Starting phenix.real_space_refine on Mon Jun 16 18:03:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnp_26017/06_2025/7tnp_26017.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnp_26017/06_2025/7tnp_26017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnp_26017/06_2025/7tnp_26017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnp_26017/06_2025/7tnp_26017.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnp_26017/06_2025/7tnp_26017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnp_26017/06_2025/7tnp_26017.cif" } resolution = 3.96 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: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12218 2.51 5 N 3046 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18840 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4673 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4679 Classifications: {'peptide': 601} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Chain: "C" Number of atoms: 4673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4673 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4679 Classifications: {'peptide': 601} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.15, per 1000 atoms: 0.64 Number of scatterers: 18840 At special positions: 0 Unit cell: (125.33, 115.37, 134.46, 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 4 17.00 S 136 16.00 O 3436 8.00 N 3046 7.00 C 12218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.04 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.04 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.11 Conformation dependent library (CDL) restraints added in 2.7 seconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4396 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 22 sheets defined 54.4% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.853A pdb=" N TYR A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.528A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.646A pdb=" N MET A 527 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 624 removed outlier: 3.666A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 660 Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.566A pdb=" N TRP A 671 " --> pdb=" O PHE A 667 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.587A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.812A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.693A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 769 removed outlier: 3.757A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 822 removed outlier: 3.502A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1028 removed outlier: 3.634A pdb=" N PHE A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A1022 " --> pdb=" O ALA A1018 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A1024 " --> pdb=" O PHE A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1103 removed outlier: 3.520A pdb=" N TYR A1095 " --> pdb=" O ASP A1091 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A1096 " --> pdb=" O THR A1092 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A1099 " --> pdb=" O TYR A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1123 removed outlier: 3.780A pdb=" N LEU A1114 " --> pdb=" O SER A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1160 removed outlier: 3.828A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A1150 " --> pdb=" O LEU A1146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A1159 " --> pdb=" O TYR A1155 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1206 removed outlier: 3.895A pdb=" N ILE A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1197 " --> pdb=" O GLY A1193 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP A1202 " --> pdb=" O HIS A1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.636A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 4.040A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.552A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 568 removed outlier: 3.792A pdb=" N SER B 567 " --> pdb=" O SER B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 598 through 617 removed outlier: 3.512A pdb=" N GLY B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 636 through 641 removed outlier: 3.522A pdb=" N SER B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.824A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.533A pdb=" N ALA B 691 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 696 " --> pdb=" O ARG B 692 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.709A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 755 removed outlier: 4.335A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 770 removed outlier: 3.601A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS B 770 " --> pdb=" O TRP B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 820 removed outlier: 3.656A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1028 removed outlier: 3.780A pdb=" N ALA B1026 " --> pdb=" O LEU B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1089 removed outlier: 3.778A pdb=" N ASP B1087 " --> pdb=" O GLU B1084 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR B1088 " --> pdb=" O ASP B1085 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU B1089 " --> pdb=" O ALA B1086 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1084 through 1089' Processing helix chain 'B' and resid 1091 through 1103 Processing helix chain 'B' and resid 1104 through 1121 removed outlier: 3.670A pdb=" N LEU B1114 " --> pdb=" O SER B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1160 removed outlier: 3.740A pdb=" N PHE B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B1158 " --> pdb=" O VAL B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1209 removed outlier: 3.511A pdb=" N GLY B1193 " --> pdb=" O ALA B1189 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 469 removed outlier: 3.854A pdb=" N TYR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.527A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.646A pdb=" N MET C 527 " --> pdb=" O TYR C 523 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 624 removed outlier: 3.666A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 660 Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.566A pdb=" N TRP C 671 " --> pdb=" O PHE C 667 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 672 " --> pdb=" O ASP C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.586A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.811A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C 712 " --> pdb=" O MET C 708 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.693A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 769 removed outlier: 3.758A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 822 removed outlier: 3.502A pdb=" N TYR C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 805 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1028 removed outlier: 3.634A pdb=" N PHE C1017 " --> pdb=" O THR C1013 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C1022 " --> pdb=" O ALA C1018 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C1024 " --> pdb=" O PHE C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1103 removed outlier: 3.521A pdb=" N TYR C1095 " --> pdb=" O ASP C1091 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C1096 " --> pdb=" O THR C1092 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C1099 " --> pdb=" O TYR C1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1123 removed outlier: 3.779A pdb=" N LEU C1114 " --> pdb=" O SER C1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1160 removed outlier: 3.829A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C1159 " --> pdb=" O TYR C1155 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA C1160 " --> pdb=" O ILE C1156 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1206 removed outlier: 3.894A pdb=" N ILE C1187 " --> pdb=" O ALA C1183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C1197 " --> pdb=" O GLY C1193 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C1202 " --> pdb=" O HIS C1198 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.635A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 4.040A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 544 removed outlier: 3.552A pdb=" N MET D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 568 removed outlier: 3.792A pdb=" N SER D 567 " --> pdb=" O SER D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 598 through 617 removed outlier: 3.511A pdb=" N GLY D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 636 through 641 removed outlier: 3.521A pdb=" N SER D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.825A pdb=" N MET D 670 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP D 671 " --> pdb=" O PHE D 667 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.533A pdb=" N ALA D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 removed outlier: 3.709A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 755 removed outlier: 4.335A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 770 removed outlier: 3.601A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS D 770 " --> pdb=" O TRP D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 820 removed outlier: 3.656A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1028 removed outlier: 3.780A pdb=" N ALA D1026 " --> pdb=" O LEU D1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1089 removed outlier: 3.778A pdb=" N ASP D1087 " --> pdb=" O GLU D1084 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR D1088 " --> pdb=" O ASP D1085 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU D1089 " --> pdb=" O ALA D1086 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1084 through 1089' Processing helix chain 'D' and resid 1091 through 1103 Processing helix chain 'D' and resid 1104 through 1121 removed outlier: 3.669A pdb=" N LEU D1114 " --> pdb=" O SER D1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1160 removed outlier: 3.739A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D1158 " --> pdb=" O VAL D1154 " (cutoff:3.500A) Processing helix chain 'D' and resid 1178 through 1209 removed outlier: 3.512A pdb=" N GLY D1193 " --> pdb=" O ALA D1189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 442 removed outlier: 6.009A pdb=" N VAL A 396 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE A 476 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N THR A 398 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA A 477 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 440 through 442 removed outlier: 6.009A pdb=" N VAL A 396 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE A 476 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N THR A 398 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA A 477 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY A 733 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 479 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY A 731 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.191A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 702 " --> pdb=" O MET A 503 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.884A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 7.284A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 489 through 498 removed outlier: 4.781A pdb=" N PHE B 491 " --> pdb=" O THR B 736 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR B 736 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LYS B 493 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE B 734 " --> pdb=" O LYS B 493 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR B 732 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER B 497 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS B 730 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.966A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 509 through 510 Processing sheet with id=AB1, first strand: chain 'B' and resid 649 through 650 removed outlier: 7.184A pdb=" N THR B 649 " --> pdb=" O VAL B 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 1076 through 1077 removed outlier: 3.515A pdb=" N SER B1174 " --> pdb=" O TYR B1034 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 440 through 442 removed outlier: 6.009A pdb=" N VAL C 396 " --> pdb=" O ILE C 474 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE C 476 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR C 398 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA C 477 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY C 733 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU C 479 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY C 731 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 440 through 442 removed outlier: 6.009A pdb=" N VAL C 396 " --> pdb=" O ILE C 474 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE C 476 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR C 398 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA C 477 " --> pdb=" O GLY C 733 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY C 733 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU C 479 " --> pdb=" O GLY C 731 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY C 731 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.191A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 702 " --> pdb=" O MET C 503 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.884A pdb=" N SER C1035 " --> pdb=" O THR C1058 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 440 through 444 removed outlier: 7.284A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 498 removed outlier: 4.781A pdb=" N PHE D 491 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR D 736 " --> pdb=" O PHE D 491 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LYS D 493 " --> pdb=" O ILE D 734 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE D 734 " --> pdb=" O LYS D 493 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR D 732 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER D 497 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS D 730 " --> pdb=" O SER D 497 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.966A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 509 through 510 Processing sheet with id=AC3, first strand: chain 'D' and resid 649 through 650 removed outlier: 7.184A pdb=" N THR D 649 " --> pdb=" O VAL D 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 1076 through 1077 removed outlier: 3.515A pdb=" N SER D1174 " --> pdb=" O TYR D1034 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2718 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: 7.03 Time building geometry restraints manager: 6.06 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: 5730 1.34 - 1.46: 5017 1.46 - 1.59: 8283 1.59 - 1.71: 8 1.71 - 1.83: 220 Bond restraints: 19258 Sorted by residual: bond pdb=" CG1 ILE C 573 " pdb=" CD1 ILE C 573 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.63e+00 bond pdb=" CG1 ILE A 573 " pdb=" CD1 ILE A 573 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.63e+00 bond pdb=" CB TRP B 606 " pdb=" CG TRP B 606 " ideal model delta sigma weight residual 1.498 1.431 0.067 3.10e-02 1.04e+03 4.62e+00 bond pdb=" CB TRP D 606 " pdb=" CG TRP D 606 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.50e+00 bond pdb=" N3 CYZ D1302 " pdb=" S2 CYZ D1302 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 19253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 24986 2.39 - 4.78: 895 4.78 - 7.17: 105 7.17 - 9.56: 28 9.56 - 11.95: 4 Bond angle restraints: 26018 Sorted by residual: angle pdb=" N ASN A1132 " pdb=" CA ASN A1132 " pdb=" C ASN A1132 " ideal model delta sigma weight residual 114.64 106.28 8.36 1.52e+00 4.33e-01 3.03e+01 angle pdb=" N ASN C1132 " pdb=" CA ASN C1132 " pdb=" C ASN C1132 " ideal model delta sigma weight residual 114.64 106.28 8.36 1.52e+00 4.33e-01 3.02e+01 angle pdb=" CA TRP D1177 " pdb=" CB TRP D1177 " pdb=" CG TRP D1177 " ideal model delta sigma weight residual 113.60 122.73 -9.13 1.90e+00 2.77e-01 2.31e+01 angle pdb=" CA TRP B1177 " pdb=" CB TRP B1177 " pdb=" CG TRP B1177 " ideal model delta sigma weight residual 113.60 122.69 -9.09 1.90e+00 2.77e-01 2.29e+01 angle pdb=" CA TYR D1031 " pdb=" CB TYR D1031 " pdb=" CG TYR D1031 " ideal model delta sigma weight residual 113.90 122.46 -8.56 1.80e+00 3.09e-01 2.26e+01 ... (remaining 26013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 10979 24.85 - 49.69: 364 49.69 - 74.54: 19 74.54 - 99.38: 12 99.38 - 124.23: 8 Dihedral angle restraints: 11382 sinusoidal: 4492 harmonic: 6890 Sorted by residual: dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 149.17 -56.17 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 149.15 -56.15 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CA SER B 635 " pdb=" C SER B 635 " pdb=" N ALA B 636 " pdb=" CA ALA B 636 " ideal model delta harmonic sigma weight residual -180.00 -148.50 -31.50 0 5.00e+00 4.00e-02 3.97e+01 ... (remaining 11379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2171 0.058 - 0.116: 600 0.116 - 0.174: 114 0.174 - 0.231: 19 0.231 - 0.289: 10 Chirality restraints: 2914 Sorted by residual: chirality pdb=" CA TYR D1031 " pdb=" N TYR D1031 " pdb=" C TYR D1031 " pdb=" CB TYR D1031 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA TYR B1031 " pdb=" N TYR B1031 " pdb=" C TYR B1031 " pdb=" CB TYR B1031 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C8 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" N2 CYZ A1302 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2911 not shown) Planarity restraints: 3194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1031 " 0.034 2.00e-02 2.50e+03 2.17e-02 9.43e+00 pdb=" CG TYR B1031 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B1031 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B1031 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B1031 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B1031 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B1031 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B1031 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D1031 " 0.033 2.00e-02 2.50e+03 2.15e-02 9.27e+00 pdb=" CG TYR D1031 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D1031 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D1031 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D1031 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D1031 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D1031 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D1031 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 403 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO D 404 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " -0.030 5.00e-02 4.00e+02 ... (remaining 3191 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5531 2.80 - 3.33: 17705 3.33 - 3.85: 30693 3.85 - 4.38: 35960 4.38 - 4.90: 59734 Nonbonded interactions: 149623 Sorted by model distance: nonbonded pdb=" O MET B1009 " pdb=" OG1 THR B1013 " model vdw 2.280 3.040 nonbonded pdb=" O MET D1009 " pdb=" OG1 THR D1013 " model vdw 2.280 3.040 nonbonded pdb=" OG SER A 597 " pdb=" O ALA B 806 " model vdw 2.318 3.040 nonbonded pdb=" OG SER C 597 " pdb=" O ALA D 806 " model vdw 2.342 3.040 nonbonded pdb=" O LEU D 639 " pdb=" OH TYR D 647 " model vdw 2.352 3.040 ... (remaining 149618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 47.180 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.008 0.100 19270 Z= 0.365 Angle : 1.089 11.952 26042 Z= 0.602 Chirality : 0.058 0.289 2914 Planarity : 0.007 0.059 3194 Dihedral : 12.458 124.225 6950 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 0.70 % Allowed : 7.13 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.96 (0.12), residues: 2364 helix: -3.84 (0.07), residues: 1292 sheet: -1.42 (0.40), residues: 148 loop : -2.47 (0.16), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A1032 HIS 0.010 0.002 HIS C1081 PHE 0.028 0.003 PHE A1126 TYR 0.050 0.003 TYR B1031 ARG 0.008 0.001 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.29518 ( 928) hydrogen bonds : angle 9.87166 ( 2718) SS BOND : bond 0.00446 ( 12) SS BOND : angle 2.13398 ( 24) covalent geometry : bond 0.00844 (19258) covalent geometry : angle 1.08751 (26018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 616 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.4899 (tptp) cc_final: 0.4513 (tptt) REVERT: A 533 TYR cc_start: 0.8893 (t80) cc_final: 0.8653 (t80) REVERT: A 671 TRP cc_start: 0.5711 (t-100) cc_final: 0.5496 (t-100) REVERT: A 674 MET cc_start: 0.7170 (mtt) cc_final: 0.6824 (mmp) REVERT: A 748 LEU cc_start: 0.8181 (mp) cc_final: 0.7804 (tt) REVERT: A 811 LEU cc_start: 0.8811 (mm) cc_final: 0.8599 (mt) REVERT: A 1195 LEU cc_start: 0.8691 (tp) cc_final: 0.8384 (tp) REVERT: B 496 MET cc_start: 0.7121 (mtp) cc_final: 0.6580 (mtp) REVERT: B 619 ASN cc_start: 0.5799 (t0) cc_final: 0.5569 (t0) REVERT: B 651 ASP cc_start: 0.7011 (t0) cc_final: 0.6422 (p0) REVERT: B 692 ARG cc_start: 0.5746 (ttt180) cc_final: 0.5437 (ttt180) REVERT: B 720 THR cc_start: 0.7927 (p) cc_final: 0.7657 (p) REVERT: B 811 LEU cc_start: 0.8620 (tt) cc_final: 0.8329 (mt) REVERT: B 1031 TYR cc_start: 0.6025 (p90) cc_final: 0.5658 (p90) REVERT: B 1040 LYS cc_start: 0.6015 (pmtt) cc_final: 0.5610 (tptt) REVERT: B 1187 ILE cc_start: 0.9037 (mt) cc_final: 0.8822 (tt) REVERT: C 601 VAL cc_start: 0.9290 (p) cc_final: 0.9003 (t) REVERT: C 671 TRP cc_start: 0.5490 (t-100) cc_final: 0.4923 (t-100) REVERT: C 693 VAL cc_start: 0.6954 (t) cc_final: 0.6370 (t) REVERT: C 1195 LEU cc_start: 0.8717 (tp) cc_final: 0.8477 (tp) REVERT: D 651 ASP cc_start: 0.7065 (t0) cc_final: 0.6155 (p0) REVERT: D 664 ILE cc_start: 0.7228 (mt) cc_final: 0.6682 (mp) REVERT: D 720 THR cc_start: 0.7873 (p) cc_final: 0.7639 (p) REVERT: D 722 LYS cc_start: 0.7683 (tttt) cc_final: 0.7253 (tttp) REVERT: D 790 SER cc_start: 0.8692 (m) cc_final: 0.8411 (t) REVERT: D 1031 TYR cc_start: 0.5561 (p90) cc_final: 0.4757 (p90) REVERT: D 1040 LYS cc_start: 0.6509 (pmtt) cc_final: 0.6140 (tptt) REVERT: D 1134 ILE cc_start: 0.8348 (mp) cc_final: 0.8053 (mm) REVERT: D 1187 ILE cc_start: 0.9168 (mt) cc_final: 0.8869 (tt) outliers start: 14 outliers final: 1 residues processed: 621 average time/residue: 0.3123 time to fit residues: 290.3304 Evaluate side-chains 330 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 704 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 217 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 791 ASN ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 ASN B 418 ASN B1132 ASN B1206 GLN C 791 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN D 586 GLN D 587 GLN D1131 HIS D1132 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.105424 restraints weight = 41804.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106717 restraints weight = 26603.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.107448 restraints weight = 19484.072| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19270 Z= 0.142 Angle : 0.685 9.231 26042 Z= 0.359 Chirality : 0.043 0.268 2914 Planarity : 0.005 0.046 3194 Dihedral : 9.764 110.014 2704 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 2.69 % Allowed : 14.51 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 2364 helix: -1.12 (0.12), residues: 1322 sheet: -0.99 (0.36), residues: 188 loop : -2.05 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D1177 HIS 0.006 0.001 HIS A1059 PHE 0.028 0.002 PHE A 659 TYR 0.034 0.002 TYR B1031 ARG 0.010 0.001 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.04950 ( 928) hydrogen bonds : angle 5.15058 ( 2718) SS BOND : bond 0.01141 ( 12) SS BOND : angle 3.23614 ( 24) covalent geometry : bond 0.00301 (19258) covalent geometry : angle 0.67870 (26018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 421 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.7890 (mmt) cc_final: 0.7041 (tpp) REVERT: A 674 MET cc_start: 0.7526 (mtt) cc_final: 0.6895 (mmp) REVERT: A 748 LEU cc_start: 0.8276 (mp) cc_final: 0.7954 (tt) REVERT: B 405 TYR cc_start: 0.7462 (m-80) cc_final: 0.7116 (m-80) REVERT: B 651 ASP cc_start: 0.6657 (t0) cc_final: 0.6169 (p0) REVERT: B 714 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7299 (mt0) REVERT: B 799 LEU cc_start: 0.8980 (tp) cc_final: 0.8769 (tt) REVERT: B 811 LEU cc_start: 0.8443 (tt) cc_final: 0.8185 (mt) REVERT: B 1008 GLN cc_start: 0.7124 (pt0) cc_final: 0.6781 (mm-40) REVERT: B 1031 TYR cc_start: 0.5880 (p90) cc_final: 0.5563 (p90) REVERT: B 1040 LYS cc_start: 0.6241 (pmtt) cc_final: 0.5656 (tptt) REVERT: B 1072 PHE cc_start: 0.6820 (m-80) cc_final: 0.5454 (m-80) REVERT: B 1096 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7980 (t80) REVERT: B 1187 ILE cc_start: 0.9181 (mt) cc_final: 0.8949 (tt) REVERT: C 424 TYR cc_start: 0.8275 (t80) cc_final: 0.8035 (t80) REVERT: C 702 TYR cc_start: 0.8346 (t80) cc_final: 0.8119 (t80) REVERT: D 460 TRP cc_start: 0.6701 (m100) cc_final: 0.6397 (m100) REVERT: D 651 ASP cc_start: 0.6851 (t0) cc_final: 0.5886 (p0) REVERT: D 673 TYR cc_start: 0.4647 (t80) cc_final: 0.4336 (t80) REVERT: D 699 LYS cc_start: 0.5415 (mttp) cc_final: 0.4376 (tptt) REVERT: D 790 SER cc_start: 0.8822 (m) cc_final: 0.8602 (t) REVERT: D 1031 TYR cc_start: 0.5142 (p90) cc_final: 0.4741 (p90) REVERT: D 1040 LYS cc_start: 0.6409 (pmtt) cc_final: 0.6138 (tptt) REVERT: D 1096 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7957 (t80) REVERT: D 1134 ILE cc_start: 0.8297 (mp) cc_final: 0.7915 (mm) REVERT: D 1199 MET cc_start: 0.7967 (mtt) cc_final: 0.7544 (mtt) REVERT: D 1204 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.6853 (t-90) outliers start: 54 outliers final: 20 residues processed: 458 average time/residue: 0.2764 time to fit residues: 197.6607 Evaluate side-chains 344 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 321 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 96 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A1204 HIS B 587 GLN B1059 HIS ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.128643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102046 restraints weight = 42916.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.101936 restraints weight = 30481.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102173 restraints weight = 25625.426| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19270 Z= 0.228 Angle : 0.718 10.490 26042 Z= 0.378 Chirality : 0.045 0.362 2914 Planarity : 0.005 0.046 3194 Dihedral : 9.517 109.271 2704 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.26 % Rotamer: Outliers : 4.19 % Allowed : 16.70 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2364 helix: -0.06 (0.14), residues: 1328 sheet: -0.91 (0.37), residues: 188 loop : -1.96 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 460 HIS 0.006 0.001 HIS C1059 PHE 0.019 0.002 PHE D 574 TYR 0.028 0.002 TYR D1031 ARG 0.012 0.001 ARG D 420 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 928) hydrogen bonds : angle 5.03671 ( 2718) SS BOND : bond 0.01099 ( 12) SS BOND : angle 3.60988 ( 24) covalent geometry : bond 0.00523 (19258) covalent geometry : angle 0.71027 (26018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 328 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 ASP cc_start: 0.6058 (m-30) cc_final: 0.5842 (m-30) REVERT: A 674 MET cc_start: 0.7353 (mtt) cc_final: 0.6876 (mmp) REVERT: A 705 GLU cc_start: 0.7699 (mp0) cc_final: 0.6781 (mp0) REVERT: A 748 LEU cc_start: 0.8341 (mp) cc_final: 0.8082 (tt) REVERT: B 651 ASP cc_start: 0.6694 (t0) cc_final: 0.6189 (p0) REVERT: B 799 LEU cc_start: 0.9038 (tp) cc_final: 0.8756 (tt) REVERT: B 1040 LYS cc_start: 0.6501 (pmtt) cc_final: 0.6037 (tptt) REVERT: B 1096 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7908 (t80) REVERT: B 1187 ILE cc_start: 0.9194 (mt) cc_final: 0.8946 (tt) REVERT: B 1191 MET cc_start: 0.8075 (mtp) cc_final: 0.7785 (mtp) REVERT: C 473 ASP cc_start: 0.6122 (m-30) cc_final: 0.5834 (m-30) REVERT: C 674 MET cc_start: 0.6606 (mtp) cc_final: 0.5943 (mmp) REVERT: D 503 MET cc_start: 0.7060 (ttm) cc_final: 0.6733 (ttt) REVERT: D 651 ASP cc_start: 0.6638 (t0) cc_final: 0.5812 (p0) REVERT: D 673 TYR cc_start: 0.4795 (t80) cc_final: 0.4037 (t80) REVERT: D 1031 TYR cc_start: 0.5873 (p90) cc_final: 0.5438 (p90) REVERT: D 1040 LYS cc_start: 0.6493 (pmtt) cc_final: 0.6216 (tptt) REVERT: D 1096 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7712 (t80) REVERT: D 1199 MET cc_start: 0.7740 (mtt) cc_final: 0.7538 (mtt) REVERT: D 1204 HIS cc_start: 0.7096 (OUTLIER) cc_final: 0.6841 (t-90) REVERT: A 1301 GLU cc_start: 0.5774 (tp30) cc_final: 0.5012 (tp30) outliers start: 84 outliers final: 48 residues processed: 392 average time/residue: 0.2653 time to fit residues: 165.7373 Evaluate side-chains 346 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 295 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 741 SER Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1195 LEU Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1177 TRP Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 164 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.128260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100920 restraints weight = 43212.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101970 restraints weight = 28304.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.102367 restraints weight = 21523.969| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 19270 Z= 0.203 Angle : 0.701 12.638 26042 Z= 0.363 Chirality : 0.045 0.314 2914 Planarity : 0.004 0.041 3194 Dihedral : 9.173 106.601 2702 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.26 % Rotamer: Outliers : 4.24 % Allowed : 17.80 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.78 (0.17), residues: 2364 helix: 0.46 (0.14), residues: 1322 sheet: -0.88 (0.38), residues: 188 loop : -1.95 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B1177 HIS 0.021 0.002 HIS A1204 PHE 0.017 0.002 PHE D 574 TYR 0.052 0.002 TYR B1031 ARG 0.004 0.000 ARG A1203 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 928) hydrogen bonds : angle 4.95793 ( 2718) SS BOND : bond 0.00899 ( 12) SS BOND : angle 3.30190 ( 24) covalent geometry : bond 0.00465 (19258) covalent geometry : angle 0.69427 (26018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 328 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 MET cc_start: 0.7245 (mtt) cc_final: 0.6741 (mmp) REVERT: A 748 LEU cc_start: 0.8399 (mp) cc_final: 0.8077 (tt) REVERT: B 651 ASP cc_start: 0.6567 (t0) cc_final: 0.6171 (p0) REVERT: B 670 MET cc_start: 0.7537 (mmm) cc_final: 0.6821 (mpp) REVERT: B 799 LEU cc_start: 0.8989 (tp) cc_final: 0.8755 (tt) REVERT: B 1040 LYS cc_start: 0.6532 (pmtt) cc_final: 0.6043 (tptt) REVERT: B 1096 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7833 (t80) REVERT: B 1136 SER cc_start: 0.8915 (m) cc_final: 0.8674 (t) REVERT: B 1187 ILE cc_start: 0.9199 (mt) cc_final: 0.8919 (tt) REVERT: C 473 ASP cc_start: 0.6054 (m-30) cc_final: 0.5820 (m-30) REVERT: C 674 MET cc_start: 0.6783 (mtp) cc_final: 0.6210 (mmp) REVERT: C 1195 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8812 (mm) REVERT: D 460 TRP cc_start: 0.6858 (m100) cc_final: 0.6189 (m100) REVERT: D 503 MET cc_start: 0.7013 (ttm) cc_final: 0.6736 (ttt) REVERT: D 549 TYR cc_start: 0.4989 (OUTLIER) cc_final: 0.4779 (m-10) REVERT: D 651 ASP cc_start: 0.6579 (t0) cc_final: 0.5924 (p0) REVERT: D 673 TYR cc_start: 0.4863 (t80) cc_final: 0.4055 (t80) REVERT: D 1031 TYR cc_start: 0.5881 (p90) cc_final: 0.5581 (p90) REVERT: D 1040 LYS cc_start: 0.6785 (pmtt) cc_final: 0.6497 (tptt) REVERT: D 1096 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7812 (t80) REVERT: D 1199 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7608 (mtt) outliers start: 85 outliers final: 50 residues processed: 391 average time/residue: 0.2666 time to fit residues: 166.0773 Evaluate side-chains 350 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1195 LEU Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1177 TRP Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1199 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 125 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 216 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: A 791 ASN B 586 GLN C 587 GLN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.128422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102368 restraints weight = 43073.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102729 restraints weight = 28686.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.103156 restraints weight = 23859.346| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19270 Z= 0.188 Angle : 0.687 13.444 26042 Z= 0.353 Chirality : 0.044 0.229 2914 Planarity : 0.004 0.039 3194 Dihedral : 8.990 103.288 2702 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.80 % Rotamer: Outliers : 4.79 % Allowed : 18.69 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.48 (0.17), residues: 2364 helix: 0.76 (0.14), residues: 1320 sheet: -0.93 (0.38), residues: 188 loop : -1.87 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 460 HIS 0.008 0.001 HIS C1059 PHE 0.017 0.002 PHE B1072 TYR 0.049 0.002 TYR B1031 ARG 0.003 0.000 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 928) hydrogen bonds : angle 4.95667 ( 2718) SS BOND : bond 0.00810 ( 12) SS BOND : angle 2.67806 ( 24) covalent geometry : bond 0.00433 (19258) covalent geometry : angle 0.68245 (26018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 314 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 LYS cc_start: 0.4907 (OUTLIER) cc_final: 0.4196 (mmtp) REVERT: A 674 MET cc_start: 0.7165 (mtt) cc_final: 0.6760 (mmp) REVERT: A 711 TYR cc_start: 0.7783 (t80) cc_final: 0.7556 (t80) REVERT: A 748 LEU cc_start: 0.8366 (mp) cc_final: 0.8038 (tt) REVERT: A 1082 PHE cc_start: 0.5726 (p90) cc_final: 0.5412 (p90) REVERT: A 1195 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8606 (mm) REVERT: B 651 ASP cc_start: 0.6530 (t0) cc_final: 0.6276 (p0) REVERT: B 767 TRP cc_start: 0.7336 (OUTLIER) cc_final: 0.6854 (t-100) REVERT: B 1040 LYS cc_start: 0.6538 (pmtt) cc_final: 0.6058 (tptt) REVERT: B 1096 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7790 (t80) REVERT: B 1136 SER cc_start: 0.8935 (m) cc_final: 0.8714 (t) REVERT: B 1177 TRP cc_start: 0.6270 (OUTLIER) cc_final: 0.5048 (m100) REVERT: B 1187 ILE cc_start: 0.9205 (mt) cc_final: 0.8904 (tt) REVERT: C 641 LYS cc_start: 0.4650 (OUTLIER) cc_final: 0.4169 (mmmm) REVERT: C 674 MET cc_start: 0.6821 (mtp) cc_final: 0.6425 (mmp) REVERT: C 1082 PHE cc_start: 0.5640 (p90) cc_final: 0.5348 (p90) REVERT: C 1195 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8852 (mm) REVERT: D 503 MET cc_start: 0.6955 (ttm) cc_final: 0.6633 (ttt) REVERT: D 651 ASP cc_start: 0.6473 (t0) cc_final: 0.5992 (p0) REVERT: D 673 TYR cc_start: 0.4744 (t80) cc_final: 0.3896 (t80) REVERT: D 1031 TYR cc_start: 0.5855 (p90) cc_final: 0.5485 (p90) REVERT: D 1040 LYS cc_start: 0.6739 (pmtt) cc_final: 0.6529 (tptt) REVERT: D 1096 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7733 (t80) REVERT: D 1199 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7640 (mtt) outliers start: 96 outliers final: 58 residues processed: 388 average time/residue: 0.2587 time to fit residues: 160.0828 Evaluate side-chains 362 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 295 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 641 LYS Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1195 LEU Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1120 CYS Chi-restraints excluded: chain D residue 1136 SER Chi-restraints excluded: chain D residue 1177 TRP Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1199 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 198 optimal weight: 0.0170 chunk 230 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 142 optimal weight: 0.0370 chunk 97 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN C 586 GLN C 619 ASN ** C1059 HIS ** 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 = 0.3882 r_free = 0.3882 target = 0.133730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.107612 restraints weight = 43292.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109748 restraints weight = 28750.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110417 restraints weight = 20343.192| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19270 Z= 0.117 Angle : 0.627 9.974 26042 Z= 0.316 Chirality : 0.041 0.166 2914 Planarity : 0.003 0.034 3194 Dihedral : 8.307 94.944 2702 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.57 % Rotamer: Outliers : 3.14 % Allowed : 20.74 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.17), residues: 2364 helix: 1.25 (0.14), residues: 1316 sheet: -0.91 (0.35), residues: 216 loop : -1.74 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 460 HIS 0.008 0.001 HIS C1059 PHE 0.013 0.001 PHE C1115 TYR 0.044 0.001 TYR B1031 ARG 0.003 0.000 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 928) hydrogen bonds : angle 4.59686 ( 2718) SS BOND : bond 0.00515 ( 12) SS BOND : angle 1.79203 ( 24) covalent geometry : bond 0.00244 (19258) covalent geometry : angle 0.62540 (26018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 356 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.4312 (mmm) cc_final: 0.4105 (mmt) REVERT: A 414 MET cc_start: 0.7160 (mmm) cc_final: 0.6612 (mmt) REVERT: A 527 MET cc_start: 0.8331 (ttp) cc_final: 0.7775 (ttm) REVERT: A 585 MET cc_start: 0.8734 (mmt) cc_final: 0.8299 (mpp) REVERT: A 705 GLU cc_start: 0.7508 (mp0) cc_final: 0.7211 (mp0) REVERT: A 711 TYR cc_start: 0.7621 (t80) cc_final: 0.7398 (t80) REVERT: A 1082 PHE cc_start: 0.5832 (p90) cc_final: 0.5551 (p90) REVERT: B 405 TYR cc_start: 0.7626 (m-80) cc_final: 0.7314 (m-80) REVERT: B 508 GLN cc_start: 0.6365 (tm-30) cc_final: 0.5505 (tp40) REVERT: B 1023 MET cc_start: 0.7376 (tpt) cc_final: 0.7142 (tpt) REVERT: B 1040 LYS cc_start: 0.6504 (pmtt) cc_final: 0.6272 (tptt) REVERT: B 1082 PHE cc_start: 0.4115 (m-80) cc_final: 0.3621 (t80) REVERT: B 1096 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7549 (t80) REVERT: B 1136 SER cc_start: 0.8973 (m) cc_final: 0.8719 (t) REVERT: B 1177 TRP cc_start: 0.5547 (OUTLIER) cc_final: 0.5156 (m100) REVERT: B 1187 ILE cc_start: 0.9184 (mt) cc_final: 0.8840 (tt) REVERT: C 431 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6146 (mm-30) REVERT: C 527 MET cc_start: 0.8352 (ttp) cc_final: 0.7802 (ttm) REVERT: C 711 TYR cc_start: 0.7676 (t80) cc_final: 0.7405 (t80) REVERT: C 768 TYR cc_start: 0.6715 (m-80) cc_final: 0.6311 (m-80) REVERT: D 503 MET cc_start: 0.6951 (ttm) cc_final: 0.6666 (ttt) REVERT: D 508 GLN cc_start: 0.6639 (tm-30) cc_final: 0.5545 (tp40) REVERT: D 651 ASP cc_start: 0.6285 (t0) cc_final: 0.5974 (p0) REVERT: D 673 TYR cc_start: 0.4561 (t80) cc_final: 0.3777 (t80) REVERT: D 1024 THR cc_start: 0.8046 (m) cc_final: 0.7761 (p) REVERT: D 1062 LEU cc_start: 0.7846 (mp) cc_final: 0.7554 (mp) REVERT: D 1096 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7573 (t80) REVERT: D 1116 MET cc_start: 0.7671 (mmt) cc_final: 0.7424 (mmm) REVERT: C 1301 GLU cc_start: 0.5964 (tp30) cc_final: 0.4985 (tp30) outliers start: 63 outliers final: 39 residues processed: 398 average time/residue: 0.2723 time to fit residues: 171.2135 Evaluate side-chains 357 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 315 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 1057 MET Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 586 GLN Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1181 PHE Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1197 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 1032 TRP Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 42 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 233 optimal weight: 0.0370 chunk 124 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 714 GLN C 619 ASN ** C1059 HIS ** 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 = 0.3882 r_free = 0.3882 target = 0.133444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.107229 restraints weight = 43174.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.108905 restraints weight = 31484.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.109828 restraints weight = 22555.143| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19270 Z= 0.120 Angle : 0.641 11.667 26042 Z= 0.319 Chirality : 0.041 0.190 2914 Planarity : 0.003 0.049 3194 Dihedral : 8.059 92.050 2702 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 3.49 % Allowed : 21.14 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.22 (0.17), residues: 2364 helix: 1.39 (0.14), residues: 1316 sheet: -0.87 (0.38), residues: 196 loop : -1.61 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 PHE 0.024 0.001 PHE D1072 TYR 0.041 0.001 TYR B1031 ARG 0.006 0.000 ARG B1098 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 928) hydrogen bonds : angle 4.52653 ( 2718) SS BOND : bond 0.00556 ( 12) SS BOND : angle 1.43427 ( 24) covalent geometry : bond 0.00267 (19258) covalent geometry : angle 0.63965 (26018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 336 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.8312 (ttp) cc_final: 0.7801 (ttm) REVERT: A 711 TYR cc_start: 0.7643 (t80) cc_final: 0.7434 (t80) REVERT: A 732 TYR cc_start: 0.7679 (m-10) cc_final: 0.7467 (m-10) REVERT: A 1082 PHE cc_start: 0.5868 (p90) cc_final: 0.5543 (p90) REVERT: B 508 GLN cc_start: 0.6381 (tm-30) cc_final: 0.5568 (tp40) REVERT: B 635 SER cc_start: 0.7540 (m) cc_final: 0.6946 (p) REVERT: B 711 TYR cc_start: 0.6380 (t80) cc_final: 0.5965 (t80) REVERT: B 1040 LYS cc_start: 0.6521 (pmtt) cc_final: 0.6283 (tptt) REVERT: B 1096 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7536 (t80) REVERT: B 1136 SER cc_start: 0.8964 (m) cc_final: 0.8668 (t) REVERT: B 1177 TRP cc_start: 0.5794 (OUTLIER) cc_final: 0.5341 (m100) REVERT: B 1187 ILE cc_start: 0.9161 (mt) cc_final: 0.8801 (tt) REVERT: C 408 MET cc_start: 0.4491 (mmm) cc_final: 0.4066 (mmt) REVERT: C 431 GLU cc_start: 0.6508 (mm-30) cc_final: 0.6087 (mm-30) REVERT: C 527 MET cc_start: 0.8334 (ttp) cc_final: 0.7826 (ttm) REVERT: C 711 TYR cc_start: 0.7712 (t80) cc_final: 0.7462 (t80) REVERT: D 503 MET cc_start: 0.6818 (ttm) cc_final: 0.6534 (ttt) REVERT: D 508 GLN cc_start: 0.6632 (tm-30) cc_final: 0.5534 (tp40) REVERT: D 651 ASP cc_start: 0.6177 (t0) cc_final: 0.5904 (p0) REVERT: D 673 TYR cc_start: 0.4458 (t80) cc_final: 0.3693 (t80) REVERT: D 1024 THR cc_start: 0.7981 (m) cc_final: 0.7749 (p) REVERT: D 1096 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7525 (t80) REVERT: D 1177 TRP cc_start: 0.6034 (t60) cc_final: 0.5090 (m100) outliers start: 70 outliers final: 38 residues processed: 384 average time/residue: 0.2701 time to fit residues: 165.4280 Evaluate side-chains 358 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 317 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 1032 TRP Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 123 optimal weight: 7.9990 chunk 105 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN C 586 GLN C 619 ASN ** C1059 HIS ** 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 = 0.3889 r_free = 0.3889 target = 0.134047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.107520 restraints weight = 43448.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.109648 restraints weight = 29674.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110609 restraints weight = 20892.387| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19270 Z= 0.123 Angle : 0.652 13.665 26042 Z= 0.324 Chirality : 0.041 0.175 2914 Planarity : 0.003 0.033 3194 Dihedral : 7.909 88.706 2702 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 3.24 % Allowed : 21.78 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.31 (0.17), residues: 2364 helix: 1.50 (0.14), residues: 1304 sheet: -0.82 (0.38), residues: 196 loop : -1.60 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 PHE 0.013 0.001 PHE A1115 TYR 0.044 0.001 TYR D1031 ARG 0.004 0.000 ARG C 661 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 928) hydrogen bonds : angle 4.51614 ( 2718) SS BOND : bond 0.00590 ( 12) SS BOND : angle 1.93891 ( 24) covalent geometry : bond 0.00273 (19258) covalent geometry : angle 0.64964 (26018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 339 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.4329 (mmm) cc_final: 0.4110 (mmt) REVERT: A 414 MET cc_start: 0.7175 (mmm) cc_final: 0.6501 (mmt) REVERT: A 483 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7167 (tt) REVERT: A 527 MET cc_start: 0.8342 (ttp) cc_final: 0.7865 (ttm) REVERT: A 711 TYR cc_start: 0.7682 (t80) cc_final: 0.7476 (t80) REVERT: A 1082 PHE cc_start: 0.5892 (p90) cc_final: 0.5593 (p90) REVERT: B 508 GLN cc_start: 0.6441 (tm-30) cc_final: 0.5638 (tp40) REVERT: B 711 TYR cc_start: 0.6384 (t80) cc_final: 0.6019 (t80) REVERT: B 1040 LYS cc_start: 0.6517 (pmtt) cc_final: 0.6311 (tptt) REVERT: B 1096 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7568 (t80) REVERT: B 1136 SER cc_start: 0.8940 (m) cc_final: 0.8687 (t) REVERT: B 1177 TRP cc_start: 0.5785 (OUTLIER) cc_final: 0.5374 (m100) REVERT: C 407 MET cc_start: 0.7699 (mmm) cc_final: 0.7059 (mmm) REVERT: C 408 MET cc_start: 0.4588 (mmm) cc_final: 0.4175 (mmt) REVERT: C 438 PHE cc_start: 0.7314 (p90) cc_final: 0.6382 (p90) REVERT: C 527 MET cc_start: 0.8349 (ttp) cc_final: 0.7869 (ttm) REVERT: C 638 ASP cc_start: 0.7062 (m-30) cc_final: 0.6415 (p0) REVERT: C 711 TYR cc_start: 0.7741 (t80) cc_final: 0.7484 (t80) REVERT: C 768 TYR cc_start: 0.6551 (m-80) cc_final: 0.6050 (m-80) REVERT: D 503 MET cc_start: 0.6883 (ttm) cc_final: 0.6629 (ttt) REVERT: D 508 GLN cc_start: 0.6657 (tm-30) cc_final: 0.5602 (tp40) REVERT: D 651 ASP cc_start: 0.6297 (t0) cc_final: 0.6000 (p0) REVERT: D 673 TYR cc_start: 0.4543 (t80) cc_final: 0.3725 (t80) REVERT: D 1023 MET cc_start: 0.8086 (mmm) cc_final: 0.7813 (mmm) REVERT: D 1024 THR cc_start: 0.8086 (m) cc_final: 0.7882 (p) REVERT: D 1096 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7617 (t80) REVERT: D 1109 LEU cc_start: 0.8752 (tp) cc_final: 0.8544 (mm) REVERT: D 1177 TRP cc_start: 0.5737 (OUTLIER) cc_final: 0.5098 (m100) REVERT: C 1301 GLU cc_start: 0.6217 (tp30) cc_final: 0.5357 (tp30) outliers start: 65 outliers final: 41 residues processed: 383 average time/residue: 0.2691 time to fit residues: 164.6521 Evaluate side-chains 366 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 320 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1181 PHE Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 1032 TRP Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1177 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 218 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN D1059 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.131452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104821 restraints weight = 44111.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.106372 restraints weight = 31654.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106875 restraints weight = 24070.300| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19270 Z= 0.186 Angle : 0.708 13.024 26042 Z= 0.357 Chirality : 0.044 0.342 2914 Planarity : 0.004 0.034 3194 Dihedral : 8.066 92.514 2702 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 3.39 % Allowed : 21.98 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.12 (0.17), residues: 2364 helix: 1.38 (0.14), residues: 1288 sheet: -0.89 (0.37), residues: 204 loop : -1.68 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 PHE 0.020 0.002 PHE A1115 TYR 0.045 0.002 TYR D1031 ARG 0.005 0.000 ARG A1098 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 928) hydrogen bonds : angle 4.69407 ( 2718) SS BOND : bond 0.00597 ( 12) SS BOND : angle 2.46281 ( 24) covalent geometry : bond 0.00432 (19258) covalent geometry : angle 0.70462 (26018) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 315 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7084 (mmm) cc_final: 0.6446 (mmt) REVERT: A 491 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7399 (m-10) REVERT: A 527 MET cc_start: 0.8356 (ttp) cc_final: 0.7865 (ttm) REVERT: A 711 TYR cc_start: 0.7784 (t80) cc_final: 0.7560 (t80) REVERT: A 1082 PHE cc_start: 0.5964 (p90) cc_final: 0.5662 (p90) REVERT: B 405 TYR cc_start: 0.7559 (m-80) cc_final: 0.7298 (m-80) REVERT: B 442 LEU cc_start: 0.8812 (mt) cc_final: 0.8452 (mt) REVERT: B 508 GLN cc_start: 0.6321 (tm-30) cc_final: 0.5420 (tp40) REVERT: B 585 MET cc_start: 0.8496 (mmm) cc_final: 0.8223 (mtp) REVERT: B 711 TYR cc_start: 0.6437 (t80) cc_final: 0.6058 (t80) REVERT: B 1096 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7741 (t80) REVERT: B 1136 SER cc_start: 0.8872 (m) cc_final: 0.8645 (t) REVERT: B 1177 TRP cc_start: 0.6263 (OUTLIER) cc_final: 0.5409 (m100) REVERT: C 438 PHE cc_start: 0.7230 (p90) cc_final: 0.6269 (p90) REVERT: C 527 MET cc_start: 0.8347 (ttp) cc_final: 0.7879 (ttm) REVERT: C 690 VAL cc_start: 0.8706 (t) cc_final: 0.8460 (p) REVERT: D 405 TYR cc_start: 0.7533 (m-80) cc_final: 0.7307 (m-80) REVERT: D 503 MET cc_start: 0.6701 (ttm) cc_final: 0.6433 (ttt) REVERT: D 508 GLN cc_start: 0.6613 (tm-30) cc_final: 0.5491 (tp40) REVERT: D 651 ASP cc_start: 0.6466 (t0) cc_final: 0.6089 (p0) REVERT: D 673 TYR cc_start: 0.4528 (t80) cc_final: 0.3697 (t80) REVERT: D 1024 THR cc_start: 0.8156 (m) cc_final: 0.7909 (p) REVERT: D 1096 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7654 (t80) REVERT: D 1177 TRP cc_start: 0.6229 (OUTLIER) cc_final: 0.5203 (m100) outliers start: 68 outliers final: 47 residues processed: 359 average time/residue: 0.2629 time to fit residues: 156.3555 Evaluate side-chains 354 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1181 PHE Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1136 SER Chi-restraints excluded: chain D residue 1177 TRP Chi-restraints excluded: chain D residue 1198 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 110 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 230 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 27 optimal weight: 0.0060 chunk 126 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1148 ASN C 619 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.133038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108484 restraints weight = 43448.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108233 restraints weight = 32022.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108477 restraints weight = 27551.446| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19270 Z= 0.135 Angle : 0.690 13.601 26042 Z= 0.342 Chirality : 0.043 0.266 2914 Planarity : 0.004 0.034 3194 Dihedral : 7.653 88.260 2702 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 2.74 % Allowed : 22.88 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.26 (0.17), residues: 2364 helix: 1.52 (0.14), residues: 1288 sheet: -1.07 (0.38), residues: 194 loop : -1.60 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 PHE 0.017 0.001 PHE A1115 TYR 0.042 0.001 TYR D1031 ARG 0.009 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 928) hydrogen bonds : angle 4.61181 ( 2718) SS BOND : bond 0.00360 ( 12) SS BOND : angle 2.08576 ( 24) covalent geometry : bond 0.00305 (19258) covalent geometry : angle 0.68751 (26018) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 322 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.4673 (mmm) cc_final: 0.4406 (mmt) REVERT: A 431 GLU cc_start: 0.7839 (tp30) cc_final: 0.7479 (mm-30) REVERT: A 527 MET cc_start: 0.8372 (ttp) cc_final: 0.7885 (ttm) REVERT: A 711 TYR cc_start: 0.7676 (t80) cc_final: 0.7452 (t80) REVERT: A 1082 PHE cc_start: 0.5919 (p90) cc_final: 0.5636 (p90) REVERT: B 508 GLN cc_start: 0.6356 (tm-30) cc_final: 0.5549 (tp40) REVERT: B 585 MET cc_start: 0.8443 (mmm) cc_final: 0.8117 (mtp) REVERT: B 711 TYR cc_start: 0.6354 (t80) cc_final: 0.6001 (t80) REVERT: B 1024 THR cc_start: 0.8019 (m) cc_final: 0.7766 (p) REVERT: B 1096 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7658 (t80) REVERT: B 1136 SER cc_start: 0.8839 (m) cc_final: 0.8600 (t) REVERT: B 1177 TRP cc_start: 0.6080 (OUTLIER) cc_final: 0.5446 (m100) REVERT: C 407 MET cc_start: 0.7886 (mmm) cc_final: 0.7399 (mmm) REVERT: C 438 PHE cc_start: 0.7160 (p90) cc_final: 0.6240 (p90) REVERT: C 527 MET cc_start: 0.8349 (ttp) cc_final: 0.7873 (ttm) REVERT: C 711 TYR cc_start: 0.7725 (t80) cc_final: 0.7485 (t80) REVERT: D 503 MET cc_start: 0.6550 (ttm) cc_final: 0.6264 (ttt) REVERT: D 508 GLN cc_start: 0.6612 (tm-30) cc_final: 0.5573 (tp40) REVERT: D 585 MET cc_start: 0.8372 (mmm) cc_final: 0.7941 (mtp) REVERT: D 651 ASP cc_start: 0.6356 (t0) cc_final: 0.6072 (p0) REVERT: D 673 TYR cc_start: 0.4488 (t80) cc_final: 0.3694 (t80) REVERT: D 1096 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7607 (t80) REVERT: D 1177 TRP cc_start: 0.5881 (OUTLIER) cc_final: 0.5238 (m100) REVERT: C 1301 GLU cc_start: 0.6450 (tp30) cc_final: 0.5662 (tp30) outliers start: 55 outliers final: 41 residues processed: 358 average time/residue: 0.2646 time to fit residues: 154.8782 Evaluate side-chains 352 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 307 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1194 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1181 PHE Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1177 TRP Chi-restraints excluded: chain D residue 1198 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 112 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN B1148 ASN C 619 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1078 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 = 0.3868 r_free = 0.3868 target = 0.132641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.107976 restraints weight = 43799.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107825 restraints weight = 31442.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108030 restraints weight = 27944.838| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19270 Z= 0.144 Angle : 0.702 13.353 26042 Z= 0.345 Chirality : 0.043 0.248 2914 Planarity : 0.004 0.037 3194 Dihedral : 7.309 87.253 2702 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 2.89 % Allowed : 23.13 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.30 (0.17), residues: 2364 helix: 1.55 (0.15), residues: 1288 sheet: -1.07 (0.38), residues: 194 loop : -1.59 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 PHE 0.018 0.001 PHE A1115 TYR 0.041 0.001 TYR D1031 ARG 0.007 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 928) hydrogen bonds : angle 4.60682 ( 2718) SS BOND : bond 0.00456 ( 12) SS BOND : angle 2.22173 ( 24) covalent geometry : bond 0.00332 (19258) covalent geometry : angle 0.69863 (26018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6229.16 seconds wall clock time: 109 minutes 59.20 seconds (6599.20 seconds total)