Starting phenix.real_space_refine on Wed Mar 4 15:28:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qd7_4520/03_2026/6qd7_4520.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qd7_4520/03_2026/6qd7_4520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qd7_4520/03_2026/6qd7_4520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qd7_4520/03_2026/6qd7_4520.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qd7_4520/03_2026/6qd7_4520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qd7_4520/03_2026/6qd7_4520.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.103 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 9123 2.51 5 N 2466 2.21 5 O 2805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14445 Number of models: 1 Model: "" Number of chains: 24 Chain: "L" Number of atoms: 827 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} bond proxies already assigned to first conformer: 839 Chain: "H" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 909 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1928 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 44 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "C" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1928 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 44 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1928 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 44 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "F" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1032 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "X" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 909 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "U" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 909 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "Z" Number of atoms: 827 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} bond proxies already assigned to first conformer: 839 Chain: "P" Number of atoms: 827 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Conformer: "B" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} bond proxies already assigned to first conformer: 839 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.51, per 1000 atoms: 0.24 Number of scatterers: 14445 At special positions: 0 Unit cell: (133.45, 123.25, 126.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2805 8.00 N 2466 7.00 C 9123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 93 " distance=2.05 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.01 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.04 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS D 609 " distance=2.20 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.04 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.04 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS F 609 " distance=1.90 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.04 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 93 " distance=2.05 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 93 " distance=2.05 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 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 Links applied ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 701 " - " ASN B 618 " " NAG D 701 " - " ASN D 618 " " NAG F 701 " - " ASN F 618 " " NAG G 1 " - " ASN B 563 " " NAG I 1 " - " ASN D 563 " " NAG J 1 " - " ASN F 563 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 515.3 milliseconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 33 sheets defined 19.2% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.591A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 removed outlier: 3.676A pdb=" N LYS A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'B' and resid 538 through 541 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.565A pdb=" N GLN B 560 " --> pdb=" O CYS B 556 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 598 Processing helix chain 'B' and resid 612 through 622 Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.520A pdb=" N ILE B 627 " --> pdb=" O ILE B 623 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS B 628 " --> pdb=" O ASP B 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 623 through 628' Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.676A pdb=" N LYS C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 84 removed outlier: 3.676A pdb=" N LYS E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 264 Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 3.565A pdb=" N GLN D 560 " --> pdb=" O CYS D 556 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 Processing helix chain 'D' and resid 612 through 622 Processing helix chain 'D' and resid 623 through 628 removed outlier: 3.520A pdb=" N ILE D 627 " --> pdb=" O ILE D 623 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS D 628 " --> pdb=" O ASP D 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 623 through 628' Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 3.565A pdb=" N GLN F 560 " --> pdb=" O CYS F 556 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 Processing helix chain 'F' and resid 612 through 622 Processing helix chain 'F' and resid 623 through 628 removed outlier: 3.520A pdb=" N ILE F 627 " --> pdb=" O ILE F 623 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS F 628 " --> pdb=" O ASP F 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 623 through 628' Processing helix chain 'X' and resid 28 through 32 Processing helix chain 'X' and resid 62 through 65 Processing helix chain 'X' and resid 74 through 76 No H-bonds generated for 'chain 'X' and resid 74 through 76' Processing helix chain 'X' and resid 84 through 88 Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 62 through 65 Processing helix chain 'U' and resid 74 through 76 No H-bonds generated for 'chain 'U' and resid 74 through 76' Processing helix chain 'U' and resid 84 through 88 Processing helix chain 'Z' and resid 79 through 83 removed outlier: 3.549A pdb=" N VAL Z 83 " --> pdb=" O PRO Z 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.555A pdb=" N VAL P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.882A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.882A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU H 107 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 45 Processing sheet with id=AA8, first strand: chain 'A' and resid 42 through 45 removed outlier: 7.026A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.091A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 232 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 241 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP A 275 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 243 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS A 272 " --> pdb=" O UNK A 472 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N UNK A 474 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 274 " --> pdb=" O UNK A 474 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N UNK A 476 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 42 through 45 Processing sheet with id=AB4, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.831A pdb=" N VAL C 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AB7, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.091A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR C 232 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 241 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP C 275 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN C 243 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS C 272 " --> pdb=" O UNK C 472 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N UNK C 474 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 274 " --> pdb=" O UNK C 474 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N UNK C 476 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 45 Processing sheet with id=AB9, first strand: chain 'E' and resid 42 through 45 removed outlier: 7.032A pdb=" N VAL E 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AC2, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AC3, first strand: chain 'E' and resid 105 through 114 removed outlier: 6.091A pdb=" N GLU E 106 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS E 139 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU E 112 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR E 232 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR E 241 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP E 275 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN E 243 " --> pdb=" O TRP E 275 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS E 272 " --> pdb=" O UNK E 472 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N UNK E 474 " --> pdb=" O LYS E 272 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE E 274 " --> pdb=" O UNK E 474 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N UNK E 476 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'X' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY X 10 " --> pdb=" O THR X 115 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET X 34 " --> pdb=" O THR X 50 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 10 through 12 removed outlier: 5.996A pdb=" N GLY X 10 " --> pdb=" O THR X 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU X 107 " --> pdb=" O LYS X 95 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'U' and resid 10 through 12 removed outlier: 5.995A pdb=" N GLY U 10 " --> pdb=" O THR U 115 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET U 34 " --> pdb=" O THR U 50 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 10 through 12 removed outlier: 5.995A pdb=" N GLY U 10 " --> pdb=" O THR U 115 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU U 107 " --> pdb=" O LYS U 95 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'Z' and resid 10 through 13 removed outlier: 5.910A pdb=" N LEU Z 11 " --> pdb=" O GLU Z 105 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA Z 84 " --> pdb=" O VAL Z 104 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU Z 33 " --> pdb=" O TYR Z 49 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TYR Z 49 " --> pdb=" O LEU Z 33 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP Z 35 " --> pdb=" O LEU Z 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Z' and resid 10 through 13 removed outlier: 5.910A pdb=" N LEU Z 11 " --> pdb=" O GLU Z 105 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA Z 84 " --> pdb=" O VAL Z 104 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR Z 97 " --> pdb=" O GLN Z 90 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'P' and resid 10 through 13 removed outlier: 5.961A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 10 through 13 removed outlier: 5.961A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1413 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: 2.54 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4220 1.34 - 1.46: 3679 1.46 - 1.59: 6807 1.59 - 1.71: 3 1.71 - 1.83: 60 Bond restraints: 14769 Sorted by residual: bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C1 NAG F 701 " pdb=" O5 NAG F 701 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C5 MAN J 4 " pdb=" O5 MAN J 4 " ideal model delta sigma weight residual 1.418 1.492 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.418 1.492 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 14764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 19538 4.25 - 8.49: 475 8.49 - 12.74: 45 12.74 - 16.99: 12 16.99 - 21.23: 6 Bond angle restraints: 20076 Sorted by residual: angle pdb=" CA LEU A 256 " pdb=" CB LEU A 256 " pdb=" CG LEU A 256 " ideal model delta sigma weight residual 116.30 137.53 -21.23 3.50e+00 8.16e-02 3.68e+01 angle pdb=" CA LEU E 256 " pdb=" CB LEU E 256 " pdb=" CG LEU E 256 " ideal model delta sigma weight residual 116.30 137.53 -21.23 3.50e+00 8.16e-02 3.68e+01 angle pdb=" CA LEU C 256 " pdb=" CB LEU C 256 " pdb=" CG LEU C 256 " ideal model delta sigma weight residual 116.30 137.48 -21.18 3.50e+00 8.16e-02 3.66e+01 angle pdb=" CA GLU A 229 " pdb=" CB GLU A 229 " pdb=" CG GLU A 229 " ideal model delta sigma weight residual 114.10 125.69 -11.59 2.00e+00 2.50e-01 3.36e+01 angle pdb=" CA GLU C 229 " pdb=" CB GLU C 229 " pdb=" CG GLU C 229 " ideal model delta sigma weight residual 114.10 125.65 -11.55 2.00e+00 2.50e-01 3.34e+01 ... (remaining 20071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.96: 8404 22.96 - 45.92: 437 45.92 - 68.88: 82 68.88 - 91.84: 62 91.84 - 114.80: 15 Dihedral angle restraints: 9000 sinusoidal: 3735 harmonic: 5265 Sorted by residual: dihedral pdb=" C ASN F 618 " pdb=" N ASN F 618 " pdb=" CA ASN F 618 " pdb=" CB ASN F 618 " ideal model delta harmonic sigma weight residual -122.60 -135.12 12.52 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C ASN B 618 " pdb=" N ASN B 618 " pdb=" CA ASN B 618 " pdb=" CB ASN B 618 " ideal model delta harmonic sigma weight residual -122.60 -135.09 12.49 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C ASN D 618 " pdb=" N ASN D 618 " pdb=" CA ASN D 618 " pdb=" CB ASN D 618 " ideal model delta harmonic sigma weight residual -122.60 -135.09 12.49 0 2.50e+00 1.60e-01 2.49e+01 ... (remaining 8997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1784 0.097 - 0.193: 423 0.193 - 0.290: 56 0.290 - 0.387: 13 0.387 - 0.483: 10 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CB ILE E 274 " pdb=" CA ILE E 274 " pdb=" CG1 ILE E 274 " pdb=" CG2 ILE E 274 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CB ILE A 274 " pdb=" CA ILE A 274 " pdb=" CG1 ILE A 274 " pdb=" CG2 ILE A 274 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CB ILE C 274 " pdb=" CA ILE C 274 " pdb=" CG1 ILE C 274 " pdb=" CG2 ILE C 274 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 2283 not shown) Planarity restraints: 2580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 235 " 0.044 2.00e-02 2.50e+03 8.66e-02 7.49e+01 pdb=" CD GLU E 235 " -0.150 2.00e-02 2.50e+03 pdb=" OE1 GLU E 235 " 0.058 2.00e-02 2.50e+03 pdb=" OE2 GLU E 235 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 235 " -0.044 2.00e-02 2.50e+03 8.64e-02 7.47e+01 pdb=" CD GLU A 235 " 0.149 2.00e-02 2.50e+03 pdb=" OE1 GLU A 235 " -0.057 2.00e-02 2.50e+03 pdb=" OE2 GLU A 235 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 235 " -0.044 2.00e-02 2.50e+03 8.63e-02 7.44e+01 pdb=" CD GLU C 235 " 0.149 2.00e-02 2.50e+03 pdb=" OE1 GLU C 235 " -0.057 2.00e-02 2.50e+03 pdb=" OE2 GLU C 235 " -0.048 2.00e-02 2.50e+03 ... (remaining 2577 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1938 2.77 - 3.30: 12944 3.30 - 3.83: 23167 3.83 - 4.37: 27292 4.37 - 4.90: 47553 Nonbonded interactions: 112894 Sorted by model distance: nonbonded pdb=" OD2 ASP C 78 " pdb=" OG SER C 246 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP E 78 " pdb=" OG SER E 246 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP A 78 " pdb=" OG SER A 246 " model vdw 2.234 3.040 nonbonded pdb=" NZ LYS F 622 " pdb=" O7 NAG F 701 " model vdw 2.310 3.120 nonbonded pdb=" NZ LYS B 622 " pdb=" O7 NAG B 701 " model vdw 2.310 3.120 ... (remaining 112889 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'U' selection = chain 'X' } ncs_group { reference = (chain 'L' and (resid 1 through 21 or resid 23 through 108)) selection = (chain 'P' and (resid 1 through 21 or resid 23 through 108)) selection = (chain 'Z' and (resid 1 through 21 or resid 23 through 108)) } 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.360 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 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 : 0.009 0.167 14805 Z= 0.415 Angle : 1.665 21.233 20163 Z= 0.879 Chirality : 0.088 0.483 2286 Planarity : 0.010 0.087 2574 Dihedral : 16.736 114.797 5565 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.72 % Favored : 95.11 % Rotamer: Outliers : 4.53 % Allowed : 6.43 % Favored : 89.04 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.18), residues: 1782 helix: 0.20 (0.30), residues: 210 sheet: -0.42 (0.20), residues: 549 loop : -0.76 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG X 19 TYR 0.052 0.005 TYR C 241 PHE 0.078 0.005 PHE E 307 TRP 0.036 0.004 TRP Z 35 HIS 0.014 0.003 HIS B 613 Details of bonding type rmsd covalent geometry : bond 0.00862 (14769) covalent geometry : angle 1.61506 (20076) SS BOND : bond 0.04739 ( 21) SS BOND : angle 3.49351 ( 42) hydrogen bonds : bond 0.15840 ( 528) hydrogen bonds : angle 7.85565 ( 1413) link_ALPHA1-6 : bond 0.00502 ( 3) link_ALPHA1-6 : angle 5.53135 ( 9) link_BETA1-4 : bond 0.00865 ( 6) link_BETA1-4 : angle 5.56072 ( 18) link_NAG-ASN : bond 0.01419 ( 6) link_NAG-ASN : angle 10.98824 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 192 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 618 ASN cc_start: -0.2380 (OUTLIER) cc_final: -0.3042 (p0) REVERT: D 618 ASN cc_start: -0.2241 (OUTLIER) cc_final: -0.2828 (p0) REVERT: F 618 ASN cc_start: -0.1413 (OUTLIER) cc_final: -0.2105 (p0) outliers start: 66 outliers final: 31 residues processed: 252 average time/residue: 0.1427 time to fit residues: 49.8891 Evaluate side-chains 164 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain D residue 604 LEU Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain U residue 5 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 257 ASN B 516 HIS ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 257 ASN E 61 ASN E 257 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.229427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.182726 restraints weight = 29553.335| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 5.82 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4099 r_free = 0.4099 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14805 Z= 0.174 Angle : 0.793 13.456 20163 Z= 0.400 Chirality : 0.049 0.197 2286 Planarity : 0.006 0.085 2574 Dihedral : 11.716 91.367 2410 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.56 % Allowed : 11.09 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.19), residues: 1782 helix: 1.01 (0.35), residues: 219 sheet: -0.34 (0.20), residues: 540 loop : -0.18 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Z 61 TYR 0.016 0.002 TYR X 80 PHE 0.015 0.002 PHE A 194 TRP 0.012 0.002 TRP L 35 HIS 0.006 0.001 HIS F 613 Details of bonding type rmsd covalent geometry : bond 0.00382 (14769) covalent geometry : angle 0.76034 (20076) SS BOND : bond 0.00590 ( 21) SS BOND : angle 1.42044 ( 42) hydrogen bonds : bond 0.05352 ( 528) hydrogen bonds : angle 6.16531 ( 1413) link_ALPHA1-6 : bond 0.01316 ( 3) link_ALPHA1-6 : angle 2.69829 ( 9) link_BETA1-4 : bond 0.00913 ( 6) link_BETA1-4 : angle 3.25665 ( 18) link_NAG-ASN : bond 0.00949 ( 6) link_NAG-ASN : angle 6.38364 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.5851 (p0) cc_final: 0.5626 (p0) REVERT: H 80 TYR cc_start: 0.7365 (m-80) cc_final: 0.6779 (m-80) REVERT: B 618 ASN cc_start: -0.1656 (OUTLIER) cc_final: -0.2301 (p0) REVERT: D 618 ASN cc_start: -0.2470 (OUTLIER) cc_final: -0.3397 (p0) REVERT: F 618 ASN cc_start: -0.1593 (OUTLIER) cc_final: -0.2135 (p0) outliers start: 36 outliers final: 16 residues processed: 188 average time/residue: 0.1355 time to fit residues: 35.7624 Evaluate side-chains 152 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 609 CYS Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 115 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 151 optimal weight: 0.0060 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 HIS ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN F 567 GLN F 595 GLN Z 6 GLN Z 38 HIS P 38 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.229832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.185508 restraints weight = 29901.130| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 4.74 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4140 r_free = 0.4140 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4140 r_free = 0.4140 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14805 Z= 0.183 Angle : 0.765 12.578 20163 Z= 0.379 Chirality : 0.048 0.229 2286 Planarity : 0.006 0.067 2574 Dihedral : 9.637 78.929 2371 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.82 % Allowed : 11.09 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.19), residues: 1782 helix: 1.06 (0.35), residues: 219 sheet: -0.34 (0.22), residues: 510 loop : -0.33 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 596 TYR 0.015 0.002 TYR E 232 PHE 0.014 0.002 PHE C 194 TRP 0.016 0.002 TRP B 531 HIS 0.005 0.001 HIS F 613 Details of bonding type rmsd covalent geometry : bond 0.00425 (14769) covalent geometry : angle 0.73135 (20076) SS BOND : bond 0.00442 ( 21) SS BOND : angle 1.51252 ( 42) hydrogen bonds : bond 0.05080 ( 528) hydrogen bonds : angle 6.01930 ( 1413) link_ALPHA1-6 : bond 0.01171 ( 3) link_ALPHA1-6 : angle 3.01954 ( 9) link_BETA1-4 : bond 0.00580 ( 6) link_BETA1-4 : angle 3.36346 ( 18) link_NAG-ASN : bond 0.00902 ( 6) link_NAG-ASN : angle 6.12033 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.433 Fit side-chains REVERT: B 618 ASN cc_start: -0.1523 (OUTLIER) cc_final: -0.2626 (p0) REVERT: D 618 ASN cc_start: -0.2314 (OUTLIER) cc_final: -0.3226 (p0) REVERT: F 591 ASP cc_start: 0.7506 (m-30) cc_final: 0.7265 (m-30) REVERT: F 618 ASN cc_start: -0.1240 (OUTLIER) cc_final: -0.1899 (p0) outliers start: 40 outliers final: 25 residues processed: 177 average time/residue: 0.1412 time to fit residues: 35.1105 Evaluate side-chains 157 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 609 CYS Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain X residue 93 CYS Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 91 optimal weight: 0.4980 chunk 77 optimal weight: 9.9990 chunk 5 optimal weight: 0.0370 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN F 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.232600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.193867 restraints weight = 30542.314| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 4.20 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4218 r_free = 0.4218 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4218 r_free = 0.4218 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14805 Z= 0.132 Angle : 0.679 11.519 20163 Z= 0.334 Chirality : 0.046 0.209 2286 Planarity : 0.005 0.044 2574 Dihedral : 7.835 66.962 2369 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.76 % Allowed : 12.60 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1782 helix: 0.99 (0.34), residues: 219 sheet: -0.32 (0.22), residues: 546 loop : -0.46 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.012 0.001 TYR A 232 PHE 0.013 0.001 PHE A 234 TRP 0.019 0.001 TRP B 531 HIS 0.006 0.001 HIS D 602 Details of bonding type rmsd covalent geometry : bond 0.00286 (14769) covalent geometry : angle 0.64820 (20076) SS BOND : bond 0.00358 ( 21) SS BOND : angle 1.27032 ( 42) hydrogen bonds : bond 0.04083 ( 528) hydrogen bonds : angle 5.65192 ( 1413) link_ALPHA1-6 : bond 0.01454 ( 3) link_ALPHA1-6 : angle 3.09279 ( 9) link_BETA1-4 : bond 0.00707 ( 6) link_BETA1-4 : angle 2.86703 ( 18) link_NAG-ASN : bond 0.00818 ( 6) link_NAG-ASN : angle 5.52953 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 618 ASN cc_start: -0.1706 (OUTLIER) cc_final: -0.2396 (p0) REVERT: D 618 ASN cc_start: -0.2237 (OUTLIER) cc_final: -0.3081 (p0) REVERT: F 618 ASN cc_start: -0.1152 (OUTLIER) cc_final: -0.1757 (p0) outliers start: 39 outliers final: 24 residues processed: 173 average time/residue: 0.1311 time to fit residues: 32.8028 Evaluate side-chains 159 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 609 CYS Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 137 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 162 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 163 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN P 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.228471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.187171 restraints weight = 31467.343| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 4.68 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4178 r_free = 0.4178 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4178 r_free = 0.4178 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14805 Z= 0.148 Angle : 0.688 10.662 20163 Z= 0.338 Chirality : 0.046 0.195 2286 Planarity : 0.005 0.040 2574 Dihedral : 7.130 56.590 2368 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.48 % Allowed : 12.53 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.19), residues: 1782 helix: 1.19 (0.34), residues: 219 sheet: -0.40 (0.22), residues: 546 loop : -0.54 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.014 0.001 TYR U 80 PHE 0.011 0.002 PHE U 92 TRP 0.021 0.001 TRP B 531 HIS 0.005 0.001 HIS F 613 Details of bonding type rmsd covalent geometry : bond 0.00339 (14769) covalent geometry : angle 0.66052 (20076) SS BOND : bond 0.00346 ( 21) SS BOND : angle 1.06087 ( 42) hydrogen bonds : bond 0.04263 ( 528) hydrogen bonds : angle 5.65666 ( 1413) link_ALPHA1-6 : bond 0.01592 ( 3) link_ALPHA1-6 : angle 3.13069 ( 9) link_BETA1-4 : bond 0.00614 ( 6) link_BETA1-4 : angle 2.97528 ( 18) link_NAG-ASN : bond 0.00668 ( 6) link_NAG-ASN : angle 5.28873 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 TYR cc_start: 0.7426 (m-80) cc_final: 0.6851 (m-80) REVERT: B 618 ASN cc_start: -0.2012 (OUTLIER) cc_final: -0.2600 (p0) REVERT: E 258 GLU cc_start: -0.0424 (OUTLIER) cc_final: -0.3169 (tp30) REVERT: D 618 ASN cc_start: -0.2457 (OUTLIER) cc_final: -0.3279 (p0) REVERT: F 609 CYS cc_start: 0.5093 (OUTLIER) cc_final: 0.4459 (m) REVERT: F 618 ASN cc_start: -0.1226 (OUTLIER) cc_final: -0.2139 (p0) REVERT: X 87 ASP cc_start: 0.5468 (m-30) cc_final: 0.5018 (t0) REVERT: U 87 ASP cc_start: 0.5499 (m-30) cc_final: 0.5173 (t0) outliers start: 50 outliers final: 29 residues processed: 191 average time/residue: 0.1280 time to fit residues: 35.4833 Evaluate side-chains 173 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 609 CYS Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 69 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 130 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN E 61 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.224330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.184746 restraints weight = 27868.870| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 4.06 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4158 r_free = 0.4158 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4158 r_free = 0.4158 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14805 Z= 0.221 Angle : 0.770 9.849 20163 Z= 0.376 Chirality : 0.048 0.183 2286 Planarity : 0.005 0.044 2574 Dihedral : 6.785 49.827 2368 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.28 % Allowed : 13.39 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.19), residues: 1782 helix: 1.19 (0.34), residues: 219 sheet: -0.63 (0.22), residues: 555 loop : -0.72 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 61 TYR 0.015 0.002 TYR E 232 PHE 0.014 0.002 PHE A 153 TRP 0.022 0.002 TRP B 531 HIS 0.006 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00528 (14769) covalent geometry : angle 0.74431 (20076) SS BOND : bond 0.00420 ( 21) SS BOND : angle 1.22821 ( 42) hydrogen bonds : bond 0.05135 ( 528) hydrogen bonds : angle 5.95506 ( 1413) link_ALPHA1-6 : bond 0.01432 ( 3) link_ALPHA1-6 : angle 2.75970 ( 9) link_BETA1-4 : bond 0.00599 ( 6) link_BETA1-4 : angle 3.44361 ( 18) link_NAG-ASN : bond 0.00588 ( 6) link_NAG-ASN : angle 5.14917 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 TYR cc_start: 0.7532 (m-80) cc_final: 0.7043 (m-80) REVERT: B 618 ASN cc_start: -0.1966 (OUTLIER) cc_final: -0.2462 (p0) REVERT: D 618 ASN cc_start: -0.2224 (OUTLIER) cc_final: -0.3357 (p0) REVERT: F 618 ASN cc_start: -0.1552 (OUTLIER) cc_final: -0.2219 (p0) REVERT: X 51 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7628 (tt) REVERT: X 87 ASP cc_start: 0.5536 (m-30) cc_final: 0.5058 (t0) outliers start: 47 outliers final: 33 residues processed: 183 average time/residue: 0.1262 time to fit residues: 33.6442 Evaluate side-chains 175 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 41 optimal weight: 50.0000 chunk 115 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 139 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** 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 = 0.4494 r_free = 0.4494 target = 0.223515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.173025 restraints weight = 26857.599| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 5.71 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14805 Z= 0.153 Angle : 0.676 9.170 20163 Z= 0.334 Chirality : 0.045 0.175 2286 Planarity : 0.005 0.041 2574 Dihedral : 6.115 52.152 2368 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.22 % Allowed : 13.45 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 1782 helix: 1.27 (0.35), residues: 219 sheet: -0.55 (0.22), residues: 549 loop : -0.74 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 19 TYR 0.013 0.002 TYR E 232 PHE 0.011 0.001 PHE U 92 TRP 0.026 0.001 TRP B 531 HIS 0.004 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00351 (14769) covalent geometry : angle 0.65293 (20076) SS BOND : bond 0.00324 ( 21) SS BOND : angle 1.19430 ( 42) hydrogen bonds : bond 0.04272 ( 528) hydrogen bonds : angle 5.68051 ( 1413) link_ALPHA1-6 : bond 0.01467 ( 3) link_ALPHA1-6 : angle 2.09635 ( 9) link_BETA1-4 : bond 0.00603 ( 6) link_BETA1-4 : angle 2.94911 ( 18) link_NAG-ASN : bond 0.00545 ( 6) link_NAG-ASN : angle 4.70717 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.637 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: H 76 LYS cc_start: 0.7751 (ttpp) cc_final: 0.7495 (pttp) REVERT: B 618 ASN cc_start: -0.2532 (OUTLIER) cc_final: -0.3012 (p0) REVERT: D 595 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7699 (mp10) REVERT: D 618 ASN cc_start: -0.2975 (OUTLIER) cc_final: -0.4104 (p0) REVERT: F 618 ASN cc_start: -0.2385 (OUTLIER) cc_final: -0.3034 (p0) REVERT: X 51 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7628 (tt) REVERT: X 80 TYR cc_start: 0.7337 (m-80) cc_final: 0.7079 (m-80) REVERT: X 87 ASP cc_start: 0.5444 (m-30) cc_final: 0.4693 (t0) REVERT: U 87 ASP cc_start: 0.5746 (m-30) cc_final: 0.5458 (t0) outliers start: 46 outliers final: 31 residues processed: 175 average time/residue: 0.1351 time to fit residues: 34.2602 Evaluate side-chains 170 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 93 CYS Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 36 optimal weight: 0.3980 chunk 172 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 90 optimal weight: 0.3980 chunk 102 optimal weight: 50.0000 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.225192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.163814 restraints weight = 30078.973| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 5.59 r_work: 0.3486 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14805 Z= 0.148 Angle : 0.669 8.433 20163 Z= 0.332 Chirality : 0.045 0.163 2286 Planarity : 0.005 0.041 2574 Dihedral : 6.004 54.158 2368 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.15 % Allowed : 13.85 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1782 helix: 1.35 (0.35), residues: 219 sheet: -0.53 (0.22), residues: 543 loop : -0.75 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.014 0.001 TYR E 232 PHE 0.010 0.001 PHE U 92 TRP 0.029 0.001 TRP B 531 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00344 (14769) covalent geometry : angle 0.64641 (20076) SS BOND : bond 0.00331 ( 21) SS BOND : angle 1.55859 ( 42) hydrogen bonds : bond 0.04215 ( 528) hydrogen bonds : angle 5.56104 ( 1413) link_ALPHA1-6 : bond 0.01168 ( 3) link_ALPHA1-6 : angle 1.67286 ( 9) link_BETA1-4 : bond 0.00628 ( 6) link_BETA1-4 : angle 2.97375 ( 18) link_NAG-ASN : bond 0.00509 ( 6) link_NAG-ASN : angle 4.37927 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.428 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: H 54 ASN cc_start: 0.5817 (p0) cc_final: 0.5553 (t0) REVERT: H 76 LYS cc_start: 0.7755 (ttpp) cc_final: 0.7418 (pttp) REVERT: A 120 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7519 (mm-30) REVERT: B 618 ASN cc_start: -0.3927 (OUTLIER) cc_final: -0.4318 (p0) REVERT: E 120 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7493 (mm-30) REVERT: D 595 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7349 (mp10) REVERT: D 618 ASN cc_start: -0.4475 (OUTLIER) cc_final: -0.5172 (p0) REVERT: F 618 ASN cc_start: -0.3491 (OUTLIER) cc_final: -0.4011 (p0) REVERT: X 51 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7694 (tt) REVERT: X 80 TYR cc_start: 0.7647 (m-80) cc_final: 0.7397 (m-80) REVERT: X 87 ASP cc_start: 0.5317 (m-30) cc_final: 0.4303 (t0) REVERT: U 54 ASN cc_start: 0.5768 (p0) cc_final: 0.5377 (t0) REVERT: U 80 TYR cc_start: 0.7616 (m-80) cc_final: 0.6962 (m-80) REVERT: U 87 ASP cc_start: 0.5723 (m-30) cc_final: 0.5141 (t0) outliers start: 45 outliers final: 31 residues processed: 178 average time/residue: 0.1334 time to fit residues: 34.0966 Evaluate side-chains 175 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 144 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN C 154 HIS E 154 HIS ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Z 37 GLN P 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.219375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.159756 restraints weight = 30811.728| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 4.92 r_work: 0.3406 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 14805 Z= 0.318 Angle : 0.851 9.404 20163 Z= 0.420 Chirality : 0.051 0.181 2286 Planarity : 0.006 0.053 2574 Dihedral : 6.707 56.047 2368 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.82 % Allowed : 13.98 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 1782 helix: 1.71 (0.34), residues: 201 sheet: -0.48 (0.22), residues: 537 loop : -0.96 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 61 TYR 0.018 0.003 TYR E 232 PHE 0.020 0.003 PHE C 153 TRP 0.028 0.003 TRP B 531 HIS 0.009 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00775 (14769) covalent geometry : angle 0.82701 (20076) SS BOND : bond 0.00428 ( 21) SS BOND : angle 1.95510 ( 42) hydrogen bonds : bond 0.06067 ( 528) hydrogen bonds : angle 6.35070 ( 1413) link_ALPHA1-6 : bond 0.00799 ( 3) link_ALPHA1-6 : angle 1.79348 ( 9) link_BETA1-4 : bond 0.00465 ( 6) link_BETA1-4 : angle 3.94144 ( 18) link_NAG-ASN : bond 0.00394 ( 6) link_NAG-ASN : angle 4.65134 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.502 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: L 70 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6595 (mm-30) REVERT: H 73 ASP cc_start: 0.6335 (p0) cc_final: 0.6034 (p0) REVERT: H 80 TYR cc_start: 0.7904 (m-80) cc_final: 0.7536 (m-80) REVERT: B 618 ASN cc_start: -0.4018 (OUTLIER) cc_final: -0.4378 (p0) REVERT: C 103 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: D 618 ASN cc_start: -0.4499 (OUTLIER) cc_final: -0.5070 (p0) REVERT: F 618 ASN cc_start: -0.3639 (OUTLIER) cc_final: -0.4172 (p0) REVERT: X 51 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7867 (tt) REVERT: X 80 TYR cc_start: 0.7715 (m-80) cc_final: 0.7454 (m-80) REVERT: X 87 ASP cc_start: 0.5689 (m-30) cc_final: 0.4620 (t0) REVERT: U 76 LYS cc_start: 0.7848 (ttpp) cc_final: 0.7428 (ttpt) REVERT: U 87 ASP cc_start: 0.5919 (m-30) cc_final: 0.5321 (t0) outliers start: 40 outliers final: 31 residues processed: 183 average time/residue: 0.1238 time to fit residues: 33.1000 Evaluate side-chains 184 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 609 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain Z residue 27 GLN Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 49 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 129 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.226774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.174770 restraints weight = 22817.066| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 4.95 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3983 r_free = 0.3983 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3983 r_free = 0.3983 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14805 Z= 0.144 Angle : 0.669 8.001 20163 Z= 0.337 Chirality : 0.045 0.170 2286 Planarity : 0.005 0.041 2574 Dihedral : 6.054 57.792 2368 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.49 % Allowed : 14.90 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.19), residues: 1782 helix: 1.41 (0.36), residues: 219 sheet: -0.60 (0.22), residues: 543 loop : -0.91 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 587 TYR 0.015 0.002 TYR A 232 PHE 0.012 0.001 PHE U 92 TRP 0.033 0.001 TRP B 531 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00328 (14769) covalent geometry : angle 0.64938 (20076) SS BOND : bond 0.00282 ( 21) SS BOND : angle 1.52673 ( 42) hydrogen bonds : bond 0.04301 ( 528) hydrogen bonds : angle 5.74064 ( 1413) link_ALPHA1-6 : bond 0.00810 ( 3) link_ALPHA1-6 : angle 1.47956 ( 9) link_BETA1-4 : bond 0.00692 ( 6) link_BETA1-4 : angle 2.99427 ( 18) link_NAG-ASN : bond 0.00506 ( 6) link_NAG-ASN : angle 3.95039 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.520 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 120 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 618 ASN cc_start: -0.2882 (OUTLIER) cc_final: -0.3741 (p0) REVERT: E 120 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7501 (mm-30) REVERT: D 596 ARG cc_start: 0.7187 (ttt-90) cc_final: 0.6864 (ttt-90) REVERT: D 618 ASN cc_start: -0.3284 (OUTLIER) cc_final: -0.4566 (p0) REVERT: F 595 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7151 (mp10) REVERT: F 618 ASN cc_start: -0.2989 (OUTLIER) cc_final: -0.3835 (p0) REVERT: X 51 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7684 (tt) REVERT: X 80 TYR cc_start: 0.7323 (m-80) cc_final: 0.7053 (m-80) REVERT: X 87 ASP cc_start: 0.5549 (m-30) cc_final: 0.4672 (t0) REVERT: U 87 ASP cc_start: 0.5783 (m-30) cc_final: 0.5448 (t0) outliers start: 35 outliers final: 28 residues processed: 180 average time/residue: 0.1253 time to fit residues: 32.6831 Evaluate side-chains 179 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 626 ILE Chi-restraints excluded: chain X residue 51 ILE Chi-restraints excluded: chain U residue 93 CYS Chi-restraints excluded: chain Z residue 27 GLN Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 133 optimal weight: 7.9990 chunk 85 optimal weight: 0.0980 chunk 136 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 146 optimal weight: 0.2980 chunk 157 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 134 optimal weight: 0.0980 chunk 131 optimal weight: 7.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN ** D 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.227178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.174514 restraints weight = 22996.750| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 5.19 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4012 r_free = 0.4012 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4012 r_free = 0.4012 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14805 Z= 0.121 Angle : 0.636 8.658 20163 Z= 0.321 Chirality : 0.044 0.170 2286 Planarity : 0.005 0.036 2574 Dihedral : 5.876 59.215 2368 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.69 % Allowed : 14.44 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 1782 helix: 1.46 (0.35), residues: 219 sheet: -0.54 (0.22), residues: 549 loop : -0.80 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 587 TYR 0.016 0.001 TYR U 80 PHE 0.012 0.001 PHE F 572 TRP 0.034 0.001 TRP D 531 HIS 0.003 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00268 (14769) covalent geometry : angle 0.61827 (20076) SS BOND : bond 0.00403 ( 21) SS BOND : angle 1.44182 ( 42) hydrogen bonds : bond 0.03752 ( 528) hydrogen bonds : angle 5.46427 ( 1413) link_ALPHA1-6 : bond 0.00779 ( 3) link_ALPHA1-6 : angle 1.44172 ( 9) link_BETA1-4 : bond 0.00628 ( 6) link_BETA1-4 : angle 2.73162 ( 18) link_NAG-ASN : bond 0.00407 ( 6) link_NAG-ASN : angle 3.65821 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3235.81 seconds wall clock time: 56 minutes 11.11 seconds (3371.11 seconds total)