Starting phenix.real_space_refine on Sat Jul 4 06:22:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tnp_26017/07_2026/7tnp_26017.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnp_26017/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnp_26017/07_2026/7tnp_26017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnp_26017/07_2026/7tnp_26017.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnp_26017/07_2026/7tnp_26017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnp_26017/07_2026/7tnp_26017.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tnp_26017/07_2026/7tnp_26017.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tnp_26017/07_2026/7tnp_26017.cif" } 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-6108/lib/python3.11/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: 2.97, per 1000 atoms: 0.16 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: 1.32 Conformation dependent library (CDL) restraints added in 591.1 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: 0.52 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: 3.04 Time building geometry restraints manager: 1.68 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 - 19.45: 10754 19.45 - 38.91: 444 38.91 - 58.36: 76 58.36 - 77.81: 8 77.81 - 97.27: 4 Dihedral angle restraints: 11286 sinusoidal: 4396 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 11283 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: 0.04 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: 3.280 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: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.480 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- 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 : 11.380 97.268 6854 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/Z covalent geometry : bond 0.00844 / 0.36 (19258) covalent geometry : angle 1.08751 / 0.60 (26018) SS BOND : bond 0.00446 / 0.26 ( 12) SS BOND : angle 2.13398 / 1.41 ( 24) hydrogen bonds : bond 0.29518 / 19.56 ( 928) hydrogen bonds : angle 9.87166 / 6.79 ( 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 : 0.595 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: 0.1271 time to fit residues: 120.4855 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 : 0.696 ------------------------------------------------------------------------------- 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... 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 = 0.3867 r_free = 0.3867 target = 0.132950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105140 restraints weight = 41948.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.106384 restraints weight = 27490.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.106776 restraints weight = 20771.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106920 restraints weight = 19184.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.107622 restraints weight = 18072.534| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 19270 Z= 0.153 Angle : 0.687 9.124 26042 Z= 0.361 Chirality : 0.044 0.288 2914 Planarity : 0.005 0.046 3194 Dihedral : 6.835 91.148 2608 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 2.59 % Allowed : 14.81 % Favored : 82.60 % 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: -2.38 (0.15), residues: 2364 helix: -1.23 (0.12), residues: 1324 sheet: -1.01 (0.36), residues: 188 loop : -2.05 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 453 TYR 0.033 0.002 TYR B1031 PHE 0.026 0.002 PHE A 659 TRP 0.027 0.001 TRP D1177 HIS 0.006 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (19258) covalent geometry : angle 0.68111 / 0.36 (26018) SS BOND : bond 0.00898 / 0.56 ( 12) SS BOND : angle 3.14423 / 2.12 ( 24) hydrogen bonds : bond 0.05299 / 3.49 ( 928) hydrogen bonds : angle 5.21424 / 3.60 ( 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 467 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 415 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.7847 (mmt) cc_final: 0.7332 (tpp) REVERT: A 674 MET cc_start: 0.7517 (mtt) cc_final: 0.7021 (mmp) REVERT: A 748 LEU cc_start: 0.8281 (mp) cc_final: 0.7978 (tt) REVERT: A 773 CYS cc_start: 0.5949 (OUTLIER) cc_final: 0.5221 (m) REVERT: B 405 TYR cc_start: 0.7460 (m-80) cc_final: 0.7120 (m-80) REVERT: B 651 ASP cc_start: 0.6648 (t0) cc_final: 0.6152 (p0) REVERT: B 722 LYS cc_start: 0.7206 (tttt) cc_final: 0.6965 (tttp) REVERT: B 799 LEU cc_start: 0.8954 (tp) cc_final: 0.8746 (tt) REVERT: B 811 LEU cc_start: 0.8479 (tt) cc_final: 0.8212 (mt) REVERT: B 1008 GLN cc_start: 0.7149 (pt0) cc_final: 0.6689 (mm-40) REVERT: B 1031 TYR cc_start: 0.5901 (p90) cc_final: 0.4962 (p90) REVERT: B 1040 LYS cc_start: 0.6243 (pmtt) cc_final: 0.5645 (tptt) REVERT: B 1072 PHE cc_start: 0.6765 (m-80) cc_final: 0.5415 (m-80) REVERT: B 1096 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7986 (t80) REVERT: B 1177 TRP cc_start: 0.5501 (t60) cc_final: 0.4734 (t60) REVERT: B 1187 ILE cc_start: 0.9181 (mt) cc_final: 0.8931 (tt) REVERT: C 424 TYR cc_start: 0.8280 (t80) cc_final: 0.8041 (t80) REVERT: C 671 TRP cc_start: 0.5405 (t-100) cc_final: 0.5150 (t-100) REVERT: D 651 ASP cc_start: 0.6851 (t0) cc_final: 0.5885 (p0) REVERT: D 673 TYR cc_start: 0.4626 (t80) cc_final: 0.4315 (t80) REVERT: D 699 LYS cc_start: 0.5418 (mttp) cc_final: 0.4371 (tptt) REVERT: D 790 SER cc_start: 0.8803 (m) cc_final: 0.8583 (t) REVERT: D 1031 TYR cc_start: 0.5152 (p90) cc_final: 0.4777 (p90) REVERT: D 1040 LYS cc_start: 0.6405 (pmtt) cc_final: 0.6156 (tptt) REVERT: D 1096 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7959 (t80) REVERT: D 1134 ILE cc_start: 0.8343 (mp) cc_final: 0.7961 (mm) REVERT: D 1204 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.6900 (t-90) outliers start: 52 outliers final: 17 residues processed: 451 average time/residue: 0.1134 time to fit residues: 80.9255 Evaluate side-chains 336 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 315 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 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: 6.9990 chunk 81 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 33 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN A1204 HIS B 412 HIS B 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 = 0.3845 r_free = 0.3845 target = 0.131223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.103342 restraints weight = 42929.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104878 restraints weight = 29020.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.104808 restraints weight = 22692.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105081 restraints weight = 22154.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105383 restraints weight = 20586.001| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19270 Z= 0.155 Angle : 0.660 10.340 26042 Z= 0.344 Chirality : 0.043 0.348 2914 Planarity : 0.004 0.041 3194 Dihedral : 6.415 90.679 2608 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.36 % Rotamer: Outliers : 3.84 % Allowed : 16.20 % Favored : 79.96 % 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: -1.09 (0.16), residues: 2364 helix: 0.07 (0.14), residues: 1326 sheet: -0.73 (0.38), residues: 188 loop : -1.90 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 675 TYR 0.028 0.001 TYR D1031 PHE 0.014 0.002 PHE B 495 TRP 0.016 0.001 TRP B1177 HIS 0.006 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (19258) covalent geometry : angle 0.65153 / 0.34 (26018) SS BOND : bond 0.01160 / 0.74 ( 12) SS BOND : angle 3.50106 / 2.44 ( 24) hydrogen bonds : bond 0.04365 / 2.86 ( 928) hydrogen bonds : angle 4.86246 / 3.35 ( 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 425 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 348 time to evaluate : 0.608 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: 0.7415 (mtt) cc_final: 0.7023 (mmp) REVERT: A 702 TYR cc_start: 0.8531 (t80) cc_final: 0.8254 (t80) REVERT: A 748 LEU cc_start: 0.8335 (mp) cc_final: 0.8093 (tt) REVERT: B 508 GLN cc_start: 0.6517 (tm-30) cc_final: 0.5415 (pm20) REVERT: B 651 ASP cc_start: 0.6714 (t0) cc_final: 0.6235 (p0) REVERT: B 670 MET cc_start: 0.7384 (mmm) cc_final: 0.6745 (mpp) REVERT: B 799 LEU cc_start: 0.9000 (tp) cc_final: 0.8728 (tt) REVERT: B 811 LEU cc_start: 0.8492 (tt) cc_final: 0.8252 (mt) REVERT: B 1040 LYS cc_start: 0.6419 (pmtt) cc_final: 0.5866 (tptt) REVERT: B 1096 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7946 (t80) REVERT: B 1177 TRP cc_start: 0.5479 (t60) cc_final: 0.4339 (t-100) REVERT: B 1187 ILE cc_start: 0.9206 (mt) cc_final: 0.8951 (tt) REVERT: B 1191 MET cc_start: 0.8203 (mtp) cc_final: 0.7982 (mtp) REVERT: C 431 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6397 (mm-30) REVERT: C 473 ASP cc_start: 0.5964 (m-30) cc_final: 0.5708 (m-30) REVERT: C 674 MET cc_start: 0.6669 (mtp) cc_final: 0.6040 (mmp) REVERT: D 503 MET cc_start: 0.7247 (ttm) cc_final: 0.6942 (ttt) REVERT: D 508 GLN cc_start: 0.6592 (tm-30) cc_final: 0.5286 (pm20) REVERT: D 549 TYR cc_start: 0.4640 (m-10) cc_final: 0.4271 (m-10) REVERT: D 651 ASP cc_start: 0.6735 (t0) cc_final: 0.5838 (p0) REVERT: D 673 TYR cc_start: 0.4818 (t80) cc_final: 0.4140 (t80) REVERT: D 797 TYR cc_start: 0.8950 (m-80) cc_final: 0.8664 (m-80) REVERT: D 1031 TYR cc_start: 0.5637 (p90) cc_final: 0.5285 (p90) REVERT: D 1040 LYS cc_start: 0.6534 (pmtt) cc_final: 0.6304 (tptt) REVERT: D 1096 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7874 (t80) REVERT: D 1204 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6856 (t-90) outliers start: 77 outliers final: 38 residues processed: 403 average time/residue: 0.1082 time to fit residues: 70.1997 Evaluate side-chains 342 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 CYS 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 1119 LEU 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 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 467 LEU Chi-restraints excluded: chain C residue 521 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 1104 SER 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 693 VAL Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 191 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 791 ASN B 764 ASN B1059 HIS ** 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 = 0.3836 r_free = 0.3836 target = 0.130371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103835 restraints weight = 43066.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105131 restraints weight = 28970.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105301 restraints weight = 22576.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.105709 restraints weight = 20854.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105853 restraints weight = 20102.509| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19270 Z= 0.171 Angle : 0.679 13.355 26042 Z= 0.349 Chirality : 0.044 0.321 2914 Planarity : 0.004 0.039 3194 Dihedral : 6.342 91.813 2606 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 3.94 % Allowed : 17.05 % Favored : 79.01 % 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: -0.56 (0.17), residues: 2364 helix: 0.64 (0.14), residues: 1314 sheet: -0.63 (0.40), residues: 172 loop : -1.85 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 675 TYR 0.052 0.002 TYR B1031 PHE 0.016 0.002 PHE A 659 TRP 0.015 0.001 TRP C 460 HIS 0.019 0.002 HIS A1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (19258) covalent geometry : angle 0.67340 / 0.35 (26018) SS BOND : bond 0.01136 / 0.75 ( 12) SS BOND : angle 2.92037 / 1.80 ( 24) hydrogen bonds : bond 0.04056 / 2.68 ( 928) hydrogen bonds : angle 4.83585 / 3.34 ( 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 411 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 332 time to evaluate : 0.779 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 674 MET cc_start: 0.7160 (mtt) cc_final: 0.6803 (mmp) REVERT: A 748 LEU cc_start: 0.8317 (mp) cc_final: 0.7976 (tt) REVERT: A 1195 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8568 (mm) REVERT: B 405 TYR cc_start: 0.7673 (m-80) cc_final: 0.7457 (m-80) REVERT: B 651 ASP cc_start: 0.6441 (t0) cc_final: 0.6154 (p0) REVERT: B 670 MET cc_start: 0.7626 (mmm) cc_final: 0.6942 (mpp) REVERT: B 1040 LYS cc_start: 0.6491 (pmtt) cc_final: 0.6061 (tptt) REVERT: B 1096 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7782 (t80) REVERT: B 1136 SER cc_start: 0.8936 (m) cc_final: 0.8687 (t) REVERT: B 1187 ILE cc_start: 0.9198 (mt) cc_final: 0.8892 (tt) REVERT: C 674 MET cc_start: 0.6684 (mtp) cc_final: 0.6173 (mmp) REVERT: C 1195 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8840 (mm) REVERT: D 503 MET cc_start: 0.6969 (ttm) cc_final: 0.6681 (ttt) REVERT: D 651 ASP cc_start: 0.6496 (t0) cc_final: 0.5876 (p0) REVERT: D 673 TYR cc_start: 0.4712 (t80) cc_final: 0.3909 (t80) REVERT: D 674 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6479 (ttm) REVERT: D 1096 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7613 (t80) outliers start: 79 outliers final: 46 residues processed: 384 average time/residue: 0.1283 time to fit residues: 79.3662 Evaluate side-chains 347 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 296 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 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 643 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 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 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 467 LEU Chi-restraints excluded: chain C residue 519 ASP 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 1195 LEU Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 720 THR 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 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: 10.0000 chunk 177 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 204 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 133 optimal weight: 0.7980 chunk 132 optimal weight: 0.4980 chunk 206 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3858 r_free = 0.3858 target = 0.132044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105850 restraints weight = 42655.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106662 restraints weight = 28842.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107060 restraints weight = 24389.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107506 restraints weight = 20952.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107631 restraints weight = 19729.453| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19270 Z= 0.123 Angle : 0.646 13.215 26042 Z= 0.327 Chirality : 0.042 0.278 2914 Planarity : 0.003 0.035 3194 Dihedral : 6.213 88.733 2606 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.15 % Rotamer: Outliers : 3.49 % Allowed : 18.69 % Favored : 77.82 % 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: -0.10 (0.17), residues: 2364 helix: 1.08 (0.14), residues: 1314 sheet: -0.71 (0.37), residues: 202 loop : -1.73 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 661 TYR 0.046 0.001 TYR D1031 PHE 0.014 0.001 PHE A 659 TRP 0.015 0.001 TRP C 460 HIS 0.008 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (19258) covalent geometry : angle 0.64130 / 0.32 (26018) SS BOND : bond 0.00564 / 0.37 ( 12) SS BOND : angle 2.68484 / 1.67 ( 24) hydrogen bonds : bond 0.03669 / 2.42 ( 928) hydrogen bonds : angle 4.67678 / 3.24 ( 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 417 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 347 time to evaluate : 0.770 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 414 MET cc_start: 0.7151 (mmm) cc_final: 0.6637 (mmt) REVERT: A 527 MET cc_start: 0.8384 (ttp) cc_final: 0.7817 (ttm) REVERT: A 1082 PHE cc_start: 0.5715 (p90) cc_final: 0.5361 (p90) REVERT: A 1195 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8532 (mm) REVERT: B 508 GLN cc_start: 0.6427 (tm-30) cc_final: 0.5542 (tp40) REVERT: B 651 ASP cc_start: 0.6335 (t0) cc_final: 0.6122 (p0) REVERT: B 670 MET cc_start: 0.7703 (mmm) cc_final: 0.7129 (mpp) REVERT: B 767 TRP cc_start: 0.7184 (OUTLIER) cc_final: 0.6777 (t-100) REVERT: B 1023 MET cc_start: 0.7504 (tpt) cc_final: 0.7159 (mmt) REVERT: B 1040 LYS cc_start: 0.6520 (pmtt) cc_final: 0.6154 (tptt) REVERT: B 1096 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7709 (t80) REVERT: B 1136 SER cc_start: 0.8955 (m) cc_final: 0.8716 (t) REVERT: B 1187 ILE cc_start: 0.9208 (mt) cc_final: 0.8868 (tt) REVERT: C 408 MET cc_start: 0.4564 (mmm) cc_final: 0.4107 (mmt) REVERT: C 431 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6210 (mm-30) REVERT: C 527 MET cc_start: 0.8382 (ttp) cc_final: 0.7866 (ttm) REVERT: C 670 MET cc_start: 0.6491 (mmt) cc_final: 0.6161 (mmm) REVERT: C 674 MET cc_start: 0.6633 (mtp) cc_final: 0.6350 (mmp) REVERT: D 503 MET cc_start: 0.7042 (ttm) cc_final: 0.6754 (ttt) REVERT: D 508 GLN cc_start: 0.6665 (tm-30) cc_final: 0.5366 (pm20) REVERT: D 651 ASP cc_start: 0.6347 (t0) cc_final: 0.5851 (p0) REVERT: D 673 TYR cc_start: 0.4664 (t80) cc_final: 0.3812 (t80) REVERT: D 1096 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7707 (t80) REVERT: D 1177 TRP cc_start: 0.5974 (OUTLIER) cc_final: 0.4898 (m100) outliers start: 70 outliers final: 41 residues processed: 391 average time/residue: 0.1258 time to fit residues: 79.7105 Evaluate side-chains 357 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 311 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 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 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 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 422 GLU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 519 ASP 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 1081 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 168 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1204 HIS B 586 GLN B 764 ASN 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 = 0.3824 r_free = 0.3824 target = 0.129435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103584 restraints weight = 42900.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104239 restraints weight = 31830.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104576 restraints weight = 25141.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105015 restraints weight = 21827.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105273 restraints weight = 20702.325| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19270 Z= 0.187 Angle : 0.662 10.352 26042 Z= 0.341 Chirality : 0.043 0.180 2914 Planarity : 0.004 0.036 3194 Dihedral : 6.384 92.541 2606 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 4.19 % Allowed : 19.24 % Favored : 76.57 % 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: -0.13 (0.17), residues: 2364 helix: 1.09 (0.14), residues: 1316 sheet: -0.96 (0.39), residues: 180 loop : -1.76 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 692 TYR 0.052 0.002 TYR D1031 PHE 0.016 0.002 PHE B 495 TRP 0.014 0.001 TRP C 460 HIS 0.008 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (19258) covalent geometry : angle 0.65961 / 0.34 (26018) SS BOND : bond 0.00554 / 0.35 ( 12) SS BOND : angle 2.05601 / 1.22 ( 24) hydrogen bonds : bond 0.03871 / 2.55 ( 928) hydrogen bonds : angle 4.82046 / 3.33 ( 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 396 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 312 time to evaluate : 0.849 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 491 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7451 (m-10) REVERT: A 527 MET cc_start: 0.8424 (ttp) cc_final: 0.7906 (ttm) REVERT: A 1082 PHE cc_start: 0.5747 (p90) cc_final: 0.5402 (p90) REVERT: A 1195 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8588 (mm) REVERT: B 767 TRP cc_start: 0.7431 (OUTLIER) cc_final: 0.7067 (t-100) REVERT: B 1040 LYS cc_start: 0.6427 (pmtt) cc_final: 0.6099 (tptt) REVERT: B 1096 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7677 (t80) REVERT: B 1136 SER cc_start: 0.8973 (m) cc_final: 0.8762 (t) REVERT: B 1187 ILE cc_start: 0.9194 (mt) cc_final: 0.8868 (tt) REVERT: C 431 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6315 (mm-30) REVERT: C 527 MET cc_start: 0.8418 (ttp) cc_final: 0.7930 (ttm) REVERT: C 674 MET cc_start: 0.6658 (mtp) cc_final: 0.6411 (mmp) REVERT: D 503 MET cc_start: 0.6898 (ttm) cc_final: 0.6610 (ttt) REVERT: D 597 SER cc_start: 0.9273 (p) cc_final: 0.9048 (p) REVERT: D 651 ASP cc_start: 0.6355 (t0) cc_final: 0.5954 (p0) REVERT: D 673 TYR cc_start: 0.4597 (t80) cc_final: 0.3711 (t80) REVERT: D 1096 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7678 (t80) REVERT: A 1301 GLU cc_start: 0.6044 (mm-30) cc_final: 0.5591 (tm-30) REVERT: C 1301 GLU cc_start: 0.6070 (tp30) cc_final: 0.5324 (tp30) outliers start: 84 outliers final: 51 residues processed: 372 average time/residue: 0.1297 time to fit residues: 77.6870 Evaluate side-chains 357 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 301 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 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 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 767 TRP Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 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 633 ILE Chi-restraints excluded: chain C residue 792 VAL 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 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 767 TRP Chi-restraints excluded: chain D residue 790 SER 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 1105 ILE Chi-restraints excluded: chain D residue 1136 SER Chi-restraints excluded: chain D residue 1177 TRP Chi-restraints excluded: chain D residue 1184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 159 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 184 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1204 HIS ** 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 = 0.3854 r_free = 0.3854 target = 0.131836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.105788 restraints weight = 43370.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.107741 restraints weight = 33610.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108474 restraints weight = 23957.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108646 restraints weight = 20677.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108738 restraints weight = 19806.997| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19270 Z= 0.133 Angle : 0.635 12.594 26042 Z= 0.322 Chirality : 0.041 0.153 2914 Planarity : 0.003 0.032 3194 Dihedral : 6.227 90.182 2606 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.02 % Rotamer: Outliers : 3.44 % Allowed : 20.14 % Favored : 76.42 % 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: 0.06 (0.17), residues: 2364 helix: 1.28 (0.14), residues: 1320 sheet: -0.87 (0.39), residues: 176 loop : -1.74 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 675 TYR 0.047 0.001 TYR D1031 PHE 0.012 0.001 PHE C 438 TRP 0.021 0.001 TRP C 460 HIS 0.008 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (19258) covalent geometry : angle 0.63361 / 0.32 (26018) SS BOND : bond 0.00964 / 0.65 ( 12) SS BOND : angle 1.67449 / 0.98 ( 24) hydrogen bonds : bond 0.03594 / 2.37 ( 928) hydrogen bonds : angle 4.64433 / 3.21 ( 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 391 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 322 time to evaluate : 0.732 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 414 MET cc_start: 0.7038 (mmm) cc_final: 0.6426 (mmt) REVERT: A 491 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7315 (m-10) REVERT: A 527 MET cc_start: 0.8275 (ttp) cc_final: 0.7805 (ttm) REVERT: A 1082 PHE cc_start: 0.5806 (p90) cc_final: 0.5506 (p90) REVERT: A 1195 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8593 (mm) REVERT: B 508 GLN cc_start: 0.6415 (tm-30) cc_final: 0.5432 (tp40) REVERT: B 1082 PHE cc_start: 0.4107 (m-80) cc_final: 0.3502 (t80) REVERT: B 1096 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7509 (t80) REVERT: B 1136 SER cc_start: 0.8912 (m) cc_final: 0.8663 (t) REVERT: B 1187 ILE cc_start: 0.9156 (mt) cc_final: 0.8819 (tt) REVERT: C 408 MET cc_start: 0.4470 (mmm) cc_final: 0.4106 (mmt) REVERT: C 431 GLU cc_start: 0.6479 (mm-30) cc_final: 0.6058 (mm-30) REVERT: C 527 MET cc_start: 0.8315 (ttp) cc_final: 0.7859 (ttm) REVERT: C 697 LYS cc_start: 0.7269 (mttt) cc_final: 0.6413 (pttp) REVERT: C 711 TYR cc_start: 0.7651 (t80) cc_final: 0.7410 (t80) REVERT: D 503 MET cc_start: 0.6683 (ttm) cc_final: 0.6403 (ttt) REVERT: D 597 SER cc_start: 0.9185 (p) cc_final: 0.8966 (p) REVERT: D 651 ASP cc_start: 0.6143 (t0) cc_final: 0.5916 (p0) REVERT: D 673 TYR cc_start: 0.4408 (t80) cc_final: 0.3479 (t80) REVERT: D 1096 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7515 (t80) REVERT: D 1177 TRP cc_start: 0.6120 (OUTLIER) cc_final: 0.5094 (m100) REVERT: C 1301 GLU cc_start: 0.5879 (tp30) cc_final: 0.5427 (tp30) outliers start: 69 outliers final: 41 residues processed: 370 average time/residue: 0.1283 time to fit residues: 76.2512 Evaluate side-chains 350 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 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 696 SER 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 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 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 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 432 ILE 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 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 1177 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 201 optimal weight: 0.0570 chunk 192 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 37 optimal weight: 0.0050 chunk 63 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 61 optimal weight: 0.0870 chunk 30 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1204 HIS B 586 GLN B 714 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 = 0.3888 r_free = 0.3888 target = 0.134138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108034 restraints weight = 43340.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.109608 restraints weight = 29483.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110210 restraints weight = 21894.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110489 restraints weight = 22146.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.110643 restraints weight = 20070.742| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19270 Z= 0.119 Angle : 0.647 13.982 26042 Z= 0.322 Chirality : 0.041 0.205 2914 Planarity : 0.003 0.058 3194 Dihedral : 6.125 87.723 2606 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 3.09 % Allowed : 20.69 % Favored : 76.22 % 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: 0.31 (0.17), residues: 2364 helix: 1.52 (0.15), residues: 1308 sheet: -0.99 (0.41), residues: 162 loop : -1.59 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 675 TYR 0.043 0.001 TYR D1031 PHE 0.023 0.001 PHE B1082 TRP 0.022 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (19258) covalent geometry : angle 0.64390 / 0.32 (26018) SS BOND : bond 0.00648 / 0.39 ( 12) SS BOND : angle 2.12141 / 1.39 ( 24) hydrogen bonds : bond 0.03393 / 2.22 ( 928) hydrogen bonds : angle 4.50718 / 3.12 ( 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 397 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 335 time to evaluate : 0.807 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 414 MET cc_start: 0.7106 (mmm) cc_final: 0.6546 (mmt) REVERT: A 491 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7291 (m-10) REVERT: A 527 MET cc_start: 0.8288 (ttp) cc_final: 0.7852 (ttm) REVERT: A 1082 PHE cc_start: 0.5781 (p90) cc_final: 0.5459 (p90) REVERT: B 508 GLN cc_start: 0.6335 (tm-30) cc_final: 0.5489 (tp40) REVERT: B 585 MET cc_start: 0.8407 (mmm) cc_final: 0.8047 (mtp) REVERT: B 711 TYR cc_start: 0.6407 (t80) cc_final: 0.6064 (t80) REVERT: B 1096 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7514 (t80) REVERT: B 1136 SER cc_start: 0.8955 (m) cc_final: 0.8666 (t) REVERT: B 1187 ILE cc_start: 0.9157 (mt) cc_final: 0.8800 (tt) REVERT: C 408 MET cc_start: 0.4656 (mmm) cc_final: 0.4253 (mmt) REVERT: C 431 GLU cc_start: 0.6503 (mm-30) cc_final: 0.6162 (mm-30) REVERT: C 527 MET cc_start: 0.8357 (ttp) cc_final: 0.7904 (ttm) REVERT: C 711 TYR cc_start: 0.7681 (t80) cc_final: 0.7457 (t80) REVERT: D 405 TYR cc_start: 0.7554 (m-80) cc_final: 0.7123 (m-80) REVERT: D 503 MET cc_start: 0.6915 (ttm) cc_final: 0.6479 (ttt) REVERT: D 508 GLN cc_start: 0.6214 (tm-30) cc_final: 0.5332 (tp40) REVERT: D 597 SER cc_start: 0.9167 (p) cc_final: 0.8921 (p) REVERT: D 651 ASP cc_start: 0.6229 (t0) cc_final: 0.5987 (p0) REVERT: D 673 TYR cc_start: 0.4540 (t80) cc_final: 0.3587 (t80) REVERT: D 1096 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7516 (t80) REVERT: D 1115 PHE cc_start: 0.7950 (t80) cc_final: 0.7596 (t80) REVERT: D 1177 TRP cc_start: 0.5884 (OUTLIER) cc_final: 0.5226 (m100) REVERT: C 1301 GLU cc_start: 0.5909 (tp30) cc_final: 0.5460 (tp30) outliers start: 62 outliers final: 35 residues processed: 376 average time/residue: 0.1232 time to fit residues: 75.5978 Evaluate side-chains 339 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 300 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 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 1105 ILE Chi-restraints excluded: chain A residue 1114 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 586 GLN 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 1065 THR Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 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 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 1177 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 108 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 141 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1204 HIS B 508 GLN B 714 GLN B1148 ASN C 791 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.101851 restraints weight = 43778.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101944 restraints weight = 35855.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102637 restraints weight = 34191.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102892 restraints weight = 26562.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103053 restraints weight = 24663.542| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 19270 Z= 0.310 Angle : 0.794 11.654 26042 Z= 0.412 Chirality : 0.048 0.215 2914 Planarity : 0.005 0.049 3194 Dihedral : 6.802 96.096 2606 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.25 % Favored : 94.59 % Rotamer: Outliers : 3.29 % Allowed : 20.94 % Favored : 75.77 % 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: -0.43 (0.17), residues: 2364 helix: 0.85 (0.14), residues: 1306 sheet: -1.66 (0.37), residues: 178 loop : -1.70 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1098 TYR 0.047 0.003 TYR D1031 PHE 0.021 0.002 PHE B 495 TRP 0.022 0.002 TRP A 767 HIS 0.015 0.002 HIS A1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.31 (19258) covalent geometry : angle 0.79045 / 0.41 (26018) SS BOND : bond 0.00418 / 0.30 ( 12) SS BOND : angle 2.44112 / 1.55 ( 24) hydrogen bonds : bond 0.04404 / 2.90 ( 928) hydrogen bonds : angle 5.05245 / 3.49 ( 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 363 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 297 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7393 (m-10) REVERT: A 527 MET cc_start: 0.8394 (ttp) cc_final: 0.7961 (ttm) REVERT: A 1207 LEU cc_start: 0.7618 (mt) cc_final: 0.7385 (tt) REVERT: B 405 TYR cc_start: 0.8080 (m-80) cc_final: 0.7856 (m-80) REVERT: B 670 MET cc_start: 0.7791 (mmm) cc_final: 0.7098 (mpp) REVERT: B 711 TYR cc_start: 0.6634 (t80) cc_final: 0.6166 (t80) REVERT: B 1096 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7744 (t80) REVERT: B 1187 ILE cc_start: 0.9156 (mt) cc_final: 0.8874 (tt) REVERT: C 527 MET cc_start: 0.8383 (ttp) cc_final: 0.7957 (ttm) REVERT: C 674 MET cc_start: 0.7154 (mtp) cc_final: 0.6718 (mmp) REVERT: D 503 MET cc_start: 0.6352 (ttm) cc_final: 0.6094 (ttt) REVERT: D 651 ASP cc_start: 0.6361 (t0) cc_final: 0.5988 (p0) REVERT: D 673 TYR cc_start: 0.4655 (t80) cc_final: 0.3676 (t80) REVERT: D 1096 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7764 (t80) REVERT: D 1109 LEU cc_start: 0.8746 (tp) cc_final: 0.8537 (mm) outliers start: 66 outliers final: 44 residues processed: 343 average time/residue: 0.1255 time to fit residues: 69.9286 Evaluate side-chains 332 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 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 1105 ILE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1199 MET 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 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 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 619 ASN 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 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 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1136 SER Chi-restraints excluded: chain D residue 1177 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 34 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1204 HIS ** 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 = 0.3867 r_free = 0.3867 target = 0.132631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105725 restraints weight = 43389.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108032 restraints weight = 31600.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108711 restraints weight = 21883.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.108803 restraints weight = 20837.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.108863 restraints weight = 18956.978| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19270 Z= 0.135 Angle : 0.699 13.468 26042 Z= 0.347 Chirality : 0.043 0.262 2914 Planarity : 0.004 0.065 3194 Dihedral : 6.469 90.326 2606 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 2.14 % Allowed : 22.43 % Favored : 75.42 % 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: 1.32 (0.14), residues: 1300 sheet: -1.26 (0.36), residues: 204 loop : -1.62 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1098 TYR 0.043 0.001 TYR D1031 PHE 0.017 0.001 PHE A1115 TRP 0.023 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (19258) covalent geometry : angle 0.69468 / 0.34 (26018) SS BOND : bond 0.00363 / 0.23 ( 12) SS BOND : angle 2.63138 / 1.61 ( 24) hydrogen bonds : bond 0.03658 / 2.40 ( 928) hydrogen bonds : angle 4.65655 / 3.23 ( 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 355 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 312 time to evaluate : 0.744 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 414 MET cc_start: 0.7154 (mmm) cc_final: 0.6667 (mmt) REVERT: A 431 GLU cc_start: 0.7804 (tp30) cc_final: 0.7483 (mm-30) REVERT: A 491 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.7328 (m-10) REVERT: A 527 MET cc_start: 0.8330 (ttp) cc_final: 0.7775 (ttm) REVERT: A 1082 PHE cc_start: 0.5924 (p90) cc_final: 0.5691 (p90) REVERT: B 405 TYR cc_start: 0.7973 (m-80) cc_final: 0.7745 (m-80) REVERT: B 508 GLN cc_start: 0.6347 (tm-30) cc_final: 0.5425 (tp40) REVERT: B 585 MET cc_start: 0.8411 (mtp) cc_final: 0.8184 (mtp) REVERT: B 635 SER cc_start: 0.7689 (m) cc_final: 0.7115 (p) REVERT: B 670 MET cc_start: 0.7783 (mmm) cc_final: 0.7235 (mpp) REVERT: B 711 TYR cc_start: 0.6544 (t80) cc_final: 0.6099 (t80) REVERT: B 1096 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7505 (t80) REVERT: B 1187 ILE cc_start: 0.9165 (mt) cc_final: 0.8833 (tt) REVERT: C 431 GLU cc_start: 0.6567 (mm-30) cc_final: 0.6182 (mm-30) REVERT: C 527 MET cc_start: 0.8319 (ttp) cc_final: 0.7762 (ttm) REVERT: C 674 MET cc_start: 0.7211 (mtp) cc_final: 0.6867 (mmp) REVERT: C 711 TYR cc_start: 0.7746 (t80) cc_final: 0.7448 (t80) REVERT: C 1082 PHE cc_start: 0.5762 (p90) cc_final: 0.5503 (p90) REVERT: D 651 ASP cc_start: 0.6358 (t0) cc_final: 0.6092 (p0) REVERT: D 673 TYR cc_start: 0.4613 (t80) cc_final: 0.3716 (t80) REVERT: D 1023 MET cc_start: 0.7875 (mmm) cc_final: 0.7591 (mmm) REVERT: D 1096 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7612 (t80) REVERT: D 1177 TRP cc_start: 0.6250 (OUTLIER) cc_final: 0.5154 (m100) REVERT: C 1301 GLU cc_start: 0.6579 (tp30) cc_final: 0.5708 (tp30) outliers start: 43 outliers final: 34 residues processed: 341 average time/residue: 0.1146 time to fit residues: 63.1856 Evaluate side-chains 336 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 298 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 514 VAL 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 1105 ILE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 720 THR 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 1204 HIS Chi-restraints excluded: chain C residue 454 ASP 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 586 GLN Chi-restraints excluded: chain D residue 693 VAL 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 1177 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 148 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 0.0070 chunk 220 optimal weight: 7.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1204 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN ** D1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.131936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107135 restraints weight = 43724.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106900 restraints weight = 33306.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107195 restraints weight = 28791.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107630 restraints weight = 25203.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107833 restraints weight = 23398.915| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19270 Z= 0.148 Angle : 0.690 13.061 26042 Z= 0.344 Chirality : 0.043 0.232 2914 Planarity : 0.004 0.051 3194 Dihedral : 6.462 90.817 2606 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 2.24 % Allowed : 22.83 % Favored : 74.93 % 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: 0.15 (0.17), residues: 2364 helix: 1.40 (0.14), residues: 1300 sheet: -1.25 (0.36), residues: 204 loop : -1.60 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1098 TYR 0.040 0.002 TYR D1031 PHE 0.016 0.001 PHE A1115 TRP 0.042 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (19258) covalent geometry : angle 0.68642 / 0.34 (26018) SS BOND : bond 0.00347 / 0.22 ( 12) SS BOND : angle 2.33673 / 1.43 ( 24) hydrogen bonds : bond 0.03623 / 2.38 ( 928) hydrogen bonds : angle 4.64455 / 3.23 ( 2718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.80 seconds wall clock time: 53 minutes 35.72 seconds (3215.72 seconds total)