Starting phenix.real_space_refine on Mon Dec 11 19:14:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnp_26017/12_2023/7tnp_26017_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnp_26017/12_2023/7tnp_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_26017/12_2023/7tnp_26017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnp_26017/12_2023/7tnp_26017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnp_26017/12_2023/7tnp_26017_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnp_26017/12_2023/7tnp_26017_updated.pdb" } 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 Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1203": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "B ARG 1005": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B TYR 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1203": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1203": "NH1" <-> "NH2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 819": "NH1" <-> "NH2" Residue "D ARG 1005": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D TYR 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1203": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 18840 Number of models: 1 Model: "" Number of chains: 8 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Time building chain proxies: 10.20, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.41 Conformation dependent library (CDL) restraints added in 3.9 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... running ksdssp... Secondary structure from input PDB file: 86 helices and 18 sheets defined 48.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 523 through 544 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 573 through 584 Processing helix chain 'A' and resid 596 through 623 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 654 through 661 removed outlier: 4.390A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 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 686 through 696 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 713 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 741 through 755 removed outlier: 4.106A pdb=" N THR A 744 " --> pdb=" O SER A 741 " (cutoff:3.500A) Proline residue: A 745 - end of helix removed outlier: 3.879A pdb=" N LEU A 751 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 755 " --> pdb=" O LYS A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 768 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 794 through 821 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 1007 through 1027 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 1092 through 1102 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 1105 through 1124 removed outlier: 3.780A pdb=" N LEU A1114 " --> pdb=" O SER A1110 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A1124 " --> pdb=" O CYS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1159 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) Processing helix chain 'A' and resid 1179 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 424 through 436 removed outlier: 3.566A pdb=" N LYS B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 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 516 through 519 Processing helix chain 'B' and resid 523 through 543 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) Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 599 through 616 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 620 through 625 removed outlier: 3.604A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 640 No H-bonds generated for 'chain 'B' and resid 637 through 640' Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 675 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) Processing helix chain 'B' and resid 686 through 696 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) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.709A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 755 removed outlier: 3.765A pdb=" N THR B 744 " --> pdb=" O SER B 741 " (cutoff:3.500A) Proline residue: B 745 - end of helix removed outlier: 3.788A pdb=" N LEU B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 750 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 751 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 755 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 769 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) Processing helix chain 'B' and resid 794 through 819 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 1005 through 1027 removed outlier: 3.780A pdb=" N ALA B1026 " --> pdb=" O LEU B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1088 removed outlier: 4.399A pdb=" N TYR B1088 " --> pdb=" O ASP B1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1085 through 1088' Processing helix chain 'B' and resid 1092 through 1102 Processing helix chain 'B' and resid 1105 through 1120 removed outlier: 3.670A pdb=" N LEU B1114 " --> pdb=" O SER B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1159 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 1179 through 1208 removed outlier: 3.511A pdb=" N GLY B1193 " --> pdb=" O ALA B1189 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 523 through 544 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 573 through 584 Processing helix chain 'C' and resid 596 through 623 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 654 through 661 removed outlier: 4.390A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 675 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 686 through 696 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 713 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 741 through 755 removed outlier: 4.105A pdb=" N THR C 744 " --> pdb=" O SER C 741 " (cutoff:3.500A) Proline residue: C 745 - end of helix removed outlier: 3.879A pdb=" N LEU C 751 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 754 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 755 " --> pdb=" O LYS C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 768 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 794 through 821 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 1007 through 1027 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 1092 through 1102 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 1105 through 1124 removed outlier: 3.779A pdb=" N LEU C1114 " --> pdb=" O SER C1110 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C1124 " --> pdb=" O CYS C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1159 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) Processing helix chain 'C' and resid 1179 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 424 through 436 removed outlier: 3.566A pdb=" N LYS D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 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 516 through 519 Processing helix chain 'D' and resid 523 through 543 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) Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 599 through 616 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 620 through 625 removed outlier: 3.604A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 640 No H-bonds generated for 'chain 'D' and resid 637 through 640' Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 665 through 675 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) Processing helix chain 'D' and resid 686 through 696 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) Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.709A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 755 removed outlier: 3.764A pdb=" N THR D 744 " --> pdb=" O SER D 741 " (cutoff:3.500A) Proline residue: D 745 - end of helix removed outlier: 3.788A pdb=" N LEU D 748 " --> pdb=" O PRO D 745 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 750 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU D 751 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU D 755 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 769 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) Processing helix chain 'D' and resid 794 through 819 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 1005 through 1027 removed outlier: 3.780A pdb=" N ALA D1026 " --> pdb=" O LEU D1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1088 removed outlier: 4.399A pdb=" N TYR D1088 " --> pdb=" O ASP D1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1085 through 1088' Processing helix chain 'D' and resid 1092 through 1102 Processing helix chain 'D' and resid 1105 through 1120 removed outlier: 3.669A pdb=" N LEU D1114 " --> pdb=" O SER D1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1159 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 1179 through 1208 removed outlier: 3.512A pdb=" N GLY D1193 " --> pdb=" O ALA D1189 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 474 through 476 Processing sheet with id= C, first strand: chain 'A' and resid 721 through 723 removed outlier: 3.732A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 702 " --> pdb=" O MET A 503 " (cutoff:3.500A) 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) Processing sheet with id= D, 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= E, first strand: chain 'B' and resid 395 through 397 Processing sheet with id= F, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= G, 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= H, first strand: chain 'B' and resid 1033 through 1036 Processing sheet with id= I, first strand: chain 'B' and resid 494 through 498 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= J, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= K, first strand: chain 'C' and resid 474 through 476 Processing sheet with id= L, first strand: chain 'C' and resid 721 through 723 removed outlier: 3.732A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 702 " --> pdb=" O MET C 503 " (cutoff:3.500A) 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) Processing sheet with id= M, 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= N, first strand: chain 'D' and resid 395 through 397 Processing sheet with id= O, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= P, 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= Q, first strand: chain 'D' and resid 1033 through 1036 Processing sheet with id= R, first strand: chain 'D' and resid 494 through 498 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) 772 hydrogen bonds defined for protein. 2226 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: 5.71 Time building geometry restraints manager: 7.97 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: 93.20 - 101.59: 94 101.59 - 109.97: 3324 109.97 - 118.35: 11418 118.35 - 126.73: 10945 126.73 - 135.11: 237 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: 5549 2.80 - 3.33: 17821 3.33 - 3.85: 30817 3.85 - 4.38: 36258 4.38 - 4.90: 59802 Nonbonded interactions: 150247 Sorted by model distance: nonbonded pdb=" O MET B1009 " pdb=" OG1 THR B1013 " model vdw 2.280 2.440 nonbonded pdb=" O MET D1009 " pdb=" OG1 THR D1013 " model vdw 2.280 2.440 nonbonded pdb=" OG SER A 597 " pdb=" O ALA B 806 " model vdw 2.318 2.440 nonbonded pdb=" OG SER C 597 " pdb=" O ALA D 806 " model vdw 2.342 2.440 nonbonded pdb=" O LEU D 639 " pdb=" OH TYR D 647 " model vdw 2.352 2.440 ... (remaining 150242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 820 or resid 1002 through 1169 or resid 1171 t \ hrough 1208 or resid 1301 through 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 through 1302)) selection = (chain 'C' and (resid 394 through 820 or resid 1002 through 1169 or resid 1171 t \ hrough 1208 or resid 1301 through 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 through 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: 3.360 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: 8.080 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 51.680 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.130 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.160 ------------------------------------------------------------------------------- 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= 0.546 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 : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 621 average time/residue: 0.3067 time to fit residues: 285.1030 Evaluate side-chains 313 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 1.925 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1627 time to fit residues: 2.9012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19258 Z= 0.197 Angle : 0.669 9.994 26018 Z= 0.349 Chirality : 0.043 0.337 2914 Planarity : 0.005 0.047 3194 Dihedral : 9.909 114.227 2702 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 2.84 % Allowed : 15.05 % Favored : 82.10 % 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: -2.52 (0.15), residues: 2364 helix: -1.44 (0.12), residues: 1306 sheet: -1.19 (0.38), residues: 168 loop : -1.91 (0.18), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D1177 HIS 0.005 0.001 HIS A1059 PHE 0.026 0.002 PHE A 659 TYR 0.051 0.002 TYR B1031 ARG 0.008 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 458 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 401 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 23 residues processed: 439 average time/residue: 0.2847 time to fit residues: 194.6670 Evaluate side-chains 334 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 311 time to evaluate : 2.153 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1783 time to fit residues: 10.3112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.0000 chunk 67 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.0870 chunk 235 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.1966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN 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: 0.7626 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19258 Z= 0.202 Angle : 0.625 10.566 26018 Z= 0.325 Chirality : 0.042 0.227 2914 Planarity : 0.004 0.050 3194 Dihedral : 9.317 109.132 2702 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 2.69 % Allowed : 17.85 % Favored : 79.46 % 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: -1.35 (0.16), residues: 2364 helix: -0.24 (0.14), residues: 1302 sheet: -0.90 (0.37), residues: 188 loop : -1.78 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1177 HIS 0.006 0.001 HIS C1059 PHE 0.015 0.002 PHE B 495 TYR 0.047 0.002 TYR B1031 ARG 0.005 0.000 ARG C 453 *********************** 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 406 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 352 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 21 residues processed: 391 average time/residue: 0.2815 time to fit residues: 173.2782 Evaluate side-chains 327 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 306 time to evaluate : 2.047 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1699 time to fit residues: 9.4386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 207 optimal weight: 0.0370 chunk 62 optimal weight: 0.0000 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19258 Z= 0.164 Angle : 0.591 8.307 26018 Z= 0.302 Chirality : 0.041 0.255 2914 Planarity : 0.003 0.037 3194 Dihedral : 8.768 104.503 2702 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 2.59 % Allowed : 18.79 % Favored : 78.61 % 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: -0.68 (0.17), residues: 2364 helix: 0.44 (0.14), residues: 1300 sheet: -0.75 (0.37), residues: 198 loop : -1.70 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 460 HIS 0.006 0.001 HIS C1059 PHE 0.015 0.001 PHE C1115 TYR 0.042 0.001 TYR D1031 ARG 0.005 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 361 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 19 residues processed: 394 average time/residue: 0.2838 time to fit residues: 178.1537 Evaluate side-chains 334 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 315 time to evaluate : 2.251 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1865 time to fit residues: 9.5810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 3 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 95 optimal weight: 0.3980 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19258 Z= 0.192 Angle : 0.600 9.426 26018 Z= 0.309 Chirality : 0.041 0.199 2914 Planarity : 0.003 0.036 3194 Dihedral : 8.586 101.194 2702 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 2.04 % Allowed : 19.64 % Favored : 78.32 % 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: -0.23 (0.17), residues: 2364 helix: 0.90 (0.14), residues: 1286 sheet: -1.09 (0.39), residues: 164 loop : -1.48 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 460 HIS 0.005 0.001 HIS C1059 PHE 0.014 0.001 PHE B 495 TYR 0.039 0.001 TYR D1031 ARG 0.004 0.000 ARG C 675 *********************** 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 366 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 325 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 13 residues processed: 348 average time/residue: 0.2858 time to fit residues: 159.5043 Evaluate side-chains 315 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 302 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1737 time to fit residues: 7.0157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 45 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 192 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 791 ASN B 764 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7680 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19258 Z= 0.265 Angle : 0.625 9.009 26018 Z= 0.323 Chirality : 0.042 0.203 2914 Planarity : 0.004 0.039 3194 Dihedral : 8.732 101.818 2702 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 2.49 % Allowed : 20.39 % Favored : 77.12 % 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: -0.23 (0.17), residues: 2364 helix: 0.92 (0.14), residues: 1294 sheet: -1.19 (0.39), residues: 164 loop : -1.51 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 671 HIS 0.008 0.002 HIS C1204 PHE 0.017 0.002 PHE B 495 TYR 0.034 0.002 TYR D1031 ARG 0.004 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 358 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 308 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 17 residues processed: 339 average time/residue: 0.2850 time to fit residues: 153.0103 Evaluate side-chains 312 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 295 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1794 time to fit residues: 8.4056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 0.0980 chunk 129 optimal weight: 0.6980 chunk 231 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 106 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 619 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19258 Z= 0.148 Angle : 0.611 10.497 26018 Z= 0.302 Chirality : 0.040 0.215 2914 Planarity : 0.003 0.032 3194 Dihedral : 8.183 94.614 2702 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 1.60 % Allowed : 21.09 % Favored : 77.32 % 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: 0.07 (0.17), residues: 2364 helix: 1.25 (0.15), residues: 1288 sheet: -1.14 (0.40), residues: 148 loop : -1.48 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 671 HIS 0.005 0.001 HIS A 412 PHE 0.017 0.001 PHE A1115 TYR 0.033 0.001 TYR D1031 ARG 0.005 0.000 ARG D 485 *********************** 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 380 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 348 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 369 average time/residue: 0.2754 time to fit residues: 162.6020 Evaluate side-chains 318 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 305 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1893 time to fit residues: 7.7881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.0870 chunk 92 optimal weight: 0.3980 chunk 138 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1008 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19258 Z= 0.235 Angle : 0.620 10.690 26018 Z= 0.315 Chirality : 0.042 0.165 2914 Planarity : 0.003 0.035 3194 Dihedral : 8.269 98.236 2702 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.26 % Rotamer: Outliers : 1.40 % Allowed : 22.53 % Favored : 76.07 % 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: 0.04 (0.17), residues: 2364 helix: 1.22 (0.15), residues: 1292 sheet: -1.31 (0.36), residues: 180 loop : -1.46 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 671 HIS 0.006 0.001 HIS A1204 PHE 0.019 0.002 PHE A1072 TYR 0.031 0.002 TYR D1031 ARG 0.003 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 328 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 300 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 316 average time/residue: 0.2713 time to fit residues: 137.2879 Evaluate side-chains 292 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 283 time to evaluate : 2.081 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1802 time to fit residues: 5.7552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1204 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19258 Z= 0.204 Angle : 0.627 11.949 26018 Z= 0.314 Chirality : 0.041 0.170 2914 Planarity : 0.003 0.035 3194 Dihedral : 8.161 97.234 2702 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 0.55 % Allowed : 23.18 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.08 (0.17), residues: 2364 helix: 1.24 (0.15), residues: 1292 sheet: -1.31 (0.36), residues: 180 loop : -1.40 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 671 HIS 0.004 0.001 HIS A1059 PHE 0.024 0.001 PHE B1082 TYR 0.030 0.002 TYR D1031 ARG 0.005 0.000 ARG A 661 *********************** 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 312 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 301 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 307 average time/residue: 0.2894 time to fit residues: 140.7967 Evaluate side-chains 287 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 283 time to evaluate : 2.323 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1990 time to fit residues: 4.3871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1078 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19258 Z= 0.303 Angle : 0.679 12.226 26018 Z= 0.347 Chirality : 0.044 0.202 2914 Planarity : 0.004 0.038 3194 Dihedral : 8.512 102.261 2702 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 0.55 % Allowed : 23.78 % Favored : 75.67 % 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: -0.16 (0.17), residues: 2364 helix: 1.03 (0.14), residues: 1288 sheet: -1.57 (0.36), residues: 168 loop : -1.46 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 460 HIS 0.006 0.001 HIS C1081 PHE 0.044 0.002 PHE D1186 TYR 0.035 0.002 TYR B 673 ARG 0.004 0.000 ARG C 675 ********************** 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 300 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 289 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 295 average time/residue: 0.2848 time to fit residues: 132.4789 Evaluate side-chains 284 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 277 time to evaluate : 2.117 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1873 time to fit residues: 5.1636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 52 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1204 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.133346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108722 restraints weight = 42810.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108536 restraints weight = 37589.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109111 restraints weight = 29458.751| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19258 Z= 0.174 Angle : 0.631 12.658 26018 Z= 0.313 Chirality : 0.041 0.185 2914 Planarity : 0.003 0.031 3194 Dihedral : 8.020 95.420 2702 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.98 % Rotamer: Outliers : 0.35 % Allowed : 23.98 % Favored : 75.67 % 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: 0.08 (0.17), residues: 2364 helix: 1.25 (0.15), residues: 1288 sheet: -1.28 (0.40), residues: 148 loop : -1.45 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 460 HIS 0.004 0.001 HIS A1059 PHE 0.032 0.001 PHE D1186 TYR 0.029 0.001 TYR B 673 ARG 0.004 0.000 ARG C 675 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4012.13 seconds wall clock time: 73 minutes 57.17 seconds (4437.17 seconds total)