Starting phenix.real_space_refine on Sat Jul 20 21:05:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgp_37229/07_2024/8kgp_37229.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgp_37229/07_2024/8kgp_37229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgp_37229/07_2024/8kgp_37229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgp_37229/07_2024/8kgp_37229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgp_37229/07_2024/8kgp_37229.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgp_37229/07_2024/8kgp_37229.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7822 2.51 5 N 2092 2.21 5 O 2204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 422": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 526": "NH1" <-> "NH2" Residue "B PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 718": "NH1" <-> "NH2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 873": "NH1" <-> "NH2" Residue "B ARG 900": "NH1" <-> "NH2" Residue "B ARG 912": "NH1" <-> "NH2" Residue "B ARG 929": "NH1" <-> "NH2" Residue "B ARG 940": "NH1" <-> "NH2" Residue "B ARG 956": "NH1" <-> "NH2" Residue "B ARG 1004": "NH1" <-> "NH2" Residue "B ARG 1006": "NH1" <-> "NH2" Residue "B TYR 1038": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1066": "NH1" <-> "NH2" Residue "B PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 718": "NH1" <-> "NH2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "A ARG 900": "NH1" <-> "NH2" Residue "A ARG 912": "NH1" <-> "NH2" Residue "A ARG 929": "NH1" <-> "NH2" Residue "A ARG 940": "NH1" <-> "NH2" Residue "A ARG 956": "NH1" <-> "NH2" Residue "A ARG 1004": "NH1" <-> "NH2" Residue "A ARG 1006": "NH1" <-> "NH2" Residue "A TYR 1038": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1066": "NH1" <-> "NH2" Residue "A PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12168 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6084 Classifications: {'peptide': 749} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 718} Chain breaks: 2 Chain: "A" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6084 Classifications: {'peptide': 749} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 718} Chain breaks: 2 Time building chain proxies: 9.10, per 1000 atoms: 0.75 Number of scatterers: 12168 At special positions: 0 Unit cell: (113.75, 117.65, 113.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2204 8.00 N 2092 7.00 C 7822 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: 4.31 Conformation dependent library (CDL) restraints added in 2.0 seconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 14 sheets defined 46.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'B' and resid 441 through 451 removed outlier: 3.780A pdb=" N THR B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 513 removed outlier: 3.768A pdb=" N GLN B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 511 " --> pdb=" O GLY B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 560 removed outlier: 4.506A pdb=" N LEU B 549 " --> pdb=" O CYS B 545 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY B 550 " --> pdb=" O GLY B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 565 removed outlier: 4.184A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 565' Processing helix chain 'B' and resid 593 through 601 removed outlier: 3.749A pdb=" N TRP B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.901A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.695A pdb=" N PHE B 629 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.576A pdb=" N PHE B 653 " --> pdb=" O PHE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 664 Processing helix chain 'B' and resid 672 through 683 removed outlier: 3.970A pdb=" N VAL B 682 " --> pdb=" O SER B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 695 through 703 removed outlier: 3.747A pdb=" N ILE B 703 " --> pdb=" O LYS B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 755 through 766 removed outlier: 3.780A pdb=" N ALA B 766 " --> pdb=" O ILE B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 791 removed outlier: 3.857A pdb=" N LEU B 790 " --> pdb=" O SER B 787 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY B 791 " --> pdb=" O ARG B 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 787 through 791' Processing helix chain 'B' and resid 809 through 814 removed outlier: 3.812A pdb=" N PHE B 814 " --> pdb=" O ILE B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.601A pdb=" N SER B 819 " --> pdb=" O ALA B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 877 removed outlier: 3.812A pdb=" N ALA B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 877 " --> pdb=" O ARG B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 888 removed outlier: 3.652A pdb=" N LEU B 885 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 886 " --> pdb=" O HIS B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 953 removed outlier: 3.821A pdb=" N SER B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 982 through 990 removed outlier: 3.845A pdb=" N VAL B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU B 988 " --> pdb=" O ASN B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1003 removed outlier: 3.513A pdb=" N PHE B1002 " --> pdb=" O SER B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1070 removed outlier: 3.662A pdb=" N LEU B1032 " --> pdb=" O TYR B1028 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 3.694A pdb=" N ARG B1040 " --> pdb=" O LEU B1036 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B1041 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1092 removed outlier: 3.577A pdb=" N GLU B1091 " --> pdb=" O ARG B1087 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS B1092 " --> pdb=" O ILE B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1109 through 1117 Processing helix chain 'B' and resid 1134 through 1159 removed outlier: 3.742A pdb=" N LYS B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR B1139 " --> pdb=" O ILE B1135 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ARG B1140 " --> pdb=" O ALA B1136 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1186 removed outlier: 4.152A pdb=" N GLU B1172 " --> pdb=" O SER B1168 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B1186 " --> pdb=" O ILE B1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.705A pdb=" N SER A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 513 removed outlier: 3.772A pdb=" N GLN A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 560 removed outlier: 4.508A pdb=" N LEU A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 550 " --> pdb=" O GLY A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 removed outlier: 4.183A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 565' Processing helix chain 'A' and resid 593 through 601 removed outlier: 3.751A pdb=" N TRP A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.905A pdb=" N HIS A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.711A pdb=" N PHE A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 644 through 653 removed outlier: 3.575A pdb=" N PHE A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 672 through 683 removed outlier: 3.970A pdb=" N VAL A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.747A pdb=" N ILE A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 755 through 765 Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.909A pdb=" N LEU A 790 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 791 " --> pdb=" O ARG A 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 787 through 791' Processing helix chain 'A' and resid 809 through 814 removed outlier: 3.812A pdb=" N PHE A 814 " --> pdb=" O ILE A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.600A pdb=" N SER A 819 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 removed outlier: 3.814A pdb=" N ALA A 870 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 888 removed outlier: 3.652A pdb=" N LEU A 885 " --> pdb=" O LYS A 882 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 886 " --> pdb=" O HIS A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.823A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.502A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 990 removed outlier: 3.850A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1028 through 1070 removed outlier: 3.660A pdb=" N LEU A1032 " --> pdb=" O TYR A1028 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 3.698A pdb=" N ARG A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A1041 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1079 removed outlier: 3.837A pdb=" N HIS A1078 " --> pdb=" O ASN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1092 removed outlier: 3.565A pdb=" N GLU A1091 " --> pdb=" O ARG A1087 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1117 Processing helix chain 'A' and resid 1134 through 1159 removed outlier: 3.745A pdb=" N LYS A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A1139 " --> pdb=" O ILE A1135 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ARG A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A1141 " --> pdb=" O ALA A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1186 removed outlier: 4.153A pdb=" N GLU A1172 " --> pdb=" O SER A1168 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A1186 " --> pdb=" O ILE A1182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 465 through 469 removed outlier: 5.764A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ILE B 685 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N THR B 638 " --> pdb=" O ILE B 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'B' and resid 824 through 827 removed outlier: 5.059A pdb=" N GLU B 833 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU B 827 " --> pdb=" O ARG B 831 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ARG B 831 " --> pdb=" O GLU B 827 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 909 through 913 removed outlier: 3.680A pdb=" N HIS B 909 " --> pdb=" O TYR B 920 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 916 " --> pdb=" O PHE B 913 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 922 through 925 removed outlier: 6.155A pdb=" N THR B 922 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1013 through 1015 removed outlier: 4.513A pdb=" N LEU B1013 " --> pdb=" O PHE B1025 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 465 through 469 removed outlier: 5.765A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ILE A 685 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N THR A 638 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AB1, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AB2, first strand: chain 'A' and resid 824 through 827 removed outlier: 5.048A pdb=" N GLU A 833 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU A 827 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ARG A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 909 through 913 removed outlier: 3.680A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 916 " --> pdb=" O PHE A 913 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.156A pdb=" N THR A 922 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1013 through 1015 removed outlier: 4.513A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1338 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: 3.63 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3304 1.33 - 1.45: 2369 1.45 - 1.57: 6707 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12458 Sorted by residual: bond pdb=" N LEU B1036 " pdb=" CA LEU B1036 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.04e-02 9.25e+03 9.23e+00 bond pdb=" N ILE B 763 " pdb=" CA ILE B 763 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.79e+00 bond pdb=" N LEU A1036 " pdb=" CA LEU A1036 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.04e-02 9.25e+03 8.68e+00 bond pdb=" N ILE A1031 " pdb=" CA ILE A1031 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.50e+00 bond pdb=" N TYR A 848 " pdb=" CA TYR A 848 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.23e-02 6.61e+03 7.23e+00 ... (remaining 12453 not shown) Histogram of bond angle deviations from ideal: 97.38 - 104.75: 196 104.75 - 112.13: 5783 112.13 - 119.51: 4681 119.51 - 126.88: 5999 126.88 - 134.26: 167 Bond angle restraints: 16826 Sorted by residual: angle pdb=" C ARG A 929 " pdb=" N ASN A 930 " pdb=" CA ASN A 930 " ideal model delta sigma weight residual 122.82 129.74 -6.92 1.42e+00 4.96e-01 2.37e+01 angle pdb=" C ARG B 929 " pdb=" N ASN B 930 " pdb=" CA ASN B 930 " ideal model delta sigma weight residual 122.82 129.73 -6.91 1.42e+00 4.96e-01 2.37e+01 angle pdb=" C SER A 902 " pdb=" N ASN A 903 " pdb=" CA ASN A 903 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C SER B 902 " pdb=" N ASN B 903 " pdb=" CA ASN B 903 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C ILE A 565 " pdb=" N HIS A 566 " pdb=" CA HIS A 566 " ideal model delta sigma weight residual 121.54 129.36 -7.82 1.91e+00 2.74e-01 1.68e+01 ... (remaining 16821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 6868 14.26 - 28.51: 447 28.51 - 42.77: 129 42.77 - 57.02: 20 57.02 - 71.28: 10 Dihedral angle restraints: 7474 sinusoidal: 3086 harmonic: 4388 Sorted by residual: dihedral pdb=" CA PRO A 901 " pdb=" C PRO A 901 " pdb=" N SER A 902 " pdb=" CA SER A 902 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA PRO B 901 " pdb=" C PRO B 901 " pdb=" N SER B 902 " pdb=" CA SER B 902 " ideal model delta harmonic sigma weight residual -180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA THR A 695 " pdb=" C THR A 695 " pdb=" N LYS A 696 " pdb=" CA LYS A 696 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 7471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1420 0.074 - 0.149: 359 0.149 - 0.223: 23 0.223 - 0.298: 14 0.298 - 0.372: 2 Chirality restraints: 1818 Sorted by residual: chirality pdb=" CB ILE A 963 " pdb=" CA ILE A 963 " pdb=" CG1 ILE A 963 " pdb=" CG2 ILE A 963 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB ILE B 685 " pdb=" CA ILE B 685 " pdb=" CG1 ILE B 685 " pdb=" CG2 ILE B 685 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE A 685 " pdb=" CA ILE A 685 " pdb=" CG1 ILE A 685 " pdb=" CG2 ILE A 685 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1815 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1170 " -0.023 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP B1170 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP B1170 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1170 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B1170 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1170 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1170 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B1170 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1170 " 0.023 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP A1170 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A1170 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A1170 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1170 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1170 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1170 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1170 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1170 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A1170 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 824 " -0.027 2.00e-02 2.50e+03 2.38e-02 1.13e+01 pdb=" CG TYR A 824 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 824 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 824 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 824 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 824 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 824 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 824 " -0.004 2.00e-02 2.50e+03 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3771 2.83 - 3.35: 10055 3.35 - 3.87: 18690 3.87 - 4.38: 21819 4.38 - 4.90: 38780 Nonbonded interactions: 93115 Sorted by model distance: nonbonded pdb=" OH TYR A 946 " pdb=" O LEU A1003 " model vdw 2.314 2.440 nonbonded pdb=" OH TYR B 946 " pdb=" O LEU B1003 " model vdw 2.318 2.440 nonbonded pdb=" O VAL B 840 " pdb=" CH2 TRP B1035 " model vdw 2.330 3.340 nonbonded pdb=" OG1 THR A 922 " pdb=" OG1 THR A 935 " model vdw 2.340 2.440 nonbonded pdb=" OG1 THR B 922 " pdb=" OG1 THR B 935 " model vdw 2.341 2.440 ... (remaining 93110 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: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.870 Find NCS groups from input model: 0.360 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.075 12458 Z= 0.705 Angle : 1.053 11.602 16826 Z= 0.590 Chirality : 0.066 0.372 1818 Planarity : 0.007 0.065 2144 Dihedral : 11.202 71.281 4662 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.76 % Allowed : 4.96 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -3.96 (0.18), residues: 1486 helix: -2.64 (0.16), residues: 598 sheet: -1.81 (0.35), residues: 218 loop : -2.81 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP A1170 HIS 0.015 0.002 HIS B1192 PHE 0.046 0.004 PHE B 785 TYR 0.057 0.004 TYR A 824 ARG 0.015 0.002 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 276 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 747 ASP cc_start: 0.8578 (t70) cc_final: 0.8336 (t0) REVERT: B 977 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7577 (tttm) REVERT: A 573 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7715 (mp) REVERT: A 747 ASP cc_start: 0.8591 (t70) cc_final: 0.8370 (t0) REVERT: A 964 ILE cc_start: 0.8994 (mt) cc_final: 0.8729 (mm) REVERT: A 977 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7330 (tttm) outliers start: 10 outliers final: 1 residues processed: 282 average time/residue: 0.2914 time to fit residues: 111.1996 Evaluate side-chains 147 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain A residue 573 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 620 HIS B 634 ASN B1119 GLN B1157 GLN A 620 HIS A 634 ASN A 677 GLN A1051 HIS A1119 GLN A1157 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12458 Z= 0.186 Angle : 0.573 8.925 16826 Z= 0.296 Chirality : 0.042 0.181 1818 Planarity : 0.005 0.041 2144 Dihedral : 4.934 36.247 1665 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.53 % Allowed : 10.61 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.20), residues: 1486 helix: -0.87 (0.20), residues: 614 sheet: -1.29 (0.36), residues: 202 loop : -2.30 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1170 HIS 0.005 0.001 HIS A 650 PHE 0.013 0.001 PHE B 559 TYR 0.015 0.001 TYR B 888 ARG 0.005 0.001 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 551 LEU cc_start: 0.8843 (mp) cc_final: 0.8522 (tt) REVERT: B 747 ASP cc_start: 0.8610 (t70) cc_final: 0.8328 (t0) REVERT: B 977 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7493 (tttm) REVERT: B 1134 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6061 (pp) REVERT: A 551 LEU cc_start: 0.8831 (mp) cc_final: 0.8518 (tt) REVERT: A 747 ASP cc_start: 0.8575 (t70) cc_final: 0.8332 (t0) REVERT: A 957 MET cc_start: 0.9071 (mmm) cc_final: 0.8728 (tpt) REVERT: A 964 ILE cc_start: 0.8922 (mt) cc_final: 0.8661 (mm) REVERT: A 977 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7354 (tttp) REVERT: A 1134 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6049 (pp) outliers start: 20 outliers final: 10 residues processed: 200 average time/residue: 0.2403 time to fit residues: 69.1406 Evaluate side-chains 157 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 108 optimal weight: 0.0020 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 12458 Z= 0.410 Angle : 0.647 12.230 16826 Z= 0.327 Chirality : 0.047 0.156 1818 Planarity : 0.005 0.046 2144 Dihedral : 4.786 18.647 1662 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.82 % Allowed : 11.98 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.21), residues: 1486 helix: -0.10 (0.21), residues: 618 sheet: -1.28 (0.35), residues: 206 loop : -2.11 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B1170 HIS 0.008 0.001 HIS A1192 PHE 0.017 0.002 PHE B 785 TYR 0.024 0.002 TYR A 824 ARG 0.004 0.001 ARG B 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 582 LYS cc_start: 0.8148 (mttm) cc_final: 0.7860 (mtmm) REVERT: B 747 ASP cc_start: 0.8664 (t70) cc_final: 0.8382 (t0) REVERT: B 833 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7439 (pp20) REVERT: B 977 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7542 (tttm) REVERT: B 1134 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6132 (pp) REVERT: A 747 ASP cc_start: 0.8635 (t70) cc_final: 0.8430 (t0) REVERT: A 756 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.7016 (mtp) REVERT: A 833 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7491 (pp20) REVERT: A 977 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7428 (tttm) REVERT: A 1134 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6105 (pp) outliers start: 50 outliers final: 29 residues processed: 183 average time/residue: 0.2331 time to fit residues: 63.9131 Evaluate side-chains 173 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain B residue 1142 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1142 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12458 Z= 0.226 Angle : 0.543 10.612 16826 Z= 0.274 Chirality : 0.042 0.140 1818 Planarity : 0.004 0.034 2144 Dihedral : 4.338 16.509 1662 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.13 % Allowed : 13.36 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.22), residues: 1486 helix: 0.47 (0.22), residues: 616 sheet: -0.97 (0.36), residues: 202 loop : -1.92 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1170 HIS 0.004 0.001 HIS A 650 PHE 0.011 0.001 PHE A 710 TYR 0.012 0.001 TYR A 888 ARG 0.003 0.000 ARG A 530 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 515 ASP cc_start: 0.7730 (t0) cc_final: 0.7487 (t70) REVERT: B 582 LYS cc_start: 0.8116 (mttm) cc_final: 0.7839 (mtmm) REVERT: B 747 ASP cc_start: 0.8672 (t70) cc_final: 0.8361 (t0) REVERT: B 833 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7285 (pp20) REVERT: B 890 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7716 (tt) REVERT: B 977 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7528 (tttm) REVERT: B 1134 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.6063 (pp) REVERT: A 515 ASP cc_start: 0.7741 (t0) cc_final: 0.7493 (t70) REVERT: A 747 ASP cc_start: 0.8635 (t70) cc_final: 0.8418 (t0) REVERT: A 833 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7341 (pp20) REVERT: A 890 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7698 (tt) REVERT: A 977 LYS cc_start: 0.8025 (ttmt) cc_final: 0.7412 (tttp) REVERT: A 1134 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.6059 (pp) outliers start: 41 outliers final: 27 residues processed: 193 average time/residue: 0.2192 time to fit residues: 62.9751 Evaluate side-chains 179 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1026 ASN Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1026 ASN Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 0.0980 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 36 optimal weight: 0.0670 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12458 Z= 0.149 Angle : 0.482 9.411 16826 Z= 0.245 Chirality : 0.041 0.135 1818 Planarity : 0.003 0.030 2144 Dihedral : 3.908 13.331 1662 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.44 % Allowed : 14.73 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.69 (0.22), residues: 1486 helix: 0.85 (0.22), residues: 618 sheet: -0.46 (0.36), residues: 196 loop : -1.73 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1170 HIS 0.007 0.001 HIS A 650 PHE 0.011 0.001 PHE A 710 TYR 0.010 0.001 TYR A 888 ARG 0.003 0.000 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 1.302 Fit side-chains REVERT: B 582 LYS cc_start: 0.8099 (mttm) cc_final: 0.7839 (mtmm) REVERT: B 747 ASP cc_start: 0.8680 (t70) cc_final: 0.8354 (t0) REVERT: B 833 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: B 890 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7686 (tt) REVERT: B 977 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7542 (tttm) REVERT: B 1134 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6087 (pp) REVERT: A 582 LYS cc_start: 0.8115 (mttm) cc_final: 0.7867 (mtmm) REVERT: A 747 ASP cc_start: 0.8645 (t70) cc_final: 0.8399 (t0) REVERT: A 833 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7350 (pp20) REVERT: A 890 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7697 (tt) REVERT: A 977 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7385 (tttp) REVERT: A 1134 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6028 (pp) outliers start: 32 outliers final: 19 residues processed: 192 average time/residue: 0.2286 time to fit residues: 64.8692 Evaluate side-chains 168 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1046 ARG Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1119 GLN A1119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12458 Z= 0.149 Angle : 0.488 9.495 16826 Z= 0.245 Chirality : 0.041 0.133 1818 Planarity : 0.003 0.027 2144 Dihedral : 3.756 13.161 1662 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.52 % Allowed : 15.50 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.41 (0.22), residues: 1486 helix: 1.12 (0.22), residues: 616 sheet: -0.29 (0.36), residues: 196 loop : -1.63 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 820 HIS 0.007 0.001 HIS A 650 PHE 0.010 0.001 PHE A 710 TYR 0.011 0.001 TYR B 966 ARG 0.004 0.000 ARG A1046 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 747 ASP cc_start: 0.8690 (t70) cc_final: 0.8356 (t0) REVERT: B 890 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7670 (tt) REVERT: B 977 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7495 (tttm) REVERT: B 1134 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5839 (mt) REVERT: A 582 LYS cc_start: 0.8098 (mttm) cc_final: 0.7864 (mtmm) REVERT: A 747 ASP cc_start: 0.8644 (t70) cc_final: 0.8404 (t0) REVERT: A 890 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7662 (tt) REVERT: A 977 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7382 (tttp) REVERT: A 1134 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.5901 (mt) outliers start: 33 outliers final: 25 residues processed: 172 average time/residue: 0.2218 time to fit residues: 57.4295 Evaluate side-chains 173 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12458 Z= 0.349 Angle : 0.589 15.532 16826 Z= 0.294 Chirality : 0.045 0.143 1818 Planarity : 0.004 0.042 2144 Dihedral : 4.177 17.072 1662 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.13 % Allowed : 15.27 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.54 (0.22), residues: 1486 helix: 1.10 (0.22), residues: 620 sheet: -0.53 (0.37), residues: 200 loop : -1.76 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1170 HIS 0.006 0.001 HIS A1192 PHE 0.012 0.001 PHE A 739 TYR 0.015 0.002 TYR A 824 ARG 0.004 0.000 ARG A1046 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 582 LYS cc_start: 0.8110 (mttm) cc_final: 0.7839 (mtmm) REVERT: B 747 ASP cc_start: 0.8689 (t70) cc_final: 0.8376 (t0) REVERT: B 833 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7386 (pp20) REVERT: B 950 ILE cc_start: 0.8977 (mm) cc_final: 0.8725 (mt) REVERT: B 977 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7564 (tttm) REVERT: B 1134 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6165 (pp) REVERT: A 582 LYS cc_start: 0.8112 (mttm) cc_final: 0.7861 (mtmm) REVERT: A 747 ASP cc_start: 0.8635 (t70) cc_final: 0.8431 (t0) REVERT: A 833 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7492 (pp20) REVERT: A 977 LYS cc_start: 0.8043 (ttmt) cc_final: 0.7403 (tttp) REVERT: A 1134 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6189 (pp) outliers start: 41 outliers final: 31 residues processed: 176 average time/residue: 0.2093 time to fit residues: 56.1276 Evaluate side-chains 176 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12458 Z= 0.174 Angle : 0.495 11.005 16826 Z= 0.248 Chirality : 0.041 0.132 1818 Planarity : 0.003 0.029 2144 Dihedral : 3.840 14.715 1662 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.67 % Allowed : 16.26 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1486 helix: 1.20 (0.22), residues: 634 sheet: -0.48 (0.37), residues: 202 loop : -1.62 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.005 0.001 HIS B 650 PHE 0.010 0.001 PHE A 710 TYR 0.013 0.001 TYR A 888 ARG 0.003 0.000 ARG A1046 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 150 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 551 LEU cc_start: 0.8888 (mp) cc_final: 0.8604 (tt) REVERT: B 582 LYS cc_start: 0.8087 (mttm) cc_final: 0.7836 (mtmm) REVERT: B 747 ASP cc_start: 0.8703 (t70) cc_final: 0.8365 (t0) REVERT: B 833 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7250 (pp20) REVERT: B 890 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7653 (tt) REVERT: B 977 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7510 (tttm) REVERT: B 1134 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6172 (pp) REVERT: A 551 LEU cc_start: 0.8902 (mp) cc_final: 0.8613 (tt) REVERT: A 582 LYS cc_start: 0.8087 (mttm) cc_final: 0.7864 (mtmm) REVERT: A 747 ASP cc_start: 0.8654 (t70) cc_final: 0.8423 (t0) REVERT: A 833 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7352 (pp20) REVERT: A 890 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7644 (tt) REVERT: A 977 LYS cc_start: 0.7986 (ttmt) cc_final: 0.7348 (tttp) REVERT: A 1134 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6163 (pp) outliers start: 35 outliers final: 27 residues processed: 173 average time/residue: 0.2192 time to fit residues: 57.6415 Evaluate side-chains 178 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 998 SER Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 132 optimal weight: 0.0060 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12458 Z= 0.131 Angle : 0.459 9.359 16826 Z= 0.232 Chirality : 0.040 0.131 1818 Planarity : 0.003 0.028 2144 Dihedral : 3.580 13.578 1662 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.75 % Allowed : 16.03 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.11 (0.23), residues: 1486 helix: 1.39 (0.22), residues: 632 sheet: -0.24 (0.38), residues: 198 loop : -1.51 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 820 HIS 0.004 0.001 HIS B 650 PHE 0.010 0.001 PHE A 710 TYR 0.011 0.001 TYR A 888 ARG 0.003 0.000 ARG A1046 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 551 LEU cc_start: 0.8870 (mp) cc_final: 0.8602 (tt) REVERT: B 747 ASP cc_start: 0.8701 (t70) cc_final: 0.8353 (t0) REVERT: B 833 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7286 (pp20) REVERT: B 890 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7606 (tt) REVERT: B 977 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7438 (tttm) REVERT: B 1134 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6172 (pp) REVERT: A 551 LEU cc_start: 0.8867 (mp) cc_final: 0.8598 (tt) REVERT: A 747 ASP cc_start: 0.8661 (t70) cc_final: 0.8416 (t0) REVERT: A 833 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7350 (pp20) REVERT: A 890 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7601 (tt) REVERT: A 977 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7337 (tttm) REVERT: A 1134 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6122 (pp) outliers start: 36 outliers final: 28 residues processed: 178 average time/residue: 0.2182 time to fit residues: 60.1170 Evaluate side-chains 179 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12458 Z= 0.299 Angle : 0.555 14.691 16826 Z= 0.278 Chirality : 0.044 0.142 1818 Planarity : 0.004 0.039 2144 Dihedral : 3.964 15.908 1662 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.90 % Allowed : 15.95 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1486 helix: 1.29 (0.22), residues: 632 sheet: -0.37 (0.38), residues: 202 loop : -1.63 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.005 0.001 HIS A1192 PHE 0.013 0.001 PHE A 739 TYR 0.014 0.001 TYR A 848 ARG 0.005 0.000 ARG A1046 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 145 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 551 LEU cc_start: 0.8867 (mp) cc_final: 0.8550 (tt) REVERT: B 747 ASP cc_start: 0.8698 (t70) cc_final: 0.8373 (t0) REVERT: B 833 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7376 (pp20) REVERT: B 977 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7497 (tttm) REVERT: B 1134 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6201 (pp) REVERT: A 551 LEU cc_start: 0.8874 (mp) cc_final: 0.8575 (tt) REVERT: A 572 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8816 (mp) REVERT: A 747 ASP cc_start: 0.8634 (t70) cc_final: 0.8424 (t0) REVERT: A 833 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7422 (pp20) REVERT: A 977 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7365 (tttm) REVERT: A 1134 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6149 (pp) outliers start: 38 outliers final: 28 residues processed: 172 average time/residue: 0.2080 time to fit residues: 54.2072 Evaluate side-chains 174 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 833 GLU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1119 GLN Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.0770 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 0.0030 chunk 21 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.094139 restraints weight = 16380.738| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.24 r_work: 0.2837 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12458 Z= 0.133 Angle : 0.486 10.993 16826 Z= 0.245 Chirality : 0.040 0.131 1818 Planarity : 0.003 0.028 2144 Dihedral : 3.722 13.548 1662 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.98 % Allowed : 17.71 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.23), residues: 1486 helix: 1.43 (0.22), residues: 630 sheet: -0.22 (0.39), residues: 202 loop : -1.54 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 820 HIS 0.008 0.001 HIS B 650 PHE 0.010 0.001 PHE B 710 TYR 0.011 0.001 TYR A 888 ARG 0.003 0.000 ARG A1046 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2903.06 seconds wall clock time: 52 minutes 21.65 seconds (3141.65 seconds total)