Starting phenix.real_space_refine on Sat Aug 23 16:07:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i10_35115/08_2025/8i10_35115.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i10_35115/08_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_35115/08_2025/8i10_35115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i10_35115/08_2025/8i10_35115.map" model { file = "/net/cci-nas-00/data/ceres_data/8i10_35115/08_2025/8i10_35115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i10_35115/08_2025/8i10_35115.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3} 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: {'ASP:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2, 'GLU:plan': 3} 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: {'ASP:plan': 4, 'ARG:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1, 'HIS:plan': 2} 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: 3.46, per 1000 atoms: 0.26 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: 0.93 Conformation dependent library (CDL) restraints added in 435.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.47 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: 2.24 Time building geometry restraints manager: 1.20 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: 3.310 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.240 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG L 62 TYR 0.061 0.003 TYR A 209 PHE 0.089 0.003 PHE H 71 TRP 0.018 0.002 TRP L 36 HIS 0.011 0.002 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00589 (13504) covalent geometry : angle 0.95138 (18403) SS BOND : bond 0.00979 ( 6) SS BOND : angle 3.59328 ( 12) hydrogen bonds : bond 0.19791 ( 469) hydrogen bonds : angle 9.40929 ( 1272) *********************** 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 : 0.496 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: 0.0901 time to fit residues: 24.3955 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 : 0.450 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0070 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 B 182 GLN C 249 GLN D 42 GLN H 85 GLN M 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.170188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139308 restraints weight = 22073.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140189 restraints weight = 25393.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141305 restraints weight = 20521.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141420 restraints weight = 16792.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141464 restraints weight = 15594.245| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13510 Z= 0.135 Angle : 0.687 9.790 18415 Z= 0.352 Chirality : 0.047 0.169 2089 Planarity : 0.005 0.058 2344 Dihedral : 7.098 88.869 1921 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.18 % Allowed : 14.97 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.20), residues: 1681 helix: 0.54 (0.84), residues: 36 sheet: 0.01 (0.19), residues: 770 loop : -0.88 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 8 TYR 0.016 0.001 TYR N 92 PHE 0.027 0.002 PHE C 278 TRP 0.011 0.001 TRP M 50 HIS 0.006 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00298 (13504) covalent geometry : angle 0.68620 (18403) SS BOND : bond 0.00731 ( 6) SS BOND : angle 1.61631 ( 12) hydrogen bonds : bond 0.04289 ( 469) hydrogen bonds : angle 6.34832 ( 1272) *********************** 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 229 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.320 Fit side-chains REVERT: A 39 ASP cc_start: 0.8383 (p0) cc_final: 0.8077 (p0) REVERT: B 296 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.6945 (m-70) REVERT: C 39 ASP cc_start: 0.8679 (p0) cc_final: 0.8467 (p0) REVERT: C 266 SER cc_start: 0.7896 (m) cc_final: 0.7571 (p) REVERT: D 9 GLU cc_start: 0.7428 (pm20) cc_final: 0.7029 (pm20) REVERT: D 81 THR cc_start: 0.8511 (m) cc_final: 0.8300 (p) REVERT: L 13 SER cc_start: 0.8368 (t) cc_final: 0.7795 (m) REVERT: M 21 LEU cc_start: 0.7851 (tp) cc_final: 0.7553 (tt) outliers start: 44 outliers final: 27 residues processed: 210 average time/residue: 0.0813 time to fit residues: 26.3406 Evaluate side-chains 180 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 106 LEU 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 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 54 SER 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 L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 23 THR 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 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 157 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 76 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 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 211 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 M 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.166940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139311 restraints weight = 22300.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138264 restraints weight = 31155.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139460 restraints weight = 28679.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139600 restraints weight = 22121.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139768 restraints weight = 19898.340| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13510 Z= 0.177 Angle : 0.665 9.585 18415 Z= 0.341 Chirality : 0.047 0.167 2089 Planarity : 0.005 0.056 2344 Dihedral : 6.693 87.505 1913 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.54 % Allowed : 16.63 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.20), residues: 1681 helix: 1.20 (0.87), residues: 36 sheet: 0.01 (0.19), residues: 772 loop : -0.81 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 8 TYR 0.018 0.002 TYR N 92 PHE 0.027 0.002 PHE B 88 TRP 0.009 0.002 TRP M 39 HIS 0.004 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00412 (13504) covalent geometry : angle 0.66351 (18403) SS BOND : bond 0.00813 ( 6) SS BOND : angle 1.71941 ( 12) hydrogen bonds : bond 0.03763 ( 469) hydrogen bonds : angle 5.89989 ( 1272) *********************** 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 209 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 0.392 Fit side-chains REVERT: A 39 ASP cc_start: 0.8357 (p0) cc_final: 0.8075 (p0) REVERT: B 296 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.7167 (m-70) REVERT: C 39 ASP cc_start: 0.8707 (p0) cc_final: 0.8432 (p0) REVERT: C 301 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8827 (mt) REVERT: D 9 GLU cc_start: 0.7369 (pm20) cc_final: 0.7161 (pt0) REVERT: L 5 MET cc_start: 0.8445 (tpp) cc_final: 0.7933 (tpp) REVERT: L 13 SER cc_start: 0.8408 (t) cc_final: 0.7794 (m) REVERT: M 21 LEU cc_start: 0.7920 (tp) cc_final: 0.7393 (tt) REVERT: N 6 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8617 (p) outliers start: 49 outliers final: 36 residues processed: 190 average time/residue: 0.0835 time to fit residues: 24.5794 Evaluate side-chains 185 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 324 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 205 ASP 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 C residue 301 LEU 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 6 THR Chi-restraints excluded: chain E residue 49 ILE 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 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 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 117 THR Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 129 optimal weight: 0.0670 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 H 85 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 = 0.4029 r_free = 0.4029 target = 0.166265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136486 restraints weight = 22278.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136053 restraints weight = 26652.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137647 restraints weight = 25042.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.137965 restraints weight = 19927.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138163 restraints weight = 17786.164| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2428 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= 0.124 Angle : 0.602 8.990 18415 Z= 0.305 Chirality : 0.045 0.175 2089 Planarity : 0.005 0.055 2344 Dihedral : 6.267 87.641 1913 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.47 % Allowed : 18.22 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.21), residues: 1681 helix: 1.62 (0.88), residues: 36 sheet: 0.24 (0.19), residues: 753 loop : -0.75 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 8 TYR 0.013 0.001 TYR D 83 PHE 0.034 0.002 PHE E 84 TRP 0.009 0.001 TRP H 39 HIS 0.005 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00285 (13504) covalent geometry : angle 0.60092 (18403) SS BOND : bond 0.00733 ( 6) SS BOND : angle 1.30764 ( 12) hydrogen bonds : bond 0.03198 ( 469) hydrogen bonds : angle 5.42063 ( 1272) *********************** 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: 48 poor density : 166 time to evaluate : 0.542 Fit side-chains REVERT: A 39 ASP cc_start: 0.8403 (p0) cc_final: 0.8081 (p0) REVERT: B 296 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7228 (m-70) REVERT: C 39 ASP cc_start: 0.8730 (p0) cc_final: 0.8449 (p0) REVERT: C 210 TYR cc_start: 0.8686 (m-80) cc_final: 0.8390 (m-80) REVERT: D 14 LEU cc_start: 0.8208 (mt) cc_final: 0.7960 (mp) REVERT: D 80 ASN cc_start: 0.7213 (t0) cc_final: 0.6950 (t0) REVERT: H 8 VAL cc_start: 0.8959 (t) cc_final: 0.8717 (m) REVERT: H 85 GLN cc_start: 0.7140 (tp-100) cc_final: 0.6551 (tm-30) REVERT: L 5 MET cc_start: 0.8300 (tpp) cc_final: 0.7181 (tpp) REVERT: L 13 SER cc_start: 0.8350 (t) cc_final: 0.7732 (m) REVERT: M 21 LEU cc_start: 0.7773 (tp) cc_final: 0.7321 (tt) REVERT: M 33 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.7657 (m-10) outliers start: 48 outliers final: 35 residues processed: 197 average time/residue: 0.0735 time to fit residues: 22.6300 Evaluate side-chains 182 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 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 252 VAL Chi-restraints excluded: chain B residue 296 HIS 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 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 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 23 THR Chi-restraints excluded: chain L residue 49 ILE 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 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 149 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** ** 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 = 0.4034 r_free = 0.4034 target = 0.166036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.139998 restraints weight = 22308.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139075 restraints weight = 30675.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140463 restraints weight = 28034.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.140243 restraints weight = 22403.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.140344 restraints weight = 21986.721| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13510 Z= 0.178 Angle : 0.629 9.183 18415 Z= 0.321 Chirality : 0.045 0.164 2089 Planarity : 0.005 0.054 2344 Dihedral : 6.262 84.267 1913 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.56 % Allowed : 18.15 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.21), residues: 1681 helix: 1.78 (0.87), residues: 36 sheet: 0.24 (0.20), residues: 725 loop : -0.76 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 8 TYR 0.018 0.002 TYR N 92 PHE 0.036 0.002 PHE C 278 TRP 0.010 0.002 TRP M 39 HIS 0.005 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00415 (13504) covalent geometry : angle 0.62744 (18403) SS BOND : bond 0.01136 ( 6) SS BOND : angle 1.67329 ( 12) hydrogen bonds : bond 0.03339 ( 469) hydrogen bonds : angle 5.50548 ( 1272) *********************** 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 222 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 159 time to evaluate : 0.333 Fit side-chains REVERT: A 39 ASP cc_start: 0.8351 (p0) cc_final: 0.8096 (p0) REVERT: B 296 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7422 (m-70) REVERT: C 39 ASP cc_start: 0.8638 (p0) cc_final: 0.8397 (p0) REVERT: C 210 TYR cc_start: 0.8668 (m-80) cc_final: 0.8322 (m-80) REVERT: D 14 LEU cc_start: 0.8351 (mt) cc_final: 0.8103 (mp) REVERT: H 8 VAL cc_start: 0.9024 (t) cc_final: 0.8782 (m) REVERT: H 21 LEU cc_start: 0.7040 (tt) cc_final: 0.6714 (tt) REVERT: M 21 LEU cc_start: 0.7817 (tp) cc_final: 0.7418 (tt) REVERT: M 33 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7535 (m-10) REVERT: N 19 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7638 (ttt-90) outliers start: 63 outliers final: 51 residues processed: 204 average time/residue: 0.0768 time to fit residues: 24.4315 Evaluate side-chains 193 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 140 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 205 ASP 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 35 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 296 HIS 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 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 E residue 34 VAL 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 72 THR 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 47 LEU 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 72 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 117 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 95 VAL Chi-restraints excluded: chain N residue 97 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 117 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 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 ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.165379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140460 restraints weight = 22227.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139197 restraints weight = 33584.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.140296 restraints weight = 29952.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.140113 restraints weight = 22404.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140482 restraints weight = 22186.517| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2898 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= 0.177 Angle : 0.625 9.102 18415 Z= 0.319 Chirality : 0.045 0.164 2089 Planarity : 0.005 0.053 2344 Dihedral : 6.197 81.268 1913 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.92 % Allowed : 18.44 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.21), residues: 1681 helix: 2.05 (0.87), residues: 36 sheet: 0.18 (0.19), residues: 746 loop : -0.79 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 8 TYR 0.017 0.002 TYR H 98 PHE 0.034 0.002 PHE E 84 TRP 0.008 0.002 TRP H 39 HIS 0.005 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00415 (13504) covalent geometry : angle 0.62429 (18403) SS BOND : bond 0.00900 ( 6) SS BOND : angle 1.58163 ( 12) hydrogen bonds : bond 0.03240 ( 469) hydrogen bonds : angle 5.43549 ( 1272) *********************** 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 230 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 162 time to evaluate : 0.437 Fit side-chains REVERT: A 39 ASP cc_start: 0.8380 (p0) cc_final: 0.8105 (p0) REVERT: A 278 PHE cc_start: 0.8715 (p90) cc_final: 0.8317 (p90) REVERT: B 296 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7459 (m-70) REVERT: C 39 ASP cc_start: 0.8638 (p0) cc_final: 0.8400 (p0) REVERT: C 210 TYR cc_start: 0.8683 (m-80) cc_final: 0.8389 (m-80) REVERT: H 85 GLN cc_start: 0.7138 (tp-100) cc_final: 0.6533 (tm-30) REVERT: M 33 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: N 19 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7519 (ttt-90) outliers start: 68 outliers final: 56 residues processed: 209 average time/residue: 0.0905 time to fit residues: 29.7535 Evaluate side-chains 206 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 148 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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 205 ASP 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 35 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 60 VAL 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 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 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 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 E residue 97 VAL Chi-restraints excluded: chain H residue 10 SER 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 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 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 33 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 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 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 155 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.166996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139046 restraints weight = 22046.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138214 restraints weight = 25909.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139734 restraints weight = 24830.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.139726 restraints weight = 17877.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139942 restraints weight = 16976.727| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13510 Z= 0.137 Angle : 0.607 9.093 18415 Z= 0.306 Chirality : 0.044 0.160 2089 Planarity : 0.004 0.052 2344 Dihedral : 6.026 78.785 1913 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.34 % Allowed : 19.60 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.21), residues: 1681 helix: 2.30 (0.87), residues: 36 sheet: 0.28 (0.19), residues: 746 loop : -0.78 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 90 TYR 0.014 0.001 TYR H 98 PHE 0.036 0.002 PHE E 84 TRP 0.007 0.001 TRP M 39 HIS 0.005 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00318 (13504) covalent geometry : angle 0.60581 (18403) SS BOND : bond 0.00810 ( 6) SS BOND : angle 1.38970 ( 12) hydrogen bonds : bond 0.03019 ( 469) hydrogen bonds : angle 5.25512 ( 1272) *********************** 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 224 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 0.541 Fit side-chains REVERT: A 39 ASP cc_start: 0.8387 (p0) cc_final: 0.8100 (p0) REVERT: A 49 LEU cc_start: 0.7067 (pt) cc_final: 0.6847 (pt) REVERT: A 278 PHE cc_start: 0.8677 (p90) cc_final: 0.8319 (p90) REVERT: B 296 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7509 (m-70) REVERT: C 39 ASP cc_start: 0.8649 (p0) cc_final: 0.8400 (p0) REVERT: C 210 TYR cc_start: 0.8681 (m-80) cc_final: 0.8360 (m-80) REVERT: H 42 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7440 (tm-30) REVERT: L 13 SER cc_start: 0.8422 (t) cc_final: 0.7803 (m) REVERT: M 33 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7643 (m-10) REVERT: N 19 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7573 (ttt-90) outliers start: 60 outliers final: 50 residues processed: 210 average time/residue: 0.0956 time to fit residues: 31.2770 Evaluate side-chains 200 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 A residue 340 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 60 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 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 54 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 79 LEU 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 5 VAL Chi-restraints excluded: chain H residue 31 ASN 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 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 33 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 59 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 ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN H 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.164808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138422 restraints weight = 22041.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.137153 restraints weight = 33174.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138506 restraints weight = 30282.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138697 restraints weight = 23143.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.138914 restraints weight = 20771.524| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13510 Z= 0.179 Angle : 0.638 9.271 18415 Z= 0.324 Chirality : 0.045 0.165 2089 Planarity : 0.005 0.052 2344 Dihedral : 6.082 73.408 1913 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.84 % Allowed : 19.96 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.21), residues: 1681 helix: 2.39 (0.87), residues: 36 sheet: 0.30 (0.20), residues: 726 loop : -0.80 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 90 TYR 0.019 0.002 TYR N 92 PHE 0.036 0.002 PHE E 84 TRP 0.010 0.002 TRP H 39 HIS 0.004 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00418 (13504) covalent geometry : angle 0.63663 (18403) SS BOND : bond 0.00814 ( 6) SS BOND : angle 1.81143 ( 12) hydrogen bonds : bond 0.03179 ( 469) hydrogen bonds : angle 5.32449 ( 1272) *********************** 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 228 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 161 time to evaluate : 0.570 Fit side-chains REVERT: A 39 ASP cc_start: 0.8393 (p0) cc_final: 0.8109 (p0) REVERT: A 278 PHE cc_start: 0.8696 (p90) cc_final: 0.8265 (p90) REVERT: B 85 TYR cc_start: 0.6061 (t80) cc_final: 0.5768 (t80) REVERT: C 39 ASP cc_start: 0.8637 (p0) cc_final: 0.8400 (p0) REVERT: C 210 TYR cc_start: 0.8665 (m-80) cc_final: 0.8332 (m-80) REVERT: C 273 TYR cc_start: 0.7634 (m-10) cc_final: 0.7140 (m-10) REVERT: M 33 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.7706 (m-10) REVERT: M 49 GLU cc_start: 0.7440 (tp30) cc_final: 0.6844 (tt0) REVERT: N 28 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7943 (tm-30) outliers start: 67 outliers final: 57 residues processed: 208 average time/residue: 0.0935 time to fit residues: 30.6516 Evaluate side-chains 212 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 205 ASP 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 35 VAL Chi-restraints excluded: chain B residue 60 VAL 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 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 118 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 79 LEU 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 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 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 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 33 TYR Chi-restraints excluded: chain M residue 72 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 9 optimal weight: 0.0980 chunk 144 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.166223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.138330 restraints weight = 22307.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137749 restraints weight = 29260.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.139001 restraints weight = 26772.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139303 restraints weight = 20287.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.139640 restraints weight = 18429.096| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3397 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= 0.140 Angle : 0.617 9.102 18415 Z= 0.312 Chirality : 0.044 0.164 2089 Planarity : 0.004 0.054 2344 Dihedral : 5.916 69.372 1913 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.34 % Allowed : 20.68 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.21), residues: 1681 helix: 2.64 (0.88), residues: 36 sheet: 0.37 (0.20), residues: 714 loop : -0.74 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 90 TYR 0.019 0.001 TYR H 60 PHE 0.037 0.002 PHE E 84 TRP 0.007 0.001 TRP H 39 HIS 0.005 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00324 (13504) covalent geometry : angle 0.61604 (18403) SS BOND : bond 0.00819 ( 6) SS BOND : angle 1.65266 ( 12) hydrogen bonds : bond 0.02972 ( 469) hydrogen bonds : angle 5.14441 ( 1272) *********************** 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 220 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 160 time to evaluate : 0.535 Fit side-chains REVERT: A 39 ASP cc_start: 0.8383 (p0) cc_final: 0.8101 (p0) REVERT: A 278 PHE cc_start: 0.8626 (p90) cc_final: 0.8298 (p90) REVERT: B 85 TYR cc_start: 0.6129 (t80) cc_final: 0.5831 (t80) REVERT: C 39 ASP cc_start: 0.8652 (p0) cc_final: 0.8405 (p0) REVERT: C 210 TYR cc_start: 0.8646 (m-80) cc_final: 0.8312 (m-80) REVERT: C 273 TYR cc_start: 0.7582 (m-10) cc_final: 0.7220 (m-10) REVERT: H 42 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7505 (tm-30) REVERT: L 13 SER cc_start: 0.8417 (t) cc_final: 0.7807 (m) REVERT: M 33 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: N 28 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7914 (tm-30) outliers start: 60 outliers final: 55 residues processed: 205 average time/residue: 0.0936 time to fit residues: 30.3700 Evaluate side-chains 213 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 A residue 340 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 60 VAL 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 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 118 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 79 LEU 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 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 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 75 THR 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 33 TYR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 77 THR 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 48 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 138 optimal weight: 0.0570 chunk 105 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 132 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.167797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.141989 restraints weight = 22140.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.141196 restraints weight = 30775.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142715 restraints weight = 26744.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142282 restraints weight = 19808.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142507 restraints weight = 20288.506| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.003 0.029 13510 Z= 0.120 Angle : 0.604 8.883 18415 Z= 0.305 Chirality : 0.044 0.157 2089 Planarity : 0.004 0.052 2344 Dihedral : 5.747 65.447 1913 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.27 % Allowed : 20.97 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.21), residues: 1681 helix: 2.78 (0.89), residues: 36 sheet: 0.51 (0.20), residues: 704 loop : -0.70 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 90 TYR 0.018 0.001 TYR N 94 PHE 0.048 0.002 PHE N 84 TRP 0.006 0.001 TRP M 50 HIS 0.004 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00276 (13504) covalent geometry : angle 0.60301 (18403) SS BOND : bond 0.00775 ( 6) SS BOND : angle 1.53460 ( 12) hydrogen bonds : bond 0.02804 ( 469) hydrogen bonds : angle 4.98204 ( 1272) ********************** 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: 59 poor density : 163 time to evaluate : 0.589 Fit side-chains REVERT: A 39 ASP cc_start: 0.8359 (p0) cc_final: 0.8079 (p0) REVERT: A 278 PHE cc_start: 0.8551 (p90) cc_final: 0.8292 (p90) REVERT: B 85 TYR cc_start: 0.6022 (t80) cc_final: 0.5733 (t80) REVERT: C 39 ASP cc_start: 0.8628 (p0) cc_final: 0.8381 (p0) REVERT: C 210 TYR cc_start: 0.8647 (m-80) cc_final: 0.8269 (m-80) REVERT: C 273 TYR cc_start: 0.7497 (m-10) cc_final: 0.7123 (m-10) REVERT: H 42 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7565 (tm-30) REVERT: L 5 MET cc_start: 0.7521 (tpp) cc_final: 0.7078 (tpp) REVERT: L 6 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8849 (p) REVERT: L 13 SER cc_start: 0.8365 (t) cc_final: 0.7792 (m) REVERT: M 83 TYR cc_start: 0.7727 (m-80) cc_final: 0.7455 (m-80) outliers start: 59 outliers final: 53 residues processed: 206 average time/residue: 0.0856 time to fit residues: 28.6603 Evaluate side-chains 205 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 A residue 340 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 60 VAL 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 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 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 118 LEU 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 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 23 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 75 THR 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 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 34 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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** C 102 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 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 = 0.3967 r_free = 0.3967 target = 0.160310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133747 restraints weight = 22354.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.131896 restraints weight = 30001.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133046 restraints weight = 31973.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.133267 restraints weight = 21422.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133458 restraints weight = 20669.677| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 13510 Z= 0.340 Angle : 0.760 9.447 18415 Z= 0.394 Chirality : 0.048 0.163 2089 Planarity : 0.005 0.055 2344 Dihedral : 6.367 60.983 1913 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.41 % Allowed : 20.82 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.21), residues: 1681 helix: 2.45 (0.87), residues: 36 sheet: 0.07 (0.20), residues: 730 loop : -0.97 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 90 TYR 0.033 0.003 TYR N 92 PHE 0.044 0.003 PHE N 84 TRP 0.014 0.003 TRP H 39 HIS 0.003 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00801 (13504) covalent geometry : angle 0.75840 (18403) SS BOND : bond 0.01115 ( 6) SS BOND : angle 2.29710 ( 12) hydrogen bonds : bond 0.03877 ( 469) hydrogen bonds : angle 5.69957 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1710.17 seconds wall clock time: 30 minutes 31.10 seconds (1831.10 seconds total)