 539 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 12.346A pdb=" N PHE A 557 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 12.371A pdb=" N LEU A 537 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU A 559 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 12.866A pdb=" N VAL A 535 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 11.497A pdb=" N GLY A 561 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 12.490A pdb=" N ALA A 533 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 385 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ARG A 536 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A 387 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG A 538 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU A 389 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA A 540 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352 removed outlier: 6.367A pdb=" N TRP A 340 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 369 removed outlier: 3.603A pdb=" N VAL B 610 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 610 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1069 through 1071 removed outlier: 6.973A pdb=" N VAL A1070 " --> pdb=" O GLN A1084 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 350 through 352 removed outlier: 6.926A pdb=" N LEU B 327 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG B 345 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 325 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N CYS B 523 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA B 516 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 555 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 561 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 554 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 556 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG B 538 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 352 removed outlier: 6.476A pdb=" N TRP B 340 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1069 through 1071 removed outlier: 7.105A pdb=" N VAL B1070 " --> pdb=" O GLN B1084 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1842 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: 3.50 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3861 1.34 - 1.46: 1894 1.46 - 1.57: 6586 1.57 - 1.69: 1 1.69 - 1.81: 102 Bond restraints: 12444 Sorted by residual: bond pdb=" CA LEU B 591 " pdb=" C LEU B 591 " ideal model delta sigma weight residual 1.528 1.579 -0.051 1.04e-02 9.25e+03 2.36e+01 bond pdb=" CA ASN A 923 " pdb=" C ASN A 923 " ideal model delta sigma weight residual 1.522 1.561 -0.039 1.37e-02 5.33e+03 8.08e+00 bond pdb=" C GLN B 336 " pdb=" N GLU B 337 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.47e-02 4.63e+03 6.26e+00 bond pdb=" CA ARG B 930 " pdb=" C ARG B 930 " ideal model delta sigma weight residual 1.524 1.551 -0.026 1.28e-02 6.10e+03 4.25e+00 bond pdb=" CA LEU B 843 " pdb=" C LEU B 843 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.35e-02 5.49e+03 3.98e+00 ... (remaining 12439 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.15: 359 106.15 - 113.13: 6815 113.13 - 120.10: 4471 120.10 - 127.08: 5088 127.08 - 134.05: 137 Bond angle restraints: 16870 Sorted by residual: angle pdb=" N ILE B 931 " pdb=" CA ILE B 931 " pdb=" C ILE B 931 " ideal model delta sigma weight residual 110.62 118.74 -8.12 1.02e+00 9.61e-01 6.34e+01 angle pdb=" N VAL B 844 " pdb=" CA VAL B 844 " pdb=" C VAL B 844 " ideal model delta sigma weight residual 110.72 103.33 7.39 1.01e+00 9.80e-01 5.35e+01 angle pdb=" N LYS B 842 " pdb=" CA LYS B 842 " pdb=" C LYS B 842 " ideal model delta sigma weight residual 111.07 118.61 -7.54 1.07e+00 8.73e-01 4.97e+01 angle pdb=" N PHE B1135 " pdb=" CA PHE B1135 " pdb=" C PHE B1135 " ideal model delta sigma weight residual 114.62 106.69 7.93 1.14e+00 7.69e-01 4.83e+01 angle pdb=" N LEU B 806 " pdb=" CA LEU B 806 " pdb=" C LEU B 806 " ideal model delta sigma weight residual 111.28 118.21 -6.93 1.09e+00 8.42e-01 4.05e+01 ... (remaining 16865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6499 17.97 - 35.94: 755 35.94 - 53.92: 173 53.92 - 71.89: 21 71.89 - 89.86: 18 Dihedral angle restraints: 7466 sinusoidal: 3024 harmonic: 4442 Sorted by residual: dihedral pdb=" CA ARG B 624 " pdb=" C ARG B 624 " pdb=" N SER B 625 " pdb=" CA SER B 625 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER A 625 " pdb=" C SER A 625 " pdb=" N VAL A 626 " pdb=" CA VAL A 626 " ideal model delta harmonic sigma weight residual -180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CB GLU A1212 " pdb=" CG GLU A1212 " pdb=" CD GLU A1212 " pdb=" OE1 GLU A1212 " ideal model delta sinusoidal sigma weight residual 0.00 89.64 -89.64 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1691 0.061 - 0.122: 256 0.122 - 0.183: 21 0.183 - 0.244: 6 0.244 - 0.305: 4 Chirality restraints: 1978 Sorted by residual: chirality pdb=" CA LYS B 842 " pdb=" N LYS B 842 " pdb=" C LYS B 842 " pdb=" CB LYS B 842 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA TYR B 590 " pdb=" N TYR B 590 " pdb=" C TYR B 590 " pdb=" CB TYR B 590 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA LEU B 591 " pdb=" N LEU B 591 " pdb=" C LEU B 591 " pdb=" CB LEU B 591 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1975 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 394 " 0.055 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO A 395 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 395 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 395 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 394 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO B 395 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 395 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 395 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 510 " 0.048 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO A 511 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " 0.039 5.00e-02 4.00e+02 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 60 2.60 - 3.18: 9792 3.18 - 3.75: 17282 3.75 - 4.33: 23625 4.33 - 4.90: 41144 Nonbonded interactions: 91903 Sorted by model distance: nonbonded pdb=" O ASN B 785 " pdb=" OD1 ASN B 785 " model vdw 2.028 3.040 nonbonded pdb=" O LEU A 730 " pdb=" OG1 THR A 734 " model vdw 2.085 2.440 nonbonded pdb=" O LEU B 591 " pdb=" CD1 LEU B 591 " model vdw 2.141 3.460 nonbonded pdb=" O ALA B1076 " pdb=" OD1 ASP B1079 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU A 350 " pdb=" OD1 ASP A 352 " model vdw 2.189 3.040 ... (remaining 91898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.710 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: 4.190 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.100 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.004 0.072 12444 Z= 0.234 Angle : 0.686 9.725 16870 Z= 0.431 Chirality : 0.046 0.305 1978 Planarity : 0.005 0.082 2110 Dihedral : 16.238 89.859 4574 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.01 % Favored : 94.79 % Rotamer: Outliers : 0.23 % Allowed : 15.04 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1516 helix: 0.72 (0.18), residues: 842 sheet: 0.48 (0.44), residues: 114 loop : -1.33 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.006 0.001 HIS B 586 PHE 0.019 0.001 PHE A1189 TYR 0.007 0.001 TYR B1154 ARG 0.003 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 1.245 Fit side-chains REVERT: B 1196 THR cc_start: 0.7948 (t) cc_final: 0.7719 (p) outliers start: 3 outliers final: 2 residues processed: 176 average time/residue: 0.2599 time to fit residues: 64.5237 Evaluate side-chains 168 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain B residue 323 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS A1089 GLN B 853 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12444 Z= 0.232 Angle : 0.556 9.191 16870 Z= 0.289 Chirality : 0.041 0.161 1978 Planarity : 0.005 0.060 2110 Dihedral : 4.191 31.289 1645 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.21 % Favored : 94.59 % Rotamer: Outliers : 2.03 % Allowed : 16.62 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1516 helix: 0.93 (0.18), residues: 864 sheet: 0.67 (0.47), residues: 110 loop : -1.45 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.008 0.001 HIS B 586 PHE 0.019 0.002 PHE A 822 TYR 0.008 0.001 TYR A 789 ARG 0.003 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 1.324 Fit side-chains REVERT: A 697 LEU cc_start: 0.8674 (mm) cc_final: 0.8373 (mm) REVERT: A 1156 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7882 (mptt) REVERT: B 321 HIS cc_start: 0.6378 (OUTLIER) cc_final: 0.6095 (m-70) REVERT: B 701 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7706 (ttm-80) REVERT: B 1156 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7638 (mptt) outliers start: 27 outliers final: 17 residues processed: 193 average time/residue: 0.2536 time to fit residues: 69.5261 Evaluate side-chains 189 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1205 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS A1089 GLN B 853 HIS B 899 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12444 Z= 0.337 Angle : 0.600 6.139 16870 Z= 0.311 Chirality : 0.044 0.173 1978 Planarity : 0.005 0.056 2110 Dihedral : 4.268 26.041 1642 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.67 % Favored : 94.13 % Rotamer: Outliers : 4.06 % Allowed : 15.49 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1516 helix: 0.67 (0.18), residues: 878 sheet: 0.72 (0.48), residues: 110 loop : -1.60 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.009 0.002 HIS B 586 PHE 0.024 0.002 PHE A1189 TYR 0.012 0.002 TYR A 789 ARG 0.004 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 185 time to evaluate : 1.422 Fit side-chains REVERT: A 697 LEU cc_start: 0.8723 (mm) cc_final: 0.8501 (mm) REVERT: A 1156 LYS cc_start: 0.8337 (mtpt) cc_final: 0.7866 (mmtt) REVERT: B 321 HIS cc_start: 0.6431 (OUTLIER) cc_final: 0.6004 (m-70) REVERT: B 743 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7879 (mp) REVERT: B 1080 LYS cc_start: 0.7385 (mmtp) cc_final: 0.6898 (mttp) REVERT: B 1141 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8096 (mp) REVERT: B 1156 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7686 (mptt) outliers start: 54 outliers final: 34 residues processed: 221 average time/residue: 0.2441 time to fit residues: 77.3319 Evaluate side-chains 218 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1137 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1205 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.0050 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.0070 chunk 146 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 HIS B1089 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12444 Z= 0.176 Angle : 0.504 6.447 16870 Z= 0.262 Chirality : 0.040 0.150 1978 Planarity : 0.005 0.054 2110 Dihedral : 4.055 23.739 1642 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.88 % Favored : 94.92 % Rotamer: Outliers : 3.68 % Allowed : 16.77 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1516 helix: 0.97 (0.18), residues: 878 sheet: 0.82 (0.48), residues: 110 loop : -1.52 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.007 0.001 HIS A 586 PHE 0.019 0.001 PHE A1189 TYR 0.007 0.001 TYR A 569 ARG 0.002 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 180 time to evaluate : 1.389 Fit side-chains REVERT: A 697 LEU cc_start: 0.8690 (mm) cc_final: 0.8484 (mm) REVERT: A 1156 LYS cc_start: 0.8330 (mtpt) cc_final: 0.7874 (mptt) REVERT: B 321 HIS cc_start: 0.6443 (OUTLIER) cc_final: 0.6046 (m-70) REVERT: B 590 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.6231 (t80) REVERT: B 1156 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7656 (mptt) outliers start: 49 outliers final: 39 residues processed: 212 average time/residue: 0.2451 time to fit residues: 74.4658 Evaluate side-chains 210 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 169 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1137 GLU Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 3.9990 chunk 83 optimal weight: 0.0970 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 HIS B1089 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12444 Z= 0.274 Angle : 0.550 6.134 16870 Z= 0.284 Chirality : 0.042 0.234 1978 Planarity : 0.005 0.054 2110 Dihedral : 4.122 25.641 1642 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.47 % Favored : 94.33 % Rotamer: Outliers : 4.51 % Allowed : 16.62 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1516 helix: 0.89 (0.18), residues: 878 sheet: 0.81 (0.48), residues: 110 loop : -1.56 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.008 0.001 HIS B 586 PHE 0.022 0.002 PHE A1189 TYR 0.010 0.001 TYR A 789 ARG 0.003 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 173 time to evaluate : 1.329 Fit side-chains REVERT: A 697 LEU cc_start: 0.8711 (mm) cc_final: 0.8475 (mm) REVERT: A 1085 GLU cc_start: 0.8092 (pt0) cc_final: 0.7794 (pt0) REVERT: A 1156 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7874 (mptt) REVERT: B 558 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7996 (tp) REVERT: B 586 HIS cc_start: 0.7225 (OUTLIER) cc_final: 0.6898 (p90) REVERT: B 590 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.6221 (t80) REVERT: B 1080 LYS cc_start: 0.7298 (mmtp) cc_final: 0.6795 (mtmm) REVERT: B 1156 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7685 (mptt) outliers start: 60 outliers final: 51 residues processed: 216 average time/residue: 0.2446 time to fit residues: 75.7463 Evaluate side-chains 226 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 172 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1215 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1137 GLU Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1205 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS A1089 GLN B 853 HIS B1089 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12444 Z= 0.200 Angle : 0.509 6.078 16870 Z= 0.264 Chirality : 0.040 0.179 1978 Planarity : 0.004 0.054 2110 Dihedral : 4.042 25.013 1642 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.01 % Favored : 94.79 % Rotamer: Outliers : 4.51 % Allowed : 17.22 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1516 helix: 1.09 (0.18), residues: 878 sheet: 0.89 (0.49), residues: 110 loop : -1.54 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.007 0.001 HIS A 586 PHE 0.020 0.001 PHE A1189 TYR 0.008 0.001 TYR B1154 ARG 0.002 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 176 time to evaluate : 1.510 Fit side-chains REVERT: A 697 LEU cc_start: 0.8700 (mm) cc_final: 0.8454 (mm) REVERT: A 1085 GLU cc_start: 0.8093 (pt0) cc_final: 0.7802 (pt0) REVERT: A 1156 LYS cc_start: 0.8303 (mtpt) cc_final: 0.7857 (mptt) REVERT: B 558 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7995 (tp) REVERT: B 586 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6929 (p90) REVERT: B 590 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6227 (t80) REVERT: B 1080 LYS cc_start: 0.7261 (mmtp) cc_final: 0.6774 (mtmm) REVERT: B 1141 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8029 (mp) REVERT: B 1156 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7663 (mptt) outliers start: 60 outliers final: 50 residues processed: 219 average time/residue: 0.2573 time to fit residues: 81.0254 Evaluate side-chains 227 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 173 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1137 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1205 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 4.9990 chunk 16 optimal weight: 0.0670 chunk 83 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS A1089 GLN B 853 HIS ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12444 Z= 0.335 Angle : 0.585 6.186 16870 Z= 0.303 Chirality : 0.044 0.187 1978 Planarity : 0.005 0.054 2110 Dihedral : 4.234 27.940 1642 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.54 % Favored : 94.26 % Rotamer: Outliers : 5.04 % Allowed : 17.07 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1516 helix: 0.80 (0.18), residues: 878 sheet: 0.86 (0.49), residues: 110 loop : -1.60 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.009 0.002 HIS B 586 PHE 0.022 0.002 PHE B1189 TYR 0.011 0.002 TYR A 789 ARG 0.004 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 178 time to evaluate : 1.349 Fit side-chains REVERT: A 518 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8776 (p) REVERT: A 1156 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7891 (mptt) REVERT: A 1194 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7159 (tp) REVERT: B 558 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8010 (tp) REVERT: B 586 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.6909 (p90) REVERT: B 1141 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8083 (mp) REVERT: B 1156 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7701 (mptt) outliers start: 67 outliers final: 55 residues processed: 230 average time/residue: 0.2361 time to fit residues: 79.4055 Evaluate side-chains 237 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 177 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1215 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1137 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1205 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 133 optimal weight: 0.0470 chunk 140 optimal weight: 3.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS A1089 GLN B 853 HIS ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12444 Z= 0.174 Angle : 0.495 6.050 16870 Z= 0.259 Chirality : 0.039 0.147 1978 Planarity : 0.004 0.053 2110 Dihedral : 4.026 24.898 1642 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.75 % Favored : 95.05 % Rotamer: Outliers : 4.06 % Allowed : 18.57 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1516 helix: 1.17 (0.18), residues: 878 sheet: 0.97 (0.49), residues: 110 loop : -1.55 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.007 0.001 HIS A 586 PHE 0.029 0.001 PHE B 921 TYR 0.007 0.001 TYR B1154 ARG 0.004 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 174 time to evaluate : 1.446 Fit side-chains REVERT: A 1085 GLU cc_start: 0.8129 (pt0) cc_final: 0.7876 (pt0) REVERT: A 1156 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7779 (mptt) REVERT: A 1172 LEU cc_start: 0.8346 (tp) cc_final: 0.8115 (tp) REVERT: B 558 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7989 (tp) REVERT: B 586 HIS cc_start: 0.7255 (OUTLIER) cc_final: 0.6926 (p90) REVERT: B 590 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.6248 (t80) REVERT: B 1156 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7670 (mptt) outliers start: 54 outliers final: 45 residues processed: 211 average time/residue: 0.2377 time to fit residues: 73.0190 Evaluate side-chains 218 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 170 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1215 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1010 MET Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS A1089 GLN B 853 HIS ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12444 Z= 0.210 Angle : 0.516 6.098 16870 Z= 0.267 Chirality : 0.041 0.148 1978 Planarity : 0.005 0.054 2110 Dihedral : 4.009 25.580 1642 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.08 % Favored : 94.72 % Rotamer: Outliers : 3.91 % Allowed : 18.80 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1516 helix: 1.14 (0.18), residues: 878 sheet: 0.94 (0.49), residues: 110 loop : -1.51 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.007 0.001 HIS A 586 PHE 0.027 0.002 PHE B 921 TYR 0.008 0.001 TYR B1154 ARG 0.004 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 175 time to evaluate : 1.446 Fit side-chains REVERT: A 1085 GLU cc_start: 0.8063 (pt0) cc_final: 0.7837 (pt0) REVERT: A 1156 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7698 (mmtt) REVERT: B 558 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7984 (tp) REVERT: B 586 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6908 (p90) REVERT: B 590 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.6313 (t80) REVERT: B 1156 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7668 (mptt) outliers start: 52 outliers final: 47 residues processed: 210 average time/residue: 0.2319 time to fit residues: 71.0062 Evaluate side-chains 222 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 172 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1152 VAL Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1215 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 VAL Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain B residue 1215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 0.0000 chunk 120 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS A1089 GLN ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 HIS ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12444 Z= 0.154 Angle : 0.478 6.065 16870 Z= 0.249 Chirality : 0.039 0.139 1978 Planarity : 0.004 0.053 2110 Dihedral : 3.867 23.090 1642 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.55 % Favored : 95.25 % Rotamer: Outliers : 3.08 % Allowed : 19.77 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1516 helix: 1.44 (0.18), residues: 878 sheet: 0.98 (0.49), residues: 110 loop : -1.45 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 795 HIS 0.007 0.001 HIS A 586 PHE 0.026 0.001 PHE B 921 TYR 0.007 0.001 TYR B1154 ARG 0.007 0.000 ARG A 701 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 169 time to evaluate : 1.325 Fit side-chains REVERT: A 1156 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7724 (mptt) REVERT: A 1172 LEU cc_start: 0.8410 (tp) cc_final: 0.8204 (tp) REVERT: B 558 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8079 (tp) REVERT: B 586 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6796 (p90) REVERT: B 590 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.6318 (t80) REVERT: B 1156 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7616 (mmtm) outliers start: 41 outliers final: 32 residues processed: 198 average time/residue: 0.2431 time to fit residues: 69.6852 Evaluate side-chains 201 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 HIS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1046 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1152 VAL Chi-restraints excluded: chain B residue 1196 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 50 optimal weight: 0.0020 chunk 124 optimal weight: 0.0980 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 853 HIS ** A1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 HIS ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.168739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126969 restraints weight = 13030.871| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.34 r_work: 0.3133 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12444 Z= 0.251 Angle : 0.535 6.123 16870 Z= 0.276 Chirality : 0.041 0.153 1978 Planarity : 0.005 0.053 2110 Dihedral : 4.011 25.704 1642 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.21 % Favored : 94.59 % Rotamer: Outliers : 3.23 % Allowed : 19.32 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1516 helix: 1.17 (0.18), residues: 880 sheet: 0.93 (0.49), residues: 110 loop : -1.48 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.007 0.001 HIS A 586 PHE 0.026 0.002 PHE B 921 TYR 0.009 0.001 TYR B1154 ARG 0.006 0.000 ARG A 701 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2585.75 seconds wall clock time: 47 minutes 40.82 seconds (2860.82 seconds total)