Starting phenix.real_space_refine on Thu May 15 13:53:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i10_35115/05_2025/8i10_35115.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i10_35115/05_2025/8i10_35115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i10_35115/05_2025/8i10_35115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i10_35115/05_2025/8i10_35115.map" model { file = "/net/cci-nas-00/data/ceres_data/8i10_35115/05_2025/8i10_35115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i10_35115/05_2025/8i10_35115.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 24 5.16 5 C 8375 2.51 5 N 2264 2.21 5 O 2518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13196 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2641 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2632 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2603 Classifications: {'peptide': 343} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 908 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 786 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 897 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 797 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "U" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "V" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 8.13, per 1000 atoms: 0.62 Number of scatterers: 13196 At special positions: 0 Unit cell: (149.274, 143.443, 90.9636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 15 15.00 O 2518 8.00 N 2264 7.00 C 8375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 99 " distance=2.04 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 89 " 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 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 33 sheets defined 3.7% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.720A pdb=" N ARG A 283 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.658A pdb=" N ARG B 283 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 110 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.776A pdb=" N ARG C 283 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.648A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 116 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.536A pdb=" N ILE A 169 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 54 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLN A 86 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 56 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASN A 84 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 58 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE A 82 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 60 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 190 Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.515A pdb=" N PHE A 342 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU A 344 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL A 320 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE A 232 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU A 258 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 234 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN A 256 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 236 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 116 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 29 removed outlier: 5.871A pdb=" N PHE B 28 " --> pdb=" O VAL B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.595A pdb=" N LYS B 78 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 60 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE B 82 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 58 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 63 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 88 removed outlier: 5.540A pdb=" N GLN B 86 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL B 56 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 63 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 128 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 184 through 190 Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.565A pdb=" N PHE B 342 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 344 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N VAL B 320 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 255 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AB4, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.176A pdb=" N PHE C 28 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 169 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL C 54 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN C 86 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL C 56 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN C 84 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU C 58 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 82 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 60 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS C 78 " --> pdb=" O PHE C 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 190 Processing sheet with id=AB7, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.523A pdb=" N PHE C 342 " --> pdb=" O TYR C 322 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU C 344 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N VAL C 320 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C 255 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN C 238 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA C 240 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS C 251 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 242 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN C 249 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 6 through 10 Processing sheet with id=AB9, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.311A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.311A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR D 112 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.655A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.608A pdb=" N GLN E 91 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AC6, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.689A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.689A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AC9, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.781A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.921A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 6 through 10 Processing sheet with id=AD3, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.366A pdb=" N GLY M 13 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE M 37 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER M 53 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TRP M 39 " --> pdb=" O VAL M 51 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.366A pdb=" N GLY M 13 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR M 112 " --> pdb=" O ARG M 101 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ARG M 103 " --> pdb=" O LEU M 110 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU M 110 " --> pdb=" O ARG M 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AD6, first strand: chain 'N' and resid 54 through 55 removed outlier: 6.605A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR N 50 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR N 103 " --> pdb=" O TYR N 87 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4025 1.33 - 1.46: 3142 1.46 - 1.58: 6265 1.58 - 1.71: 39 1.71 - 1.83: 33 Bond restraints: 13504 Sorted by residual: bond pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.717 1.597 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" OG1 TPO U 360 " pdb=" P TPO U 360 " ideal model delta sigma weight residual 1.717 1.598 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" OG1 TPO G 360 " pdb=" P TPO G 360 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" OG1 TPO G 359 " pdb=" P TPO G 359 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" OG1 TPO U 359 " pdb=" P TPO U 359 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.06e+01 ... (remaining 13499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 17521 2.00 - 3.99: 727 3.99 - 5.99: 112 5.99 - 7.98: 28 7.98 - 9.98: 15 Bond angle restraints: 18403 Sorted by residual: angle pdb=" C SEP V 363 " pdb=" N SEP V 364 " pdb=" CA SEP V 364 " ideal model delta sigma weight residual 121.70 111.72 9.98 1.80e+00 3.09e-01 3.07e+01 angle pdb=" N SER B 75 " pdb=" CA SER B 75 " pdb=" C SER B 75 " ideal model delta sigma weight residual 110.80 120.21 -9.41 2.13e+00 2.20e-01 1.95e+01 angle pdb=" CA GLN C 182 " pdb=" CB GLN C 182 " pdb=" CG GLN C 182 " ideal model delta sigma weight residual 114.10 122.72 -8.62 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CA LYS A 108 " pdb=" CB LYS A 108 " pdb=" CG LYS A 108 " ideal model delta sigma weight residual 114.10 122.23 -8.13 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CA LEU V 365 " pdb=" C LEU V 365 " pdb=" N ALA V 366 " ideal model delta sigma weight residual 116.20 124.15 -7.95 2.00e+00 2.50e-01 1.58e+01 ... (remaining 18398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7353 17.93 - 35.86: 585 35.86 - 53.79: 85 53.79 - 71.72: 15 71.72 - 89.65: 19 Dihedral angle restraints: 8057 sinusoidal: 3026 harmonic: 5031 Sorted by residual: dihedral pdb=" CA LEU A 74 " pdb=" C LEU A 74 " pdb=" N SER A 75 " pdb=" CA SER A 75 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA THR N 98 " pdb=" C THR N 98 " pdb=" N PHE N 99 " pdb=" CA PHE N 99 " ideal model delta harmonic sigma weight residual -180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA LEU C 74 " pdb=" C LEU C 74 " pdb=" N SER C 75 " pdb=" CA SER C 75 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 8054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1718 0.070 - 0.141: 332 0.141 - 0.211: 30 0.211 - 0.281: 7 0.281 - 0.351: 2 Chirality restraints: 2089 Sorted by residual: chirality pdb=" CG LEU B 49 " pdb=" CB LEU B 49 " pdb=" CD1 LEU B 49 " pdb=" CD2 LEU B 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CG LEU M 21 " pdb=" CB LEU M 21 " pdb=" CD1 LEU M 21 " pdb=" CD2 LEU M 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CG LEU A 49 " pdb=" CB LEU A 49 " pdb=" CD1 LEU A 49 " pdb=" CD2 LEU A 49 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2086 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 71 " 0.036 2.00e-02 2.50e+03 3.91e-02 2.67e+01 pdb=" CG PHE H 71 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE H 71 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE H 71 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE H 71 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE H 71 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 71 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 71 " 0.028 2.00e-02 2.50e+03 3.13e-02 1.71e+01 pdb=" CG PHE D 71 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE D 71 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 71 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE D 71 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE D 71 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 71 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 209 " 0.015 2.00e-02 2.50e+03 2.61e-02 1.36e+01 pdb=" CG TYR A 209 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 209 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 209 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 209 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 209 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 209 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 209 " -0.003 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 719 2.72 - 3.26: 13252 3.26 - 3.81: 19584 3.81 - 4.35: 23366 4.35 - 4.90: 42287 Nonbonded interactions: 99208 Sorted by model distance: nonbonded pdb=" O SER L 29 " pdb=" OG SER L 29 " model vdw 2.172 3.040 nonbonded pdb=" O SER M 34 " pdb=" OG SER M 34 " model vdw 2.211 3.040 nonbonded pdb=" O ASN D 31 " pdb=" OG SER D 35 " model vdw 2.222 3.040 nonbonded pdb=" NZ LYS C 108 " pdb=" OG SEP V 363 " model vdw 2.266 3.120 nonbonded pdb=" O SER E 32 " pdb=" OG SER E 32 " model vdw 2.268 3.040 ... (remaining 99203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 44 or (resid 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 49 or (resid 50 and \ (name N or name CA or name C or name O )) or (resid 51 and (name N or name CA or \ name C or name O or name CB )) or resid 52 through 73 or (resid 74 through 76 a \ nd (name N or name CA or name C or name O or name CB )) or resid 77 through 84 o \ r (resid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 \ through 102 or (resid 103 and (name N or name CA or name C or name O or name CB \ )) or resid 104 through 110 or (resid 111 and (name N or name CA or name C or n \ ame O or name CB )) or resid 112 through 113 or (resid 114 and (name N or name C \ A or name C or name O or name CB )) or resid 115 through 185 or (resid 186 and ( \ name N or name CA or name C or name O or name CB )) or resid 187 through 195 or \ (resid 196 and (name N or name CA or name C or name O or name CB )) or resid 197 \ through 283 or (resid 284 and (name N or name CA or name C or name O or name CB \ )) or resid 285 through 295 or (resid 296 and (name N or name CA or name C or n \ ame O or name CB )) or resid 297 through 311 or (resid 312 and (name N or name C \ A or name C or name O or name CB )) or resid 313 or (resid 314 through 315 and ( \ name N or name CA or name C or name O or name CB )) or resid 316 through 350)) selection = (chain 'B' and (resid 7 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or (resid 51 and (name N or name CA or name C or name \ O or name CB )) or resid 52 through 75 or (resid 76 and (name N or name CA or n \ ame C or name O or name CB )) or resid 77 through 84 or (resid 85 and (name N or \ name CA or name C or name O or name CB )) or resid 86 through 102 or (resid 103 \ and (name N or name CA or name C or name O or name CB )) or resid 104 through 1 \ 10 or (resid 111 and (name N or name CA or name C or name O or name CB )) or res \ id 112 through 113 or (resid 114 and (name N or name CA or name C or name O or n \ ame CB )) or resid 115 through 152 or (resid 153 and (name N or name CA or name \ C or name O or name CB )) or resid 154 through 156 or (resid 157 through 158 and \ (name N or name CA or name C or name O or name CB )) or resid 159 through 176 o \ r (resid 177 through 178 and (name N or name CA or name C or name O or name CB ) \ ) or resid 179 through 229 or (resid 230 and (name N or name CA or name C or nam \ e O or name CB )) or resid 231 through 283 or (resid 284 and (name N or name CA \ or name C or name O or name CB )) or resid 285 through 295 or (resid 296 and (na \ me N or name CA or name C or name O or name CB )) or resid 297 through 350)) selection = (chain 'C' and (resid 7 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 44 or (resid 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 92 or (resid 93 and (n \ ame N or name CA or name C or name O or name CB )) or resid 94 through 176 or (r \ esid 177 through 178 and (name N or name CA or name C or name O or name CB )) or \ resid 179 through 185 or (resid 186 and (name N or name CA or name C or name O \ or name CB )) or resid 187 through 195 or (resid 196 and (name N or name CA or n \ ame C or name O or name CB )) or resid 197 through 229 or (resid 230 and (name N \ or name CA or name C or name O or name CB )) or resid 231 through 311 or (resid \ 312 and (name N or name CA or name C or name O or name CB )) or resid 313 throu \ gh 350)) } ncs_group { reference = (chain 'D' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 13 or (resid 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 45 or (resid 46 and (name \ N or name CA or name C or name O or name CB )) or resid 47 through 121)) selection = (chain 'H' and (resid 5 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 or (resid 16 and (name N or name CA or name \ C or name O or name CB )) or resid 17 through 45 or (resid 46 and (name N or na \ me CA or name C or name O or name CB )) or resid 47 through 121)) selection = (chain 'M' and resid 5 through 121) } ncs_group { reference = (chain 'E' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 54 or (resid 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 106)) selection = (chain 'L' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 54 or (resid 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 106)) selection = (chain 'N' and resid 2 through 106) } ncs_group { reference = chain 'G' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.400 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.006 0.120 13510 Z= 0.274 Angle : 0.955 9.977 18415 Z= 0.488 Chirality : 0.055 0.351 2089 Planarity : 0.007 0.063 2344 Dihedral : 13.994 89.646 4805 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.58 % Allowed : 16.20 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 1681 helix: -0.54 (0.80), residues: 36 sheet: -0.41 (0.18), residues: 769 loop : -0.92 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 36 HIS 0.011 0.002 HIS B 112 PHE 0.089 0.003 PHE H 71 TYR 0.061 0.003 TYR A 209 ARG 0.009 0.001 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.19791 ( 469) hydrogen bonds : angle 9.40929 ( 1272) SS BOND : bond 0.00979 ( 6) SS BOND : angle 3.59328 ( 12) covalent geometry : bond 0.00589 (13504) covalent geometry : angle 0.95138 (18403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: H 80 ASN cc_start: 0.7625 (t0) cc_final: 0.7362 (t0) outliers start: 8 outliers final: 7 residues processed: 179 average time/residue: 0.2270 time to fit residues: 60.7174 Evaluate side-chains 161 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 18 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0370 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 160 HIS A 199 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 182 GLN B 199 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 42 GLN H 85 GLN M 85 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.167321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138206 restraints weight = 22026.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137362 restraints weight = 26223.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138859 restraints weight = 25837.923| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13510 Z= 0.138 Angle : 0.677 9.822 18415 Z= 0.345 Chirality : 0.047 0.174 2089 Planarity : 0.005 0.059 2344 Dihedral : 6.997 89.274 1921 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.54 % Allowed : 15.04 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1681 helix: 0.69 (0.86), residues: 36 sheet: 0.04 (0.19), residues: 746 loop : -0.90 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 50 HIS 0.005 0.001 HIS A 346 PHE 0.026 0.002 PHE C 278 TYR 0.017 0.002 TYR N 92 ARG 0.007 0.001 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 469) hydrogen bonds : angle 6.08695 ( 1272) SS BOND : bond 0.00729 ( 6) SS BOND : angle 1.52597 ( 12) covalent geometry : bond 0.00308 (13504) covalent geometry : angle 0.67582 (18403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 1.408 Fit side-chains REVERT: A 39 ASP cc_start: 0.8426 (p0) cc_final: 0.8110 (p0) REVERT: B 88 PHE cc_start: 0.7582 (t80) cc_final: 0.7269 (t80) REVERT: B 296 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.7001 (m-70) REVERT: C 39 ASP cc_start: 0.8710 (p0) cc_final: 0.8498 (p0) REVERT: C 266 SER cc_start: 0.7763 (m) cc_final: 0.7386 (p) REVERT: C 324 VAL cc_start: 0.8893 (t) cc_final: 0.8554 (m) REVERT: D 9 GLU cc_start: 0.7209 (pm20) cc_final: 0.6957 (pt0) REVERT: D 81 THR cc_start: 0.8449 (m) cc_final: 0.8233 (p) REVERT: E 64 SER cc_start: 0.8236 (p) cc_final: 0.7705 (m) REVERT: L 5 MET cc_start: 0.8337 (tpp) cc_final: 0.7491 (tpp) REVERT: L 13 SER cc_start: 0.8343 (t) cc_final: 0.7763 (m) REVERT: M 21 LEU cc_start: 0.7749 (tp) cc_final: 0.7159 (tt) REVERT: M 86 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7386 (ptp) outliers start: 49 outliers final: 29 residues processed: 218 average time/residue: 0.2114 time to fit residues: 70.7223 Evaluate side-chains 185 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 164 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN C 160 HIS H 85 GLN M 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.134503 restraints weight = 22368.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132652 restraints weight = 31084.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133658 restraints weight = 31854.743| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 13510 Z= 0.298 Angle : 0.761 10.121 18415 Z= 0.393 Chirality : 0.049 0.182 2089 Planarity : 0.005 0.056 2344 Dihedral : 7.057 87.496 1913 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.84 % Allowed : 16.99 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1681 helix: 1.10 (0.86), residues: 36 sheet: -0.20 (0.19), residues: 768 loop : -0.94 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP H 39 HIS 0.004 0.001 HIS A 211 PHE 0.020 0.002 PHE C 278 TYR 0.028 0.002 TYR N 92 ARG 0.004 0.001 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 469) hydrogen bonds : angle 6.22607 ( 1272) SS BOND : bond 0.01218 ( 6) SS BOND : angle 2.20634 ( 12) covalent geometry : bond 0.00696 (13504) covalent geometry : angle 0.75877 (18403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 162 time to evaluate : 1.508 Fit side-chains REVERT: A 38 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8828 (t) REVERT: A 39 ASP cc_start: 0.8402 (p0) cc_final: 0.8187 (p0) REVERT: B 88 PHE cc_start: 0.7404 (t80) cc_final: 0.7153 (t80) REVERT: B 296 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7479 (m-70) REVERT: C 39 ASP cc_start: 0.8625 (p0) cc_final: 0.8408 (p0) REVERT: D 9 GLU cc_start: 0.7658 (pm20) cc_final: 0.7444 (pt0) REVERT: E 2 ASP cc_start: 0.7912 (p0) cc_final: 0.7605 (p0) REVERT: L 5 MET cc_start: 0.8624 (tpp) cc_final: 0.7887 (tpp) REVERT: M 21 LEU cc_start: 0.7796 (tp) cc_final: 0.7129 (tt) REVERT: M 83 TYR cc_start: 0.7987 (m-10) cc_final: 0.7715 (m-10) REVERT: M 86 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7444 (ptp) outliers start: 67 outliers final: 48 residues processed: 209 average time/residue: 0.2077 time to fit residues: 66.6965 Evaluate side-chains 197 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 101 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 40 optimal weight: 8.9990 chunk 139 optimal weight: 0.2980 chunk 54 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN M 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.166547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.137961 restraints weight = 22032.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137527 restraints weight = 27154.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139008 restraints weight = 24966.067| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13510 Z= 0.137 Angle : 0.620 9.211 18415 Z= 0.314 Chirality : 0.045 0.164 2089 Planarity : 0.005 0.054 2344 Dihedral : 6.416 86.306 1913 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.40 % Allowed : 19.52 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1681 helix: 1.70 (0.87), residues: 36 sheet: 0.10 (0.20), residues: 730 loop : -0.81 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 39 HIS 0.005 0.001 HIS A 211 PHE 0.013 0.001 PHE C 278 TYR 0.014 0.001 TYR D 83 ARG 0.004 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 469) hydrogen bonds : angle 5.54075 ( 1272) SS BOND : bond 0.00762 ( 6) SS BOND : angle 1.29778 ( 12) covalent geometry : bond 0.00313 (13504) covalent geometry : angle 0.61975 (18403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 1.420 Fit side-chains REVERT: A 39 ASP cc_start: 0.8418 (p0) cc_final: 0.8103 (p0) REVERT: B 88 PHE cc_start: 0.7194 (t80) cc_final: 0.6960 (t80) REVERT: B 296 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7403 (m-70) REVERT: C 39 ASP cc_start: 0.8711 (p0) cc_final: 0.8422 (p0) REVERT: C 210 TYR cc_start: 0.8670 (m-80) cc_final: 0.8400 (m-80) REVERT: C 273 TYR cc_start: 0.7628 (m-10) cc_final: 0.7386 (m-10) REVERT: D 9 GLU cc_start: 0.7627 (pm20) cc_final: 0.7343 (pt0) REVERT: D 14 LEU cc_start: 0.8294 (mt) cc_final: 0.8015 (mp) REVERT: D 15 VAL cc_start: 0.6617 (t) cc_final: 0.6392 (t) REVERT: D 80 ASN cc_start: 0.7129 (t0) cc_final: 0.6894 (t0) REVERT: H 8 VAL cc_start: 0.8997 (t) cc_final: 0.8738 (m) REVERT: H 85 GLN cc_start: 0.7236 (tp-100) cc_final: 0.6594 (tm-30) REVERT: M 21 LEU cc_start: 0.7894 (tp) cc_final: 0.7246 (tt) REVERT: M 33 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.7831 (m-10) REVERT: M 83 TYR cc_start: 0.7938 (m-10) cc_final: 0.7703 (m-80) REVERT: M 86 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7414 (ptp) REVERT: N 19 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7545 (ttt-90) outliers start: 47 outliers final: 34 residues processed: 197 average time/residue: 0.2055 time to fit residues: 62.0584 Evaluate side-chains 180 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.165822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138057 restraints weight = 22352.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137111 restraints weight = 26533.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138376 restraints weight = 25024.438| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 0.029 13510 Z= 0.147 Angle : 0.617 9.062 18415 Z= 0.312 Chirality : 0.045 0.163 2089 Planarity : 0.004 0.052 2344 Dihedral : 6.234 84.348 1913 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.34 % Allowed : 19.52 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1681 helix: 1.94 (0.87), residues: 36 sheet: 0.18 (0.19), residues: 735 loop : -0.82 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 39 HIS 0.005 0.001 HIS A 211 PHE 0.035 0.002 PHE E 84 TYR 0.015 0.001 TYR H 98 ARG 0.005 0.000 ARG H 90 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 469) hydrogen bonds : angle 5.40923 ( 1272) SS BOND : bond 0.00802 ( 6) SS BOND : angle 1.39850 ( 12) covalent geometry : bond 0.00340 (13504) covalent geometry : angle 0.61655 (18403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 156 time to evaluate : 1.376 Fit side-chains REVERT: A 39 ASP cc_start: 0.8360 (p0) cc_final: 0.8068 (p0) REVERT: A 278 PHE cc_start: 0.8711 (p90) cc_final: 0.8356 (p90) REVERT: B 88 PHE cc_start: 0.7053 (t80) cc_final: 0.6681 (t80) REVERT: B 296 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7463 (m-70) REVERT: B 319 LEU cc_start: 0.8226 (tp) cc_final: 0.7885 (mt) REVERT: C 39 ASP cc_start: 0.8645 (p0) cc_final: 0.8424 (p0) REVERT: C 210 TYR cc_start: 0.8686 (m-80) cc_final: 0.8365 (m-80) REVERT: C 273 TYR cc_start: 0.7555 (m-10) cc_final: 0.7342 (m-10) REVERT: D 9 GLU cc_start: 0.7014 (pm20) cc_final: 0.6750 (pm20) REVERT: H 21 LEU cc_start: 0.6919 (tt) cc_final: 0.6596 (tt) REVERT: H 41 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7429 (ptt-90) REVERT: M 21 LEU cc_start: 0.7942 (tp) cc_final: 0.7208 (tt) REVERT: M 33 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7751 (m-10) REVERT: M 83 TYR cc_start: 0.7954 (m-10) cc_final: 0.7680 (m-80) REVERT: M 86 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7446 (ptp) REVERT: N 19 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7537 (ttt-90) outliers start: 60 outliers final: 44 residues processed: 199 average time/residue: 0.2116 time to fit residues: 66.8854 Evaluate side-chains 191 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 33 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 121 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 109 optimal weight: 0.0770 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN M 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.167842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140020 restraints weight = 22370.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139147 restraints weight = 25958.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140391 restraints weight = 26004.992| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13510 Z= 0.117 Angle : 0.589 8.782 18415 Z= 0.295 Chirality : 0.044 0.163 2089 Planarity : 0.004 0.052 2344 Dihedral : 6.015 82.730 1913 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.27 % Allowed : 19.96 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1681 helix: 2.30 (0.87), residues: 36 sheet: 0.31 (0.20), residues: 741 loop : -0.80 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 39 HIS 0.005 0.001 HIS A 211 PHE 0.036 0.001 PHE E 84 TYR 0.013 0.001 TYR N 94 ARG 0.003 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.02909 ( 469) hydrogen bonds : angle 5.18118 ( 1272) SS BOND : bond 0.00709 ( 6) SS BOND : angle 1.27152 ( 12) covalent geometry : bond 0.00267 (13504) covalent geometry : angle 0.58830 (18403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 1.361 Fit side-chains REVERT: A 39 ASP cc_start: 0.8395 (p0) cc_final: 0.8088 (p0) REVERT: A 278 PHE cc_start: 0.8650 (p90) cc_final: 0.8311 (p90) REVERT: B 85 TYR cc_start: 0.5780 (t80) cc_final: 0.5563 (t80) REVERT: B 88 PHE cc_start: 0.6940 (t80) cc_final: 0.6606 (t80) REVERT: B 296 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7462 (m-70) REVERT: C 39 ASP cc_start: 0.8647 (p0) cc_final: 0.8403 (p0) REVERT: C 210 TYR cc_start: 0.8660 (m-80) cc_final: 0.8297 (m-80) REVERT: C 273 TYR cc_start: 0.7578 (m-10) cc_final: 0.7361 (m-10) REVERT: D 9 GLU cc_start: 0.6938 (pm20) cc_final: 0.6594 (pm20) REVERT: H 41 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7316 (ptt-90) REVERT: H 42 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7559 (tm-30) REVERT: H 85 GLN cc_start: 0.7149 (tp-100) cc_final: 0.6530 (tm-30) REVERT: L 13 SER cc_start: 0.8372 (t) cc_final: 0.7743 (m) REVERT: M 21 LEU cc_start: 0.8016 (tp) cc_final: 0.7306 (tt) REVERT: M 33 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7803 (m-10) REVERT: M 83 TYR cc_start: 0.7903 (m-10) cc_final: 0.7643 (m-80) REVERT: M 86 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7399 (ptp) REVERT: N 19 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7592 (ttt-90) outliers start: 59 outliers final: 45 residues processed: 209 average time/residue: 0.1961 time to fit residues: 64.3495 Evaluate side-chains 203 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 8.9990 chunk 138 optimal weight: 0.3980 chunk 154 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.164891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140475 restraints weight = 22224.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140121 restraints weight = 30046.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.140804 restraints weight = 27376.438| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13510 Z= 0.176 Angle : 0.630 8.978 18415 Z= 0.318 Chirality : 0.045 0.161 2089 Planarity : 0.004 0.052 2344 Dihedral : 6.081 78.967 1913 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.35 % Allowed : 19.96 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1681 helix: 2.38 (0.87), residues: 36 sheet: 0.26 (0.20), residues: 741 loop : -0.84 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 39 HIS 0.004 0.001 HIS A 211 PHE 0.034 0.002 PHE E 84 TYR 0.018 0.002 TYR N 92 ARG 0.003 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 469) hydrogen bonds : angle 5.30789 ( 1272) SS BOND : bond 0.00822 ( 6) SS BOND : angle 1.49967 ( 12) covalent geometry : bond 0.00410 (13504) covalent geometry : angle 0.62902 (18403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 166 time to evaluate : 1.420 Fit side-chains REVERT: A 39 ASP cc_start: 0.8431 (p0) cc_final: 0.8131 (p0) REVERT: A 278 PHE cc_start: 0.8703 (p90) cc_final: 0.8336 (p90) REVERT: B 88 PHE cc_start: 0.6792 (t80) cc_final: 0.6492 (t80) REVERT: B 296 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7505 (m-70) REVERT: C 39 ASP cc_start: 0.8619 (p0) cc_final: 0.8380 (p0) REVERT: C 210 TYR cc_start: 0.8665 (m-80) cc_final: 0.8284 (m-80) REVERT: C 273 TYR cc_start: 0.7567 (m-10) cc_final: 0.7259 (m-10) REVERT: D 9 GLU cc_start: 0.7033 (pm20) cc_final: 0.6656 (pm20) REVERT: H 41 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7498 (ptt-90) REVERT: H 42 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7691 (tm-30) REVERT: L 5 MET cc_start: 0.7864 (tpp) cc_final: 0.6837 (tpp) REVERT: M 21 LEU cc_start: 0.8008 (tp) cc_final: 0.7306 (tt) REVERT: M 33 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7888 (m-10) REVERT: M 83 TYR cc_start: 0.7931 (m-10) cc_final: 0.7603 (m-10) REVERT: M 86 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7032 (ptp) REVERT: N 19 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7582 (ttt-90) outliers start: 74 outliers final: 56 residues processed: 220 average time/residue: 0.2220 time to fit residues: 74.6364 Evaluate side-chains 219 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 33 TYR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 0.0030 chunk 61 optimal weight: 1.9990 chunk 124 optimal weight: 0.0370 chunk 139 optimal weight: 0.0870 chunk 131 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN L 7 GLN M 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.168494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.141019 restraints weight = 22147.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140739 restraints weight = 28119.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.141995 restraints weight = 24685.065| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13510 Z= 0.103 Angle : 0.593 8.794 18415 Z= 0.294 Chirality : 0.043 0.155 2089 Planarity : 0.004 0.052 2344 Dihedral : 5.823 77.018 1913 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.90 % Allowed : 21.19 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1681 helix: 2.62 (0.88), residues: 36 sheet: 0.51 (0.20), residues: 722 loop : -0.76 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 50 HIS 0.005 0.001 HIS A 211 PHE 0.037 0.001 PHE E 84 TYR 0.009 0.001 TYR H 98 ARG 0.009 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.02756 ( 469) hydrogen bonds : angle 4.96995 ( 1272) SS BOND : bond 0.00663 ( 6) SS BOND : angle 1.10206 ( 12) covalent geometry : bond 0.00234 (13504) covalent geometry : angle 0.59220 (18403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 1.501 Fit side-chains REVERT: A 39 ASP cc_start: 0.8399 (p0) cc_final: 0.8079 (p0) REVERT: A 278 PHE cc_start: 0.8534 (p90) cc_final: 0.8246 (p90) REVERT: B 88 PHE cc_start: 0.6903 (t80) cc_final: 0.6570 (t80) REVERT: B 296 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7544 (m-70) REVERT: C 39 ASP cc_start: 0.8693 (p0) cc_final: 0.8396 (p0) REVERT: C 210 TYR cc_start: 0.8628 (m-80) cc_final: 0.8244 (m-80) REVERT: C 273 TYR cc_start: 0.7567 (m-10) cc_final: 0.7336 (m-10) REVERT: H 42 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7452 (tm-30) REVERT: L 5 MET cc_start: 0.7656 (tpp) cc_final: 0.6784 (tpp) REVERT: L 6 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8705 (p) REVERT: L 13 SER cc_start: 0.8372 (t) cc_final: 0.7819 (m) REVERT: L 82 GLU cc_start: 0.7153 (pm20) cc_final: 0.6924 (pm20) REVERT: M 21 LEU cc_start: 0.7962 (tp) cc_final: 0.7434 (tt) REVERT: M 86 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6989 (ptp) REVERT: M 90 ARG cc_start: 0.6947 (ptp90) cc_final: 0.6497 (ptp90) REVERT: N 103 THR cc_start: 0.8000 (p) cc_final: 0.7522 (p) outliers start: 54 outliers final: 42 residues processed: 208 average time/residue: 0.2069 time to fit residues: 66.9219 Evaluate side-chains 205 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 86 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 64 optimal weight: 5.9990 chunk 114 optimal weight: 0.0570 chunk 115 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 1.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.164497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139724 restraints weight = 22098.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139172 restraints weight = 30220.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139767 restraints weight = 28112.702| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13510 Z= 0.187 Angle : 0.646 9.499 18415 Z= 0.327 Chirality : 0.045 0.159 2089 Planarity : 0.005 0.053 2344 Dihedral : 6.001 72.077 1913 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.48 % Allowed : 20.46 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1681 helix: 2.61 (0.87), residues: 36 sheet: 0.34 (0.20), residues: 741 loop : -0.87 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 39 HIS 0.004 0.001 HIS A 211 PHE 0.045 0.002 PHE E 84 TYR 0.019 0.002 TYR N 92 ARG 0.007 0.001 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 469) hydrogen bonds : angle 5.27051 ( 1272) SS BOND : bond 0.00848 ( 6) SS BOND : angle 2.11799 ( 12) covalent geometry : bond 0.00438 (13504) covalent geometry : angle 0.64382 (18403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 163 time to evaluate : 1.531 Fit side-chains REVERT: A 39 ASP cc_start: 0.8433 (p0) cc_final: 0.8134 (p0) REVERT: A 278 PHE cc_start: 0.8631 (p90) cc_final: 0.8192 (p90) REVERT: B 88 PHE cc_start: 0.6815 (t80) cc_final: 0.6505 (t80) REVERT: B 153 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7484 (mmtt) REVERT: C 39 ASP cc_start: 0.8632 (p0) cc_final: 0.8396 (p0) REVERT: C 210 TYR cc_start: 0.8659 (m-80) cc_final: 0.8307 (m-80) REVERT: C 273 TYR cc_start: 0.7569 (m-10) cc_final: 0.7240 (m-10) REVERT: L 5 MET cc_start: 0.7961 (tpp) cc_final: 0.6988 (tpp) REVERT: N 103 THR cc_start: 0.8154 (p) cc_final: 0.7624 (p) outliers start: 62 outliers final: 53 residues processed: 206 average time/residue: 0.2089 time to fit residues: 67.1459 Evaluate side-chains 209 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 5 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN H 80 ASN M 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.164592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136961 restraints weight = 22092.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135712 restraints weight = 26613.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137040 restraints weight = 25454.443| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13510 Z= 0.175 Angle : 0.644 9.376 18415 Z= 0.325 Chirality : 0.045 0.215 2089 Planarity : 0.005 0.053 2344 Dihedral : 5.954 65.956 1913 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.34 % Allowed : 20.97 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1681 helix: 2.67 (0.88), residues: 36 sheet: 0.32 (0.20), residues: 735 loop : -0.83 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 39 HIS 0.005 0.001 HIS A 211 PHE 0.047 0.002 PHE C 278 TYR 0.027 0.002 TYR M 33 ARG 0.006 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 469) hydrogen bonds : angle 5.23070 ( 1272) SS BOND : bond 0.00837 ( 6) SS BOND : angle 1.82432 ( 12) covalent geometry : bond 0.00407 (13504) covalent geometry : angle 0.64266 (18403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3362 Ramachandran restraints generated. 1681 Oldfield, 0 Emsley, 1681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 1.569 Fit side-chains REVERT: A 39 ASP cc_start: 0.8458 (p0) cc_final: 0.8141 (p0) REVERT: A 278 PHE cc_start: 0.8625 (p90) cc_final: 0.8220 (p90) REVERT: B 85 TYR cc_start: 0.6327 (t80) cc_final: 0.6074 (t80) REVERT: B 88 PHE cc_start: 0.7001 (t80) cc_final: 0.6724 (t80) REVERT: C 39 ASP cc_start: 0.8669 (p0) cc_final: 0.8423 (p0) REVERT: C 210 TYR cc_start: 0.8664 (m-80) cc_final: 0.8329 (m-80) REVERT: C 273 TYR cc_start: 0.7596 (m-10) cc_final: 0.7208 (m-10) REVERT: D 42 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7496 (tm-30) REVERT: H 41 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7535 (ptt-90) REVERT: H 42 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7535 (tm-30) REVERT: L 5 MET cc_start: 0.7956 (tpp) cc_final: 0.6968 (tpp) REVERT: M 83 TYR cc_start: 0.7973 (m-10) cc_final: 0.7620 (m-10) REVERT: N 103 THR cc_start: 0.8074 (p) cc_final: 0.7577 (p) outliers start: 60 outliers final: 54 residues processed: 205 average time/residue: 0.1992 time to fit residues: 63.8086 Evaluate side-chains 213 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 150 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 116 optimal weight: 0.0770 chunk 133 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 97 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** 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 = 0.4051 r_free = 0.4051 target = 0.167680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.139642 restraints weight = 22211.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139259 restraints weight = 25226.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140558 restraints weight = 23678.145| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13510 Z= 0.110 Angle : 0.615 9.196 18415 Z= 0.305 Chirality : 0.044 0.174 2089 Planarity : 0.004 0.051 2344 Dihedral : 5.705 64.438 1913 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.54 % Allowed : 21.84 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1681 helix: 2.78 (0.89), residues: 36 sheet: 0.53 (0.20), residues: 694 loop : -0.74 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 50 HIS 0.006 0.001 HIS A 211 PHE 0.045 0.002 PHE N 84 TYR 0.017 0.001 TYR M 33 ARG 0.005 0.000 ARG M 90 Details of bonding type rmsd hydrogen bonds : bond 0.02755 ( 469) hydrogen bonds : angle 4.93808 ( 1272) SS BOND : bond 0.00755 ( 6) SS BOND : angle 1.46347 ( 12) covalent geometry : bond 0.00252 (13504) covalent geometry : angle 0.61369 (18403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3514.64 seconds wall clock time: 62 minutes 54.95 seconds (3774.95 seconds total)