Starting phenix.real_space_refine on Sat Sep 28 10:02:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnp_26017/09_2024/7tnp_26017.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnp_26017/09_2024/7tnp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnp_26017/09_2024/7tnp_26017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnp_26017/09_2024/7tnp_26017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnp_26017/09_2024/7tnp_26017.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnp_26017/09_2024/7tnp_26017.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12218 2.51 5 N 3046 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18840 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4673 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4679 Classifications: {'peptide': 601} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Chain: "C" Number of atoms: 4673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4673 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4679 Classifications: {'peptide': 601} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 585} Chain breaks: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.43, per 1000 atoms: 0.55 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: 4.61 Conformation dependent library (CDL) restraints added in 2.5 seconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4396 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 22 sheets defined 54.4% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 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: 5.82 Time building geometry restraints manager: 5.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5730 1.34 - 1.46: 5017 1.46 - 1.59: 8283 1.59 - 1.71: 8 1.71 - 1.83: 220 Bond restraints: 19258 Sorted by residual: bond pdb=" CG1 ILE C 573 " pdb=" CD1 ILE C 573 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.63e+00 bond pdb=" CG1 ILE A 573 " pdb=" CD1 ILE A 573 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.63e+00 bond pdb=" CB TRP B 606 " pdb=" CG TRP B 606 " ideal model delta sigma weight residual 1.498 1.431 0.067 3.10e-02 1.04e+03 4.62e+00 bond pdb=" CB TRP D 606 " pdb=" CG TRP D 606 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.50e+00 bond pdb=" N3 CYZ D1302 " pdb=" S2 CYZ D1302 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 19253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 24986 2.39 - 4.78: 895 4.78 - 7.17: 105 7.17 - 9.56: 28 9.56 - 11.95: 4 Bond angle restraints: 26018 Sorted by residual: angle pdb=" N ASN A1132 " pdb=" CA ASN A1132 " pdb=" C ASN A1132 " ideal model delta sigma weight residual 114.64 106.28 8.36 1.52e+00 4.33e-01 3.03e+01 angle pdb=" N ASN C1132 " pdb=" CA ASN C1132 " pdb=" C ASN C1132 " ideal model delta sigma weight residual 114.64 106.28 8.36 1.52e+00 4.33e-01 3.02e+01 angle pdb=" CA TRP D1177 " pdb=" CB TRP D1177 " pdb=" CG TRP D1177 " ideal model delta sigma weight residual 113.60 122.73 -9.13 1.90e+00 2.77e-01 2.31e+01 angle pdb=" CA TRP B1177 " pdb=" CB TRP B1177 " pdb=" CG TRP B1177 " ideal model delta sigma weight residual 113.60 122.69 -9.09 1.90e+00 2.77e-01 2.29e+01 angle pdb=" CA TYR D1031 " pdb=" CB TYR D1031 " pdb=" CG TYR D1031 " ideal model delta sigma weight residual 113.90 122.46 -8.56 1.80e+00 3.09e-01 2.26e+01 ... (remaining 26013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 10979 24.85 - 49.69: 364 49.69 - 74.54: 19 74.54 - 99.38: 12 99.38 - 124.23: 8 Dihedral angle restraints: 11382 sinusoidal: 4492 harmonic: 6890 Sorted by residual: dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 149.17 -56.17 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 149.15 -56.15 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CA SER B 635 " pdb=" C SER B 635 " pdb=" N ALA B 636 " pdb=" CA ALA B 636 " ideal model delta harmonic sigma weight residual -180.00 -148.50 -31.50 0 5.00e+00 4.00e-02 3.97e+01 ... (remaining 11379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2171 0.058 - 0.116: 600 0.116 - 0.174: 114 0.174 - 0.231: 19 0.231 - 0.289: 10 Chirality restraints: 2914 Sorted by residual: chirality pdb=" CA TYR D1031 " pdb=" N TYR D1031 " pdb=" C TYR D1031 " pdb=" CB TYR D1031 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA TYR B1031 " pdb=" N TYR B1031 " pdb=" C TYR B1031 " pdb=" CB TYR B1031 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C8 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" N2 CYZ A1302 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2911 not shown) Planarity restraints: 3194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1031 " 0.034 2.00e-02 2.50e+03 2.17e-02 9.43e+00 pdb=" CG TYR B1031 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B1031 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B1031 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B1031 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B1031 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B1031 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B1031 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D1031 " 0.033 2.00e-02 2.50e+03 2.15e-02 9.27e+00 pdb=" CG TYR D1031 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D1031 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D1031 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D1031 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D1031 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D1031 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D1031 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 403 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO D 404 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " -0.030 5.00e-02 4.00e+02 ... (remaining 3191 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5531 2.80 - 3.33: 17705 3.33 - 3.85: 30693 3.85 - 4.38: 35960 4.38 - 4.90: 59734 Nonbonded interactions: 149623 Sorted by model distance: nonbonded pdb=" O MET B1009 " pdb=" OG1 THR B1013 " model vdw 2.280 3.040 nonbonded pdb=" O MET D1009 " pdb=" OG1 THR D1013 " model vdw 2.280 3.040 nonbonded pdb=" OG SER A 597 " pdb=" O ALA B 806 " model vdw 2.318 3.040 nonbonded pdb=" OG SER C 597 " pdb=" O ALA D 806 " model vdw 2.342 3.040 nonbonded pdb=" O LEU D 639 " pdb=" OH TYR D 647 " model vdw 2.352 3.040 ... (remaining 149618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 820 or resid 1002 through 1169 or resid 1171 t \ hrough 1208 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 394 through 548 or (resid 563 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 1041 or resid 1056 through 120 \ 8 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 394 through 820 or resid 1002 through 1169 or resid 1171 t \ hrough 1208 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 394 through 548 or (resid 563 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 1041 or resid 1056 through 120 \ 8 or resid 1301 or resid 1302)) } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 40.710 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.030 ------------------------------------------------------------------------------- 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 19258 Z= 0.537 Angle : 1.088 11.952 26018 Z= 0.601 Chirality : 0.058 0.289 2914 Planarity : 0.007 0.059 3194 Dihedral : 12.458 124.225 6950 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 0.70 % Allowed : 7.13 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.12), residues: 2364 helix: -3.84 (0.07), residues: 1292 sheet: -1.42 (0.40), residues: 148 loop : -2.47 (0.16), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A1032 HIS 0.010 0.002 HIS C1081 PHE 0.028 0.003 PHE A1126 TYR 0.050 0.003 TYR B1031 ARG 0.008 0.001 ARG B 485 *********************** 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 fitting. rotamer outliers: 14 poor density : 616 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.4899 (tptp) cc_final: 0.4513 (tptt) REVERT: A 533 TYR cc_start: 0.8893 (t80) cc_final: 0.8653 (t80) REVERT: A 671 TRP cc_start: 0.5711 (t-100) cc_final: 0.5496 (t-100) REVERT: A 674 MET cc_start: 0.7170 (mtt) cc_final: 0.6824 (mmp) REVERT: A 748 LEU cc_start: 0.8181 (mp) cc_final: 0.7804 (tt) REVERT: A 811 LEU cc_start: 0.8811 (mm) cc_final: 0.8599 (mt) REVERT: A 1195 LEU cc_start: 0.8691 (tp) cc_final: 0.8384 (tp) REVERT: B 496 MET cc_start: 0.7121 (mtp) cc_final: 0.6580 (mtp) REVERT: B 619 ASN cc_start: 0.5799 (t0) cc_final: 0.5569 (t0) REVERT: B 651 ASP cc_start: 0.7011 (t0) cc_final: 0.6422 (p0) REVERT: B 692 ARG cc_start: 0.5746 (ttt180) cc_final: 0.5437 (ttt180) REVERT: B 720 THR cc_start: 0.7927 (p) cc_final: 0.7657 (p) REVERT: B 811 LEU cc_start: 0.8620 (tt) cc_final: 0.8329 (mt) REVERT: B 1031 TYR cc_start: 0.6025 (p90) cc_final: 0.5658 (p90) REVERT: B 1040 LYS cc_start: 0.6015 (pmtt) cc_final: 0.5610 (tptt) REVERT: B 1187 ILE cc_start: 0.9037 (mt) cc_final: 0.8822 (tt) REVERT: C 601 VAL cc_start: 0.9290 (p) cc_final: 0.9003 (t) REVERT: C 671 TRP cc_start: 0.5490 (t-100) cc_final: 0.4923 (t-100) REVERT: C 693 VAL cc_start: 0.6954 (t) cc_final: 0.6370 (t) REVERT: C 1195 LEU cc_start: 0.8717 (tp) cc_final: 0.8477 (tp) REVERT: D 651 ASP cc_start: 0.7065 (t0) cc_final: 0.6155 (p0) REVERT: D 664 ILE cc_start: 0.7228 (mt) cc_final: 0.6682 (mp) REVERT: D 720 THR cc_start: 0.7873 (p) cc_final: 0.7639 (p) REVERT: D 722 LYS cc_start: 0.7683 (tttt) cc_final: 0.7253 (tttp) REVERT: D 790 SER cc_start: 0.8692 (m) cc_final: 0.8411 (t) REVERT: D 1031 TYR cc_start: 0.5561 (p90) cc_final: 0.4757 (p90) REVERT: D 1040 LYS cc_start: 0.6509 (pmtt) cc_final: 0.6140 (tptt) REVERT: D 1134 ILE cc_start: 0.8348 (mp) cc_final: 0.8053 (mm) REVERT: D 1187 ILE cc_start: 0.9168 (mt) cc_final: 0.8869 (tt) outliers start: 14 outliers final: 1 residues processed: 621 average time/residue: 0.2994 time to fit residues: 278.5587 Evaluate side-chains 330 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 329 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 704 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 217 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 791 ASN ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 ASN B 418 ASN B1132 ASN B1206 GLN C 791 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 ASN D 586 GLN D 587 GLN D1131 HIS D1132 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19258 Z= 0.191 Angle : 0.679 9.231 26018 Z= 0.356 Chirality : 0.043 0.268 2914 Planarity : 0.005 0.046 3194 Dihedral : 9.764 110.015 2704 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 2.69 % Allowed : 14.51 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 2364 helix: -1.12 (0.12), residues: 1322 sheet: -0.99 (0.36), residues: 188 loop : -2.05 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D1177 HIS 0.006 0.001 HIS A1059 PHE 0.028 0.002 PHE A 659 TYR 0.034 0.002 TYR B1031 ARG 0.010 0.001 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 421 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.7647 (mmt) cc_final: 0.6876 (tpp) REVERT: A 674 MET cc_start: 0.7454 (mtt) cc_final: 0.6902 (mmp) REVERT: A 748 LEU cc_start: 0.8068 (mp) cc_final: 0.7779 (tt) REVERT: B 405 TYR cc_start: 0.7201 (m-80) cc_final: 0.6879 (m-80) REVERT: B 651 ASP cc_start: 0.6515 (t0) cc_final: 0.6125 (p0) REVERT: B 1040 LYS cc_start: 0.6202 (pmtt) cc_final: 0.5653 (tptt) REVERT: B 1072 PHE cc_start: 0.6755 (m-80) cc_final: 0.5397 (m-80) REVERT: B 1096 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7889 (t80) REVERT: B 1187 ILE cc_start: 0.9147 (mt) cc_final: 0.8929 (tt) REVERT: C 424 TYR cc_start: 0.8042 (t80) cc_final: 0.7831 (t80) REVERT: C 702 TYR cc_start: 0.8298 (t80) cc_final: 0.8093 (t80) REVERT: D 460 TRP cc_start: 0.6450 (m100) cc_final: 0.6116 (m100) REVERT: D 651 ASP cc_start: 0.6726 (t0) cc_final: 0.5852 (p0) REVERT: D 673 TYR cc_start: 0.4481 (t80) cc_final: 0.4202 (t80) REVERT: D 699 LYS cc_start: 0.5121 (mttp) cc_final: 0.4231 (tptt) REVERT: D 790 SER cc_start: 0.8617 (m) cc_final: 0.8391 (t) REVERT: D 1031 TYR cc_start: 0.5064 (p90) cc_final: 0.4842 (p90) REVERT: D 1040 LYS cc_start: 0.6402 (pmtt) cc_final: 0.6144 (tptt) REVERT: D 1096 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7885 (t80) REVERT: D 1134 ILE cc_start: 0.8336 (mp) cc_final: 0.7941 (mm) REVERT: D 1199 MET cc_start: 0.7832 (mtt) cc_final: 0.7403 (mtt) REVERT: D 1204 HIS cc_start: 0.7287 (OUTLIER) cc_final: 0.6865 (t-90) outliers start: 54 outliers final: 20 residues processed: 458 average time/residue: 0.2808 time to fit residues: 200.8790 Evaluate side-chains 340 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 317 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 1129 THR Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.4980 chunk 67 optimal weight: 0.0470 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.9084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A1204 HIS B 587 GLN B 714 GLN B1008 GLN B1059 HIS ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19258 Z= 0.259 Angle : 0.670 9.618 26018 Z= 0.352 Chirality : 0.044 0.361 2914 Planarity : 0.004 0.042 3194 Dihedral : 9.300 107.215 2704 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 4.24 % Allowed : 16.35 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2364 helix: 0.06 (0.14), residues: 1326 sheet: -0.77 (0.36), residues: 202 loop : -1.90 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 460 HIS 0.006 0.001 HIS C1059 PHE 0.017 0.002 PHE B 495 TYR 0.050 0.002 TYR B1031 ARG 0.010 0.001 ARG D 420 *********************** 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 429 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 344 time to evaluate : 1.973 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: 0.7309 (mtt) cc_final: 0.6916 (mmp) REVERT: B 651 ASP cc_start: 0.6461 (t0) cc_final: 0.6121 (p0) REVERT: B 670 MET cc_start: 0.7533 (mmm) cc_final: 0.6855 (mpp) REVERT: B 1040 LYS cc_start: 0.6397 (pmtt) cc_final: 0.6001 (tptt) REVERT: B 1096 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7863 (t80) REVERT: B 1177 TRP cc_start: 0.5811 (OUTLIER) cc_final: 0.5011 (m100) REVERT: B 1187 ILE cc_start: 0.9173 (mt) cc_final: 0.8893 (tt) REVERT: B 1191 MET cc_start: 0.7844 (mtp) cc_final: 0.7617 (mtp) REVERT: C 473 ASP cc_start: 0.5799 (m-30) cc_final: 0.5535 (m-30) REVERT: C 674 MET cc_start: 0.6519 (mtp) cc_final: 0.5962 (mmp) REVERT: D 460 TRP cc_start: 0.6543 (m100) cc_final: 0.6176 (m100) REVERT: D 503 MET cc_start: 0.6903 (ttm) cc_final: 0.6632 (ttt) REVERT: D 549 TYR cc_start: 0.4832 (m-10) cc_final: 0.4578 (m-10) REVERT: D 651 ASP cc_start: 0.6518 (t0) cc_final: 0.5760 (p0) REVERT: D 671 TRP cc_start: 0.5906 (t-100) cc_final: 0.5630 (t-100) REVERT: D 673 TYR cc_start: 0.4629 (t80) cc_final: 0.3889 (t80) REVERT: D 1040 LYS cc_start: 0.6471 (pmtt) cc_final: 0.6262 (tptt) REVERT: D 1096 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7856 (t80) REVERT: D 1204 HIS cc_start: 0.7087 (OUTLIER) cc_final: 0.6878 (t-90) outliers start: 85 outliers final: 43 residues processed: 407 average time/residue: 0.2662 time to fit residues: 171.7037 Evaluate side-chains 340 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 293 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 ASP 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 751 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 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 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 1177 TRP Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 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 1065 THR Chi-restraints excluded: chain D residue 1081 HIS Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1154 VAL Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 0.0370 chunk 146 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 207 optimal weight: 0.0570 chunk 62 optimal weight: 0.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN B 764 ASN B1008 GLN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19258 Z= 0.193 Angle : 0.658 13.183 26018 Z= 0.334 Chirality : 0.043 0.325 2914 Planarity : 0.004 0.039 3194 Dihedral : 8.825 103.295 2702 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 3.94 % Allowed : 17.70 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2364 helix: 0.67 (0.14), residues: 1326 sheet: -0.64 (0.37), residues: 202 loop : -1.86 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 460 HIS 0.008 0.001 HIS C1059 PHE 0.014 0.001 PHE B 495 TYR 0.046 0.001 TYR B1031 ARG 0.003 0.000 ARG B 594 *********************** 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 420 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 341 time to evaluate : 2.092 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: 0.7013 (mmm) cc_final: 0.6502 (mmt) REVERT: A 527 MET cc_start: 0.8227 (ttp) cc_final: 0.7679 (ttm) REVERT: A 674 MET cc_start: 0.7327 (mtt) cc_final: 0.7008 (mmp) REVERT: A 1195 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8569 (mm) REVERT: B 508 GLN cc_start: 0.6522 (tm-30) cc_final: 0.5603 (tp40) REVERT: B 651 ASP cc_start: 0.6357 (t0) cc_final: 0.6090 (p0) REVERT: B 670 MET cc_start: 0.7638 (mmm) cc_final: 0.6968 (mpp) REVERT: B 767 TRP cc_start: 0.7540 (OUTLIER) cc_final: 0.7064 (t-100) REVERT: B 1040 LYS cc_start: 0.6380 (pmtt) cc_final: 0.5998 (tptt) REVERT: B 1096 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7791 (t80) REVERT: B 1136 SER cc_start: 0.8909 (m) cc_final: 0.8643 (t) REVERT: B 1177 TRP cc_start: 0.5532 (t60) cc_final: 0.5117 (m100) REVERT: B 1187 ILE cc_start: 0.9179 (mt) cc_final: 0.8865 (tt) REVERT: C 473 ASP cc_start: 0.5483 (m-30) cc_final: 0.5277 (m-30) REVERT: C 527 MET cc_start: 0.8340 (ttp) cc_final: 0.7822 (ttm) REVERT: C 674 MET cc_start: 0.6658 (mtp) cc_final: 0.6181 (mmp) REVERT: D 503 MET cc_start: 0.6954 (ttm) cc_final: 0.6740 (ttt) REVERT: D 508 GLN cc_start: 0.6581 (tm-30) cc_final: 0.5511 (tp40) REVERT: D 651 ASP cc_start: 0.6402 (t0) cc_final: 0.5792 (p0) REVERT: D 673 TYR cc_start: 0.4630 (t80) cc_final: 0.3852 (t80) REVERT: D 1040 LYS cc_start: 0.6749 (pmtt) cc_final: 0.6526 (tptt) REVERT: D 1096 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7634 (t80) REVERT: D 1177 TRP cc_start: 0.6033 (OUTLIER) cc_final: 0.5028 (m100) outliers start: 79 outliers final: 45 residues processed: 395 average time/residue: 0.2611 time to fit residues: 165.0055 Evaluate side-chains 357 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 307 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1135 LEU 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 674 MET Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 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 467 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 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 1032 TRP Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1177 TRP Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1191 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19258 Z= 0.364 Angle : 0.738 12.968 26018 Z= 0.381 Chirality : 0.046 0.255 2914 Planarity : 0.004 0.041 3194 Dihedral : 9.111 104.834 2702 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 4.54 % Allowed : 18.54 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.17), residues: 2364 helix: 0.70 (0.14), residues: 1314 sheet: -0.98 (0.37), residues: 188 loop : -1.96 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 460 HIS 0.008 0.002 HIS C1059 PHE 0.020 0.002 PHE D 574 TYR 0.048 0.002 TYR D1031 ARG 0.004 0.001 ARG D1101 *********************** 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 401 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 310 time to evaluate : 2.112 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 641 LYS cc_start: 0.4821 (OUTLIER) cc_final: 0.4172 (mmtp) REVERT: A 674 MET cc_start: 0.7152 (mtt) cc_final: 0.6714 (mmp) REVERT: A 1195 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8667 (mm) REVERT: B 496 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6490 (ttm) REVERT: B 651 ASP cc_start: 0.6526 (t0) cc_final: 0.6286 (p0) REVERT: B 767 TRP cc_start: 0.7801 (OUTLIER) cc_final: 0.7274 (t-100) REVERT: B 1040 LYS cc_start: 0.6484 (pmtt) cc_final: 0.6052 (tptt) REVERT: B 1096 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7780 (t80) REVERT: B 1136 SER cc_start: 0.8928 (m) cc_final: 0.8689 (t) REVERT: B 1177 TRP cc_start: 0.6388 (OUTLIER) cc_final: 0.5185 (m100) REVERT: B 1187 ILE cc_start: 0.9187 (mt) cc_final: 0.8884 (tt) REVERT: C 674 MET cc_start: 0.6722 (mtp) cc_final: 0.6335 (mmp) REVERT: C 705 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6243 (mm-30) REVERT: C 1195 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8947 (mm) REVERT: D 503 MET cc_start: 0.6867 (ttm) cc_final: 0.6596 (ttt) REVERT: D 651 ASP cc_start: 0.6397 (t0) cc_final: 0.5817 (p0) REVERT: D 1040 LYS cc_start: 0.6717 (pmtt) cc_final: 0.6467 (tptt) REVERT: D 1096 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7771 (t80) REVERT: C 1301 GLU cc_start: 0.6272 (tp30) cc_final: 0.5925 (tp30) outliers start: 91 outliers final: 57 residues processed: 377 average time/residue: 0.2694 time to fit residues: 161.3355 Evaluate side-chains 363 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 298 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1195 LEU Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain D residue 676 SER Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 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 Chi-restraints excluded: chain D residue 1191 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 136 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 192 optimal weight: 0.0570 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19258 Z= 0.174 Angle : 0.642 9.784 26018 Z= 0.325 Chirality : 0.042 0.160 2914 Planarity : 0.004 0.037 3194 Dihedral : 8.520 98.280 2702 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 3.24 % Allowed : 20.24 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2364 helix: 1.15 (0.14), residues: 1318 sheet: -0.79 (0.37), residues: 202 loop : -1.77 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 460 HIS 0.008 0.001 HIS C1059 PHE 0.023 0.001 PHE B1072 TYR 0.043 0.001 TYR D1031 ARG 0.006 0.000 ARG C 661 *********************** 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 402 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 337 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7107 (mmm) cc_final: 0.6582 (mmt) REVERT: A 1082 PHE cc_start: 0.5857 (p90) cc_final: 0.5548 (p90) REVERT: A 1195 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8614 (mm) REVERT: B 405 TYR cc_start: 0.7690 (m-80) cc_final: 0.7392 (m-80) REVERT: B 407 MET cc_start: 0.6969 (mpp) cc_final: 0.6625 (mpp) REVERT: B 503 MET cc_start: 0.6667 (ttm) cc_final: 0.6347 (ttt) REVERT: B 508 GLN cc_start: 0.6419 (tm-30) cc_final: 0.5468 (tp40) REVERT: B 767 TRP cc_start: 0.7640 (OUTLIER) cc_final: 0.7248 (t-100) REVERT: B 1040 LYS cc_start: 0.6402 (pmtt) cc_final: 0.6153 (tptt) REVERT: B 1082 PHE cc_start: 0.4267 (m-80) cc_final: 0.3577 (t80) REVERT: B 1096 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7659 (t80) REVERT: B 1133 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.5874 (tp) REVERT: B 1136 SER cc_start: 0.8958 (m) cc_final: 0.8688 (t) REVERT: B 1177 TRP cc_start: 0.5816 (OUTLIER) cc_final: 0.5166 (m100) REVERT: B 1187 ILE cc_start: 0.9159 (mt) cc_final: 0.8850 (tt) REVERT: C 697 LYS cc_start: 0.7228 (mttt) cc_final: 0.6349 (pttp) REVERT: C 711 TYR cc_start: 0.7699 (t80) cc_final: 0.7465 (t80) REVERT: D 503 MET cc_start: 0.6909 (ttm) cc_final: 0.6639 (ttt) REVERT: D 651 ASP cc_start: 0.6192 (t0) cc_final: 0.5760 (p0) REVERT: D 1031 TYR cc_start: 0.5485 (p90) cc_final: 0.5058 (p90) REVERT: D 1096 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7697 (t80) REVERT: D 1177 TRP cc_start: 0.6170 (OUTLIER) cc_final: 0.5051 (m100) outliers start: 65 outliers final: 39 residues processed: 384 average time/residue: 0.2681 time to fit residues: 163.1637 Evaluate side-chains 354 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 308 time to evaluate : 2.391 ------------------------------------------------------------------------------- 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 1056 VAL 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 723 VAL Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1057 MET Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 525 ILE Chi-restraints excluded: chain D residue 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 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1177 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 141 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN B1008 GLN C 587 GLN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19258 Z= 0.343 Angle : 0.719 11.214 26018 Z= 0.369 Chirality : 0.045 0.188 2914 Planarity : 0.004 0.066 3194 Dihedral : 8.779 100.453 2702 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 4.29 % Allowed : 20.89 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2364 helix: 0.95 (0.14), residues: 1310 sheet: -1.13 (0.36), residues: 206 loop : -1.82 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 460 HIS 0.008 0.001 HIS C1059 PHE 0.019 0.002 PHE C1126 TYR 0.042 0.002 TYR D1031 ARG 0.004 0.000 ARG C 675 *********************** 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 395 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 309 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.7116 (mmm) cc_final: 0.6651 (mmt) REVERT: A 732 TYR cc_start: 0.7810 (m-10) cc_final: 0.7452 (m-10) REVERT: A 1195 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8658 (mm) REVERT: B 407 MET cc_start: 0.6924 (mpp) cc_final: 0.6674 (mpp) REVERT: B 585 MET cc_start: 0.8631 (mmm) cc_final: 0.8401 (mtp) REVERT: B 767 TRP cc_start: 0.7818 (OUTLIER) cc_final: 0.7412 (t-100) REVERT: B 1040 LYS cc_start: 0.6525 (pmtt) cc_final: 0.6268 (tptt) REVERT: B 1096 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7646 (t80) REVERT: B 1136 SER cc_start: 0.8938 (m) cc_final: 0.8720 (t) REVERT: B 1187 ILE cc_start: 0.9170 (mt) cc_final: 0.8853 (tt) REVERT: C 697 LYS cc_start: 0.7315 (mttt) cc_final: 0.6396 (pttm) REVERT: C 1195 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8921 (mm) REVERT: D 503 MET cc_start: 0.6830 (ttm) cc_final: 0.6536 (ttt) REVERT: D 597 SER cc_start: 0.9276 (p) cc_final: 0.9052 (p) REVERT: D 651 ASP cc_start: 0.6219 (t0) cc_final: 0.5814 (p0) REVERT: D 1082 PHE cc_start: 0.4162 (m-80) cc_final: 0.3666 (t80) REVERT: D 1096 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7730 (t80) REVERT: D 1204 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6831 (t-90) outliers start: 86 outliers final: 55 residues processed: 373 average time/residue: 0.2649 time to fit residues: 157.9284 Evaluate side-chains 357 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 296 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 643 THR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 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 586 GLN Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1105 ILE Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1065 THR Chi-restraints excluded: chain C residue 1104 SER Chi-restraints excluded: chain C residue 1105 ILE Chi-restraints excluded: chain C residue 1181 PHE Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1195 LEU Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 464 VAL 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 1065 THR Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1136 SER Chi-restraints excluded: chain D residue 1177 TRP Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 chunk 138 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19258 Z= 0.171 Angle : 0.668 14.105 26018 Z= 0.333 Chirality : 0.042 0.188 2914 Planarity : 0.004 0.047 3194 Dihedral : 8.226 93.841 2702 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 2.89 % Allowed : 21.98 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2364 helix: 1.34 (0.14), residues: 1316 sheet: -1.02 (0.36), residues: 210 loop : -1.69 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 PHE 0.017 0.001 PHE D1082 TYR 0.039 0.001 TYR B1031 ARG 0.006 0.000 ARG C 675 *********************** 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 385 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 327 time to evaluate : 2.104 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 697 LYS cc_start: 0.7493 (mttt) cc_final: 0.6567 (pttp) REVERT: A 1082 PHE cc_start: 0.5897 (p90) cc_final: 0.5630 (p90) REVERT: A 1195 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8607 (mm) REVERT: B 407 MET cc_start: 0.6755 (mpp) cc_final: 0.6355 (mpp) REVERT: B 508 GLN cc_start: 0.6396 (tm-30) cc_final: 0.5491 (tp40) REVERT: B 609 THR cc_start: 0.8956 (m) cc_final: 0.8752 (m) REVERT: B 722 LYS cc_start: 0.7258 (tptt) cc_final: 0.7045 (tptt) REVERT: B 767 TRP cc_start: 0.7607 (OUTLIER) cc_final: 0.7278 (t-100) REVERT: B 1096 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7525 (t80) REVERT: B 1136 SER cc_start: 0.8892 (m) cc_final: 0.8562 (t) REVERT: B 1177 TRP cc_start: 0.5974 (OUTLIER) cc_final: 0.5411 (m100) REVERT: B 1187 ILE cc_start: 0.9152 (mt) cc_final: 0.8808 (tt) REVERT: C 408 MET cc_start: 0.4591 (mmm) cc_final: 0.4288 (mmt) REVERT: C 711 TYR cc_start: 0.7690 (t80) cc_final: 0.7416 (t80) REVERT: D 405 TYR cc_start: 0.7662 (m-80) cc_final: 0.7271 (m-80) REVERT: D 407 MET cc_start: 0.7136 (mpp) cc_final: 0.6786 (mpp) REVERT: D 503 MET cc_start: 0.6908 (ttm) cc_final: 0.6467 (ttt) REVERT: D 508 GLN cc_start: 0.6267 (tm-30) cc_final: 0.5287 (tp40) REVERT: D 651 ASP cc_start: 0.6110 (t0) cc_final: 0.5835 (p0) REVERT: D 1031 TYR cc_start: 0.5528 (p90) cc_final: 0.5224 (p90) REVERT: D 1096 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7634 (t80) REVERT: D 1177 TRP cc_start: 0.6074 (OUTLIER) cc_final: 0.5069 (m100) REVERT: D 1204 HIS cc_start: 0.7106 (OUTLIER) cc_final: 0.5786 (t-90) outliers start: 58 outliers final: 35 residues processed: 369 average time/residue: 0.2632 time to fit residues: 153.8611 Evaluate side-chains 344 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 302 time to evaluate : 2.072 ------------------------------------------------------------------------------- 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 633 ILE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1129 THR Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 586 GLN Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1057 MET Chi-restraints excluded: chain B residue 1065 THR Chi-restraints excluded: chain B residue 1081 HIS Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1181 PHE Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1177 TRP Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19258 Z= 0.280 Angle : 0.719 13.390 26018 Z= 0.361 Chirality : 0.044 0.197 2914 Planarity : 0.004 0.077 3194 Dihedral : 8.354 94.841 2702 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 2.84 % Allowed : 22.53 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2364 helix: 1.23 (0.14), residues: 1306 sheet: -1.22 (0.35), residues: 210 loop : -1.76 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 PHE 0.015 0.002 PHE C1126 TYR 0.038 0.002 TYR B1031 ARG 0.012 0.000 ARG B1098 *********************** 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 367 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 310 time to evaluate : 2.811 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: 0.7135 (mmm) cc_final: 0.6737 (mmt) REVERT: A 1195 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8631 (mm) REVERT: B 508 GLN cc_start: 0.6441 (tm-30) cc_final: 0.5431 (tp40) REVERT: B 767 TRP cc_start: 0.7774 (OUTLIER) cc_final: 0.7449 (t-100) REVERT: B 1096 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7601 (t80) REVERT: B 1177 TRP cc_start: 0.6364 (OUTLIER) cc_final: 0.5272 (m100) REVERT: B 1187 ILE cc_start: 0.9140 (mt) cc_final: 0.8806 (tt) REVERT: C 408 MET cc_start: 0.4788 (mmm) cc_final: 0.4414 (mmt) REVERT: C 690 VAL cc_start: 0.8711 (t) cc_final: 0.8459 (p) REVERT: D 405 TYR cc_start: 0.7736 (m-80) cc_final: 0.7447 (m-80) REVERT: D 503 MET cc_start: 0.6703 (ttm) cc_final: 0.6427 (ttt) REVERT: D 651 ASP cc_start: 0.6309 (t0) cc_final: 0.5922 (p0) REVERT: D 1062 LEU cc_start: 0.7915 (mp) cc_final: 0.7596 (mp) REVERT: D 1096 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7645 (t80) REVERT: D 1204 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6796 (t-90) outliers start: 57 outliers final: 44 residues processed: 353 average time/residue: 0.2709 time to fit residues: 154.2511 Evaluate side-chains 346 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 296 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1204 HIS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 586 GLN 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 723 VAL 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 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1192 VAL Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1181 PHE Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 767 TRP Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1120 CYS Chi-restraints excluded: chain D residue 1177 TRP Chi-restraints excluded: chain D residue 1198 HIS Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 190 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN B1078 GLN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19258 Z= 0.182 Angle : 0.698 14.105 26018 Z= 0.342 Chirality : 0.042 0.230 2914 Planarity : 0.004 0.042 3194 Dihedral : 7.913 89.415 2702 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 2.19 % Allowed : 23.43 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2364 helix: 1.57 (0.15), residues: 1288 sheet: -1.32 (0.39), residues: 184 loop : -1.62 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 460 HIS 0.007 0.001 HIS C1059 PHE 0.011 0.001 PHE D1072 TYR 0.037 0.001 TYR B1031 ARG 0.015 0.000 ARG A 453 ********************** 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 364 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 320 time to evaluate : 1.918 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: 0.7033 (mmm) cc_final: 0.6282 (mmt) REVERT: A 453 ARG cc_start: 0.6548 (mtm110) cc_final: 0.5913 (ttm110) REVERT: A 1082 PHE cc_start: 0.5890 (p90) cc_final: 0.5678 (p90) REVERT: A 1195 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8607 (mm) REVERT: B 508 GLN cc_start: 0.6366 (tm-30) cc_final: 0.5499 (tp40) REVERT: B 767 TRP cc_start: 0.7475 (OUTLIER) cc_final: 0.7243 (t-100) REVERT: B 1096 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7581 (t80) REVERT: B 1177 TRP cc_start: 0.5965 (OUTLIER) cc_final: 0.5414 (m100) REVERT: C 408 MET cc_start: 0.4783 (mmm) cc_final: 0.4393 (mmt) REVERT: C 431 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6203 (mm-30) REVERT: C 711 TYR cc_start: 0.7725 (t80) cc_final: 0.7467 (t80) REVERT: D 549 TYR cc_start: 0.5015 (OUTLIER) cc_final: 0.4800 (m-10) REVERT: D 651 ASP cc_start: 0.6114 (t0) cc_final: 0.5816 (p0) REVERT: D 1096 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7625 (t80) REVERT: D 1177 TRP cc_start: 0.5906 (OUTLIER) cc_final: 0.5107 (m100) REVERT: D 1204 HIS cc_start: 0.7094 (OUTLIER) cc_final: 0.5724 (t-90) outliers start: 44 outliers final: 32 residues processed: 355 average time/residue: 0.2640 time to fit residues: 148.6067 Evaluate side-chains 341 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 301 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 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 723 VAL Chi-restraints excluded: chain B residue 767 TRP Chi-restraints excluded: chain B residue 1078 GLN Chi-restraints excluded: chain B residue 1096 PHE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1120 CYS Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1177 TRP Chi-restraints excluded: chain B residue 1191 MET Chi-restraints excluded: chain B residue 1204 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1181 PHE Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1204 HIS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 1065 THR Chi-restraints excluded: chain D residue 1096 PHE Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1177 TRP Chi-restraints excluded: chain D residue 1204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 175 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 190 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1078 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.132920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.106652 restraints weight = 43290.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.108175 restraints weight = 29603.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108578 restraints weight = 22757.582| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.317 19258 Z= 0.311 Angle : 0.858 59.199 26018 Z= 0.458 Chirality : 0.043 0.369 2914 Planarity : 0.004 0.039 3194 Dihedral : 7.900 89.399 2702 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 2.39 % Allowed : 23.33 % Favored : 74.28 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2364 helix: 1.57 (0.15), residues: 1288 sheet: -1.32 (0.39), residues: 184 loop : -1.62 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP D 460 HIS 0.008 0.001 HIS C1059 PHE 0.014 0.001 PHE B1186 TYR 0.036 0.001 TYR B1031 ARG 0.015 0.000 ARG A1098 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4072.68 seconds wall clock time: 74 minutes 31.47 seconds (4471.47 seconds total)