Starting phenix.real_space_refine on Thu Mar 5 03:47:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnp_26017/03_2026/7tnp_26017.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnp_26017/03_2026/7tnp_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tnp_26017/03_2026/7tnp_26017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnp_26017/03_2026/7tnp_26017.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tnp_26017/03_2026/7tnp_26017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnp_26017/03_2026/7tnp_26017.map" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.79, per 1000 atoms: 0.20 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: 1.42 Conformation dependent library (CDL) restraints added in 713.0 milliseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 0.58 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: 3.03 Time building geometry restraints manager: 1.84 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.780 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- 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 : 4.11 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.008 0.001 ARG B 485 TYR 0.050 0.003 TYR B1031 PHE 0.028 0.003 PHE A1126 TRP 0.030 0.004 TRP A1032 HIS 0.010 0.002 HIS C1081 Details of bonding type rmsd covalent geometry : bond 0.00844 (19258) covalent geometry : angle 1.08751 (26018) SS BOND : bond 0.00446 ( 12) SS BOND : angle 2.13398 ( 24) hydrogen bonds : bond 0.29518 ( 928) hydrogen bonds : angle 9.87166 ( 2718) *********************** 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 : 0.717 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: 0.4579 (tptt) REVERT: A 533 TYR cc_start: 0.8893 (t80) cc_final: 0.8654 (t80) REVERT: A 671 TRP cc_start: 0.5711 (t-100) cc_final: 0.5498 (t-100) REVERT: A 674 MET cc_start: 0.7170 (mtt) cc_final: 0.6825 (mmp) REVERT: A 748 LEU cc_start: 0.8181 (mp) cc_final: 0.7803 (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: 0.6579 (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: 0.6423 (p0) REVERT: B 692 ARG cc_start: 0.5746 (ttt180) cc_final: 0.5439 (ttt180) REVERT: B 720 THR cc_start: 0.7927 (p) cc_final: 0.7661 (p) REVERT: B 811 LEU cc_start: 0.8620 (tt) cc_final: 0.8330 (mt) REVERT: B 1031 TYR cc_start: 0.6025 (p90) cc_final: 0.5633 (p90) REVERT: B 1040 LYS cc_start: 0.6015 (pmtt) cc_final: 0.5611 (tptt) REVERT: B 1187 ILE cc_start: 0.9037 (mt) cc_final: 0.8818 (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: 0.4921 (t-100) REVERT: C 693 VAL cc_start: 0.6954 (t) cc_final: 0.6368 (t) REVERT: C 1195 LEU cc_start: 0.8717 (tp) cc_final: 0.8478 (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: 0.7640 (p) REVERT: D 722 LYS cc_start: 0.7683 (tttt) cc_final: 0.7252 (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: 0.6139 (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: 0.1357 time to fit residues: 128.2354 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 : 0.505 ------------------------------------------------------------------------------- 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 216 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.132995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105407 restraints weight = 41818.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106669 restraints weight = 26796.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107431 restraints weight = 20025.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.108057 restraints weight = 18180.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108103 restraints weight = 16568.011| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 19270 Z= 0.150 Angle : 0.693 9.286 26042 Z= 0.362 Chirality : 0.044 0.296 2914 Planarity : 0.005 0.047 3194 Dihedral : 9.841 110.872 2704 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 2.64 % Allowed : 14.61 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.15), residues: 2364 helix: -1.17 (0.12), residues: 1322 sheet: -1.01 (0.36), residues: 188 loop : -2.06 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 453 TYR 0.033 0.002 TYR B1031 PHE 0.027 0.002 PHE A 659 TRP 0.027 0.001 TRP D1177 HIS 0.006 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00330 (19258) covalent geometry : angle 0.68678 (26018) SS BOND : bond 0.00978 ( 12) SS BOND : angle 3.11898 ( 24) hydrogen bonds : bond 0.05161 ( 928) hydrogen bonds : angle 5.20134 ( 2718) *********************** 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 470 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 417 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.7861 (mmt) cc_final: 0.7348 (tpp) REVERT: A 674 MET cc_start: 0.7483 (mtt) cc_final: 0.7001 (mmp) REVERT: A 748 LEU cc_start: 0.8284 (mp) cc_final: 0.7978 (tt) REVERT: A 773 CYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5174 (m) REVERT: B 405 TYR cc_start: 0.7494 (m-80) cc_final: 0.7140 (m-80) REVERT: B 651 ASP cc_start: 0.6642 (t0) cc_final: 0.6159 (p0) REVERT: B 811 LEU cc_start: 0.8436 (tt) cc_final: 0.8179 (mt) REVERT: B 1008 GLN cc_start: 0.7121 (pt0) cc_final: 0.6712 (mm-40) REVERT: B 1031 TYR cc_start: 0.5822 (p90) cc_final: 0.4882 (p90) REVERT: B 1040 LYS cc_start: 0.6257 (pmtt) cc_final: 0.5661 (tptt) REVERT: B 1072 PHE cc_start: 0.6767 (m-80) cc_final: 0.5411 (m-80) REVERT: B 1096 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7992 (t80) REVERT: B 1177 TRP cc_start: 0.5559 (t60) cc_final: 0.4804 (t60) REVERT: B 1187 ILE cc_start: 0.9181 (mt) cc_final: 0.8948 (tt) REVERT: C 424 TYR cc_start: 0.8302 (t80) cc_final: 0.8065 (t80) REVERT: C 671 TRP cc_start: 0.5386 (t-100) cc_final: 0.5137 (t-100) REVERT: D 651 ASP cc_start: 0.6851 (t0) cc_final: 0.5891 (p0) REVERT: D 673 TYR cc_start: 0.4637 (t80) cc_final: 0.4325 (t80) REVERT: D 699 LYS cc_start: 0.5416 (mttp) cc_final: 0.4293 (tptm) REVERT: D 790 SER cc_start: 0.8814 (m) cc_final: 0.8594 (t) REVERT: D 1031 TYR cc_start: 0.5118 (p90) cc_final: 0.4750 (p90) REVERT: D 1040 LYS cc_start: 0.6384 (pmtt) cc_final: 0.6134 (tptt) REVERT: D 1096 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7959 (t80) REVERT: D 1134 ILE cc_start: 0.8335 (mp) cc_final: 0.7955 (mm) REVERT: D 1204 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6878 (t-90) outliers start: 53 outliers final: 18 residues processed: 452 average time/residue: 0.1220 time to fit residues: 87.3057 Evaluate side-chains 337 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 315 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 B residue 1133 ILE Chi-restraints excluded: chain C residue 454 ASP 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 1204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** 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 = 0.3849 r_free = 0.3849 target = 0.131639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103980 restraints weight = 42768.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.105230 restraints weight = 27696.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.106170 restraints weight = 20432.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106650 restraints weight = 19042.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.106696 restraints weight = 17118.666| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19270 Z= 0.148 Angle : 0.653 10.933 26042 Z= 0.340 Chirality : 0.042 0.314 2914 Planarity : 0.004 0.048 3194 Dihedral : 9.152 105.465 2704 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 3.74 % Allowed : 16.20 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2364 helix: 0.12 (0.14), residues: 1324 sheet: -0.73 (0.38), residues: 188 loop : -1.89 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 675 TYR 0.026 0.001 TYR D1031 PHE 0.016 0.001 PHE B 495 TRP 0.016 0.001 TRP B1177 HIS 0.006 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00329 (19258) covalent geometry : angle 0.64334 (26018) SS BOND : bond 0.01139 ( 12) SS BOND : angle 3.69912 ( 24) hydrogen bonds : bond 0.04294 ( 928) hydrogen bonds : angle 4.80632 ( 2718) *********************** 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 431 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 356 time to evaluate : 0.594 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: 0.7363 (mtt) cc_final: 0.7007 (mmp) REVERT: A 702 TYR cc_start: 0.8500 (t80) cc_final: 0.8245 (t80) REVERT: A 748 LEU cc_start: 0.8344 (mp) cc_final: 0.8118 (tt) REVERT: B 408 MET cc_start: 0.4968 (pmm) cc_final: 0.4714 (pmm) REVERT: B 508 GLN cc_start: 0.6547 (tm-30) cc_final: 0.5447 (pm20) REVERT: B 651 ASP cc_start: 0.6606 (t0) cc_final: 0.6184 (p0) REVERT: B 670 MET cc_start: 0.7409 (mmm) cc_final: 0.6750 (mpp) REVERT: B 811 LEU cc_start: 0.8486 (tt) cc_final: 0.8238 (mt) REVERT: B 1040 LYS cc_start: 0.6428 (pmtt) cc_final: 0.5892 (tptt) REVERT: B 1096 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7939 (t80) REVERT: B 1177 TRP cc_start: 0.5424 (t60) cc_final: 0.4329 (t-100) REVERT: B 1187 ILE cc_start: 0.9204 (mt) cc_final: 0.8943 (tt) REVERT: B 1191 MET cc_start: 0.8191 (mtp) cc_final: 0.7979 (mtp) REVERT: C 431 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6382 (mm-30) REVERT: C 458 LYS cc_start: 0.5456 (tptp) cc_final: 0.4845 (tttp) REVERT: C 473 ASP cc_start: 0.5876 (m-30) cc_final: 0.5598 (m-30) REVERT: C 674 MET cc_start: 0.6741 (mtp) cc_final: 0.6129 (mmp) REVERT: D 405 TYR cc_start: 0.7989 (m-80) cc_final: 0.7764 (m-80) REVERT: D 503 MET cc_start: 0.7240 (ttm) cc_final: 0.6929 (ttt) REVERT: D 508 GLN cc_start: 0.6638 (tm-30) cc_final: 0.5570 (tp40) REVERT: D 549 TYR cc_start: 0.4683 (m-10) cc_final: 0.4298 (m-10) REVERT: D 651 ASP cc_start: 0.6656 (t0) cc_final: 0.5799 (p0) REVERT: D 673 TYR cc_start: 0.4758 (t80) cc_final: 0.4077 (t80) REVERT: D 797 TYR cc_start: 0.8927 (m-80) cc_final: 0.8646 (m-80) REVERT: D 1031 TYR cc_start: 0.5584 (p90) cc_final: 0.5280 (p90) REVERT: D 1040 LYS cc_start: 0.6525 (pmtt) cc_final: 0.6311 (tptt) REVERT: D 1096 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7860 (t80) outliers start: 75 outliers final: 35 residues processed: 410 average time/residue: 0.1176 time to fit residues: 77.6853 Evaluate side-chains 351 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 314 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 773 CYS 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 1129 THR 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 643 THR 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 1204 HIS Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1129 THR 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 1032 TRP Chi-restraints excluded: chain D residue 1057 MET 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 1154 VAL Chi-restraints excluded: chain D residue 1184 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 191 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 D1204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.131990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105949 restraints weight = 43026.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106365 restraints weight = 31293.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106747 restraints weight = 24850.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107113 restraints weight = 22001.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.107403 restraints weight = 20920.058| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19270 Z= 0.143 Angle : 0.655 12.551 26042 Z= 0.335 Chirality : 0.043 0.332 2914 Planarity : 0.004 0.040 3194 Dihedral : 8.757 102.241 2702 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 4.09 % Allowed : 17.25 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2364 helix: 0.75 (0.14), residues: 1314 sheet: -0.67 (0.37), residues: 202 loop : -1.81 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 453 TYR 0.048 0.001 TYR B1031 PHE 0.015 0.001 PHE B1072 TRP 0.017 0.001 TRP C 460 HIS 0.017 0.002 HIS A1204 Details of bonding type rmsd covalent geometry : bond 0.00319 (19258) covalent geometry : angle 0.64892 (26018) SS BOND : bond 0.01078 ( 12) SS BOND : angle 3.01423 ( 24) hydrogen bonds : bond 0.03851 ( 928) hydrogen bonds : angle 4.71619 ( 2718) *********************** 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 422 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 340 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.8405 (ttp) cc_final: 0.7839 (ttm) REVERT: A 748 LEU cc_start: 0.8280 (mp) cc_final: 0.7981 (tt) REVERT: A 1195 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8532 (mm) REVERT: B 651 ASP cc_start: 0.6480 (t0) cc_final: 0.6176 (p0) REVERT: B 670 MET cc_start: 0.7608 (mmm) cc_final: 0.6938 (mpp) REVERT: B 1040 LYS cc_start: 0.6432 (pmtt) cc_final: 0.6039 (tptt) REVERT: B 1096 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7737 (t80) REVERT: B 1136 SER cc_start: 0.8860 (m) cc_final: 0.8572 (t) REVERT: B 1187 ILE cc_start: 0.9208 (mt) cc_final: 0.8870 (tt) REVERT: C 473 ASP cc_start: 0.5509 (m-30) cc_final: 0.5285 (m-30) REVERT: C 527 MET cc_start: 0.8439 (ttp) cc_final: 0.7889 (ttm) REVERT: C 674 MET cc_start: 0.6640 (mtp) cc_final: 0.6167 (mmp) REVERT: D 503 MET cc_start: 0.7054 (ttm) cc_final: 0.6818 (ttt) REVERT: D 651 ASP cc_start: 0.6475 (t0) cc_final: 0.5823 (p0) REVERT: D 673 TYR cc_start: 0.4714 (t80) cc_final: 0.3951 (t80) REVERT: D 1096 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7739 (t80) outliers start: 82 outliers final: 46 residues processed: 394 average time/residue: 0.1147 time to fit residues: 73.0092 Evaluate side-chains 348 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU 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 693 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1129 THR 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 710 GLU Chi-restraints excluded: chain B residue 723 VAL 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 422 GLU Chi-restraints excluded: chain C residue 454 ASP 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 1104 SER Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 1032 TRP Chi-restraints excluded: chain D residue 1065 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 26 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 204 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.131425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.105069 restraints weight = 42622.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.106178 restraints weight = 29095.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106523 restraints weight = 22372.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106904 restraints weight = 20698.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106982 restraints weight = 19739.509| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19270 Z= 0.151 Angle : 0.652 11.727 26042 Z= 0.333 Chirality : 0.043 0.279 2914 Planarity : 0.004 0.062 3194 Dihedral : 8.617 99.704 2702 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 3.79 % Allowed : 18.94 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2364 helix: 1.04 (0.14), residues: 1318 sheet: -0.80 (0.38), residues: 194 loop : -1.79 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 453 TYR 0.048 0.002 TYR D1031 PHE 0.015 0.001 PHE C1115 TRP 0.014 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00344 (19258) covalent geometry : angle 0.64834 (26018) SS BOND : bond 0.00865 ( 12) SS BOND : angle 2.45274 ( 24) hydrogen bonds : bond 0.03765 ( 928) hydrogen bonds : angle 4.71517 ( 2718) *********************** 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 408 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 332 time to evaluate : 0.778 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 414 MET cc_start: 0.7175 (mmm) cc_final: 0.6661 (mmt) REVERT: A 527 MET cc_start: 0.8375 (ttp) cc_final: 0.7884 (ttm) REVERT: A 748 LEU cc_start: 0.8119 (mp) cc_final: 0.7847 (tt) REVERT: A 1195 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8562 (mm) REVERT: B 508 GLN cc_start: 0.6423 (tm-30) cc_final: 0.5518 (tp40) REVERT: B 651 ASP cc_start: 0.6455 (t0) cc_final: 0.6203 (p0) REVERT: B 1040 LYS cc_start: 0.6531 (pmtt) cc_final: 0.6145 (tptt) REVERT: B 1096 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7711 (t80) REVERT: B 1136 SER cc_start: 0.8882 (m) cc_final: 0.8626 (t) REVERT: B 1187 ILE cc_start: 0.9203 (mt) cc_final: 0.8910 (tt) REVERT: C 408 MET cc_start: 0.4550 (mmm) cc_final: 0.4150 (mmt) REVERT: C 527 MET cc_start: 0.8405 (ttp) cc_final: 0.7921 (ttm) REVERT: C 670 MET cc_start: 0.6464 (mmt) cc_final: 0.6008 (mmt) REVERT: C 674 MET cc_start: 0.6623 (mtp) cc_final: 0.6391 (mmp) REVERT: D 503 MET cc_start: 0.6948 (ttm) cc_final: 0.6660 (ttt) REVERT: D 508 GLN cc_start: 0.6628 (tm-30) cc_final: 0.5580 (tp40) REVERT: D 651 ASP cc_start: 0.6382 (t0) cc_final: 0.5928 (p0) REVERT: D 673 TYR cc_start: 0.4674 (t80) cc_final: 0.3830 (t80) REVERT: D 1096 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7560 (t80) REVERT: D 1177 TRP cc_start: 0.6134 (OUTLIER) cc_final: 0.5034 (m100) outliers start: 76 outliers final: 47 residues processed: 383 average time/residue: 0.1123 time to fit residues: 69.4900 Evaluate side-chains 358 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 773 CYS 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 1114 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1129 THR 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 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 723 VAL 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 422 GLU Chi-restraints excluded: chain C residue 454 ASP 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 708 MET 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 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 527 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 168 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 135 optimal weight: 0.0970 chunk 209 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 186 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3882 r_free = 0.3882 target = 0.133878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108004 restraints weight = 43494.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.109827 restraints weight = 32875.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110622 restraints weight = 23851.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110664 restraints weight = 22053.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110715 restraints weight = 20895.344| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19270 Z= 0.116 Angle : 0.621 11.182 26042 Z= 0.313 Chirality : 0.041 0.180 2914 Planarity : 0.004 0.050 3194 Dihedral : 8.274 94.921 2702 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.36 % Rotamer: Outliers : 3.39 % Allowed : 19.99 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.17), residues: 2364 helix: 1.33 (0.14), residues: 1320 sheet: -0.87 (0.39), residues: 184 loop : -1.64 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 453 TYR 0.045 0.001 TYR D1031 PHE 0.012 0.001 PHE C1115 TRP 0.015 0.001 TRP C 460 HIS 0.008 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00248 (19258) covalent geometry : angle 0.61859 (26018) SS BOND : bond 0.00926 ( 12) SS BOND : angle 2.05720 ( 24) hydrogen bonds : bond 0.03491 ( 928) hydrogen bonds : angle 4.56752 ( 2718) *********************** 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 413 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 345 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7257 (m-10) REVERT: A 527 MET cc_start: 0.8259 (ttp) cc_final: 0.7829 (ttm) REVERT: A 1082 PHE cc_start: 0.5700 (p90) cc_final: 0.5363 (p90) REVERT: B 503 MET cc_start: 0.6489 (ttm) cc_final: 0.6077 (ttt) REVERT: B 508 GLN cc_start: 0.6381 (tm-30) cc_final: 0.5507 (tp40) REVERT: B 722 LYS cc_start: 0.7292 (tttp) cc_final: 0.7070 (tttp) REVERT: B 1040 LYS cc_start: 0.6462 (pmtt) cc_final: 0.6185 (tptt) REVERT: B 1096 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7508 (t80) REVERT: B 1136 SER cc_start: 0.8876 (m) cc_final: 0.8636 (t) REVERT: B 1187 ILE cc_start: 0.9169 (mt) cc_final: 0.8833 (tt) REVERT: C 527 MET cc_start: 0.8301 (ttp) cc_final: 0.7866 (ttm) REVERT: C 670 MET cc_start: 0.6339 (mmt) cc_final: 0.5890 (mmm) REVERT: D 503 MET cc_start: 0.6916 (ttm) cc_final: 0.6492 (ttt) REVERT: D 508 GLN cc_start: 0.6600 (tm-30) cc_final: 0.5537 (tp40) REVERT: D 597 SER cc_start: 0.9100 (p) cc_final: 0.8858 (p) REVERT: D 651 ASP cc_start: 0.6249 (t0) cc_final: 0.5927 (p0) REVERT: D 673 TYR cc_start: 0.4548 (t80) cc_final: 0.3628 (t80) REVERT: D 674 MET cc_start: 0.6396 (ttm) cc_final: 0.6156 (ttm) REVERT: D 732 TYR cc_start: 0.6889 (m-10) cc_final: 0.6672 (m-80) REVERT: D 1031 TYR cc_start: 0.5273 (p90) cc_final: 0.4816 (p90) REVERT: D 1096 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7571 (t80) REVERT: D 1177 TRP cc_start: 0.5846 (OUTLIER) cc_final: 0.4913 (m100) outliers start: 68 outliers final: 40 residues processed: 393 average time/residue: 0.1155 time to fit residues: 73.1891 Evaluate side-chains 357 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 313 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 491 PHE 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 773 CYS Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1129 THR 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 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 723 VAL 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 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE 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 521 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 1105 ILE 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 720 THR Chi-restraints excluded: chain D residue 1032 TRP Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1177 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 159 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 200 optimal weight: 0.0670 chunk 184 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN A1204 HIS B 586 GLN C 587 GLN ** 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 = 0.3895 r_free = 0.3895 target = 0.134635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.108863 restraints weight = 43229.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110339 restraints weight = 28533.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110522 restraints weight = 22395.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.110876 restraints weight = 21833.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110956 restraints weight = 20236.786| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4791 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= 0.115 Angle : 0.620 12.452 26042 Z= 0.309 Chirality : 0.041 0.222 2914 Planarity : 0.003 0.044 3194 Dihedral : 7.963 91.521 2702 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 3.64 % Allowed : 20.09 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2364 helix: 1.52 (0.14), residues: 1308 sheet: -0.82 (0.42), residues: 156 loop : -1.57 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 453 TYR 0.041 0.001 TYR D1031 PHE 0.023 0.001 PHE B1072 TRP 0.017 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00251 (19258) covalent geometry : angle 0.61925 (26018) SS BOND : bond 0.00424 ( 12) SS BOND : angle 1.42532 ( 24) hydrogen bonds : bond 0.03394 ( 928) hydrogen bonds : angle 4.47784 ( 2718) *********************** 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 416 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 343 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7210 (mmm) cc_final: 0.6605 (mmt) REVERT: A 483 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7051 (tt) REVERT: A 491 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: A 527 MET cc_start: 0.8343 (ttp) cc_final: 0.7960 (ttm) REVERT: A 1082 PHE cc_start: 0.5684 (p90) cc_final: 0.5353 (p90) REVERT: B 508 GLN cc_start: 0.6393 (tm-30) cc_final: 0.5607 (tp40) REVERT: B 1040 LYS cc_start: 0.6415 (pmtt) cc_final: 0.6215 (tptt) REVERT: B 1096 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7484 (t80) REVERT: B 1136 SER cc_start: 0.8929 (m) cc_final: 0.8693 (t) REVERT: B 1187 ILE cc_start: 0.9166 (mt) cc_final: 0.8825 (tt) REVERT: C 408 MET cc_start: 0.4661 (mmm) cc_final: 0.4306 (mmt) REVERT: C 527 MET cc_start: 0.8378 (ttp) cc_final: 0.7962 (ttm) REVERT: D 405 TYR cc_start: 0.7565 (m-80) cc_final: 0.7182 (m-80) REVERT: D 503 MET cc_start: 0.6842 (ttm) cc_final: 0.6595 (ttt) REVERT: D 508 GLN cc_start: 0.6583 (tm-30) cc_final: 0.5541 (tp40) REVERT: D 651 ASP cc_start: 0.6304 (t0) cc_final: 0.6038 (p0) REVERT: D 673 TYR cc_start: 0.4628 (t80) cc_final: 0.3696 (t80) REVERT: D 674 MET cc_start: 0.6420 (ttm) cc_final: 0.6203 (ttm) REVERT: D 1031 TYR cc_start: 0.5284 (p90) cc_final: 0.4917 (p90) REVERT: D 1096 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7549 (t80) REVERT: D 1177 TRP cc_start: 0.5917 (OUTLIER) cc_final: 0.4997 (m100) outliers start: 73 outliers final: 40 residues processed: 397 average time/residue: 0.1162 time to fit residues: 73.7544 Evaluate side-chains 364 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 319 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 491 PHE 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 1065 THR Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1129 THR 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 525 ILE 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 723 VAL Chi-restraints excluded: chain B residue 1057 MET 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 521 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 1105 ILE 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 720 THR Chi-restraints excluded: chain D residue 1032 TRP Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 201 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN B 714 GLN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.133220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.107678 restraints weight = 43671.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.108440 restraints weight = 31779.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108857 restraints weight = 26435.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.109273 restraints weight = 22575.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.109355 restraints weight = 21883.355| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19270 Z= 0.151 Angle : 0.660 13.200 26042 Z= 0.331 Chirality : 0.042 0.247 2914 Planarity : 0.004 0.040 3194 Dihedral : 7.977 93.058 2702 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 3.39 % Allowed : 20.64 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.17), residues: 2364 helix: 1.47 (0.14), residues: 1318 sheet: -0.89 (0.43), residues: 152 loop : -1.57 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 453 TYR 0.039 0.002 TYR D1031 PHE 0.013 0.001 PHE A1115 TRP 0.019 0.001 TRP C 460 HIS 0.014 0.001 HIS A1204 Details of bonding type rmsd covalent geometry : bond 0.00347 (19258) covalent geometry : angle 0.65708 (26018) SS BOND : bond 0.00460 ( 12) SS BOND : angle 2.06515 ( 24) hydrogen bonds : bond 0.03553 ( 928) hydrogen bonds : angle 4.56317 ( 2718) *********************** 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 386 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 318 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7176 (mmm) cc_final: 0.6630 (mmt) REVERT: A 491 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7351 (m-10) REVERT: A 527 MET cc_start: 0.8366 (ttp) cc_final: 0.7945 (ttm) REVERT: A 1082 PHE cc_start: 0.5748 (p90) cc_final: 0.5397 (p90) REVERT: B 508 GLN cc_start: 0.6390 (tm-30) cc_final: 0.5540 (tp40) REVERT: B 585 MET cc_start: 0.8477 (mmm) cc_final: 0.8272 (mtp) REVERT: B 767 TRP cc_start: 0.7654 (OUTLIER) cc_final: 0.7450 (t-100) REVERT: B 1040 LYS cc_start: 0.6491 (pmtt) cc_final: 0.6229 (tptt) REVERT: B 1096 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7637 (t80) REVERT: B 1136 SER cc_start: 0.8922 (m) cc_final: 0.8691 (t) REVERT: B 1187 ILE cc_start: 0.9163 (mt) cc_final: 0.8816 (tt) REVERT: C 408 MET cc_start: 0.4604 (mmm) cc_final: 0.4184 (mmt) REVERT: C 527 MET cc_start: 0.8362 (ttp) cc_final: 0.7946 (ttm) REVERT: C 674 MET cc_start: 0.7063 (mtp) cc_final: 0.6697 (mmp) REVERT: D 503 MET cc_start: 0.6630 (ttm) cc_final: 0.6398 (ttt) REVERT: D 508 GLN cc_start: 0.6592 (tm-30) cc_final: 0.5571 (tp40) REVERT: D 651 ASP cc_start: 0.6281 (t0) cc_final: 0.6047 (p0) REVERT: D 673 TYR cc_start: 0.4612 (t80) cc_final: 0.3727 (t80) REVERT: D 674 MET cc_start: 0.6438 (ttm) cc_final: 0.6215 (ttm) REVERT: D 1031 TYR cc_start: 0.5338 (p90) cc_final: 0.4992 (p90) REVERT: D 1096 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7571 (t80) REVERT: D 1177 TRP cc_start: 0.6163 (OUTLIER) cc_final: 0.5031 (m100) outliers start: 68 outliers final: 44 residues processed: 370 average time/residue: 0.1123 time to fit residues: 67.7426 Evaluate side-chains 353 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 304 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 VAL 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 1065 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1129 THR 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 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 723 VAL Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1027 VAL Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1068 LEU 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 1191 MET Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1119 LEU 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 720 THR Chi-restraints excluded: chain D residue 1065 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 108 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 228 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN B1059 HIS ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.133605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108328 restraints weight = 43637.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108697 restraints weight = 27808.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.109114 restraints weight = 22844.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109533 restraints weight = 22165.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.109647 restraints weight = 20136.837| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19270 Z= 0.136 Angle : 0.674 13.636 26042 Z= 0.334 Chirality : 0.042 0.247 2914 Planarity : 0.003 0.039 3194 Dihedral : 7.805 91.087 2702 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 3.24 % Allowed : 20.74 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2364 helix: 1.52 (0.14), residues: 1314 sheet: -0.92 (0.43), residues: 152 loop : -1.55 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 453 TYR 0.037 0.001 TYR D1031 PHE 0.018 0.001 PHE A1115 TRP 0.019 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00311 (19258) covalent geometry : angle 0.66916 (26018) SS BOND : bond 0.00502 ( 12) SS BOND : angle 2.72785 ( 24) hydrogen bonds : bond 0.03499 ( 928) hydrogen bonds : angle 4.54456 ( 2718) *********************** 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 389 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 324 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7252 (mmm) cc_final: 0.6715 (mmt) REVERT: A 491 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7295 (m-10) REVERT: A 527 MET cc_start: 0.8345 (ttp) cc_final: 0.7946 (ttm) REVERT: A 1082 PHE cc_start: 0.5693 (p90) cc_final: 0.5378 (p90) REVERT: B 508 GLN cc_start: 0.6393 (tm-30) cc_final: 0.5579 (tp40) REVERT: B 1040 LYS cc_start: 0.6491 (pmtt) cc_final: 0.6278 (tptt) REVERT: B 1082 PHE cc_start: 0.4237 (m-80) cc_final: 0.3671 (t80) REVERT: B 1096 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7673 (t80) REVERT: B 1136 SER cc_start: 0.8899 (m) cc_final: 0.8694 (t) REVERT: C 438 PHE cc_start: 0.7200 (p90) cc_final: 0.6291 (p90) REVERT: C 527 MET cc_start: 0.8380 (ttp) cc_final: 0.7948 (ttm) REVERT: C 674 MET cc_start: 0.7123 (mtp) cc_final: 0.6779 (mmp) REVERT: D 405 TYR cc_start: 0.7570 (m-80) cc_final: 0.7167 (m-80) REVERT: D 503 MET cc_start: 0.6570 (ttm) cc_final: 0.6272 (ttt) REVERT: D 508 GLN cc_start: 0.6580 (tm-30) cc_final: 0.5580 (tp40) REVERT: D 651 ASP cc_start: 0.6544 (t0) cc_final: 0.6253 (p0) REVERT: D 673 TYR cc_start: 0.4658 (t80) cc_final: 0.3777 (t80) REVERT: D 674 MET cc_start: 0.6493 (ttm) cc_final: 0.6284 (ttm) REVERT: D 1031 TYR cc_start: 0.5214 (p90) cc_final: 0.4985 (p90) REVERT: D 1096 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7673 (t80) REVERT: D 1177 TRP cc_start: 0.6105 (OUTLIER) cc_final: 0.5018 (m100) outliers start: 65 outliers final: 48 residues processed: 373 average time/residue: 0.1147 time to fit residues: 69.4871 Evaluate side-chains 365 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 313 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 VAL 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 1065 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1129 THR 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 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 1027 VAL Chi-restraints excluded: chain B residue 1057 MET Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1068 LEU 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 1191 MET Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1119 LEU 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 720 THR 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 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU 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 34 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 198 optimal weight: 0.0040 chunk 79 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.132120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106155 restraints weight = 43710.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107642 restraints weight = 33261.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108132 restraints weight = 26168.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.108184 restraints weight = 24363.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108270 restraints weight = 22763.424| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5074 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= 0.166 Angle : 0.697 13.262 26042 Z= 0.347 Chirality : 0.043 0.251 2914 Planarity : 0.004 0.055 3194 Dihedral : 7.582 91.984 2702 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 2.69 % Allowed : 21.44 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2364 helix: 1.42 (0.14), residues: 1314 sheet: -1.02 (0.39), residues: 182 loop : -1.52 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1098 TYR 0.038 0.002 TYR D1031 PHE 0.018 0.002 PHE A1115 TRP 0.018 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00387 (19258) covalent geometry : angle 0.69380 (26018) SS BOND : bond 0.00377 ( 12) SS BOND : angle 2.40116 ( 24) hydrogen bonds : bond 0.03636 ( 928) hydrogen bonds : angle 4.65006 ( 2718) ********************** 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 375 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 321 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7229 (m-10) REVERT: A 527 MET cc_start: 0.8281 (ttp) cc_final: 0.7875 (ttm) REVERT: B 412 HIS cc_start: 0.7306 (p90) cc_final: 0.6837 (t70) REVERT: B 711 TYR cc_start: 0.6524 (t80) cc_final: 0.6185 (t80) REVERT: B 1096 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7643 (t80) REVERT: B 1136 SER cc_start: 0.8858 (m) cc_final: 0.8651 (t) REVERT: C 438 PHE cc_start: 0.7100 (p90) cc_final: 0.6213 (p90) REVERT: C 527 MET cc_start: 0.8295 (ttp) cc_final: 0.7901 (ttm) REVERT: C 674 MET cc_start: 0.7052 (mtp) cc_final: 0.6712 (mmp) REVERT: C 690 VAL cc_start: 0.8698 (t) cc_final: 0.8452 (p) REVERT: D 405 TYR cc_start: 0.7444 (m-80) cc_final: 0.7194 (m-80) REVERT: D 651 ASP cc_start: 0.6341 (t0) cc_final: 0.6088 (p0) REVERT: D 670 MET cc_start: 0.7388 (mmm) cc_final: 0.6714 (mmt) REVERT: D 673 TYR cc_start: 0.4556 (t80) cc_final: 0.3638 (t80) REVERT: D 1096 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7625 (t80) REVERT: D 1177 TRP cc_start: 0.6323 (OUTLIER) cc_final: 0.5083 (m100) outliers start: 54 outliers final: 47 residues processed: 358 average time/residue: 0.1097 time to fit residues: 64.1811 Evaluate side-chains 355 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 304 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 519 ASP 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 1065 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1129 THR 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 693 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 1057 MET 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 1191 MET Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1119 LEU 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 720 THR Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU 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 148 optimal weight: 4.9990 chunk 62 optimal weight: 0.0030 chunk 151 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN D1078 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.130779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104243 restraints weight = 44288.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106111 restraints weight = 32256.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106438 restraints weight = 23197.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106745 restraints weight = 22179.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.106792 restraints weight = 20996.107| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19270 Z= 0.200 Angle : 0.736 12.678 26042 Z= 0.369 Chirality : 0.045 0.253 2914 Planarity : 0.004 0.040 3194 Dihedral : 7.356 92.860 2702 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.80 % Rotamer: Outliers : 2.79 % Allowed : 21.54 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2364 helix: 1.25 (0.14), residues: 1308 sheet: -1.03 (0.38), residues: 188 loop : -1.57 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 453 TYR 0.044 0.002 TYR D1031 PHE 0.020 0.002 PHE D1115 TRP 0.026 0.001 TRP D 671 HIS 0.007 0.001 HIS C1059 Details of bonding type rmsd covalent geometry : bond 0.00467 (19258) covalent geometry : angle 0.73339 (26018) SS BOND : bond 0.00363 ( 12) SS BOND : angle 2.21053 ( 24) hydrogen bonds : bond 0.03871 ( 928) hydrogen bonds : angle 4.80077 ( 2718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2883.64 seconds wall clock time: 51 minutes 17.91 seconds (3077.91 seconds total)