Starting phenix.real_space_refine on Sat Aug 23 16:22:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i0z_35114/08_2025/8i0z_35114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i0z_35114/08_2025/8i0z_35114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i0z_35114/08_2025/8i0z_35114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i0z_35114/08_2025/8i0z_35114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i0z_35114/08_2025/8i0z_35114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i0z_35114/08_2025/8i0z_35114.map" } resolution = 4.33 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= -0.000 sd= 0.015 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 8342 2.51 5 N 2234 2.21 5 O 2548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 13163 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2620 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2620 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2595 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'ASP:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 910 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TPO:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 771 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "M" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 920 Classifications: {'peptide': 119} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 115} Chain: "N" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 782 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "U" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 81 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TPO:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "V" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TPO:plan-1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 2.73, per 1000 atoms: 0.21 Number of scatterers: 13163 At special positions: 0 Unit cell: (149.844, 151.093, 89.9064, 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 2548 8.00 N 2234 7.00 C 8342 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=2.05 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=2.05 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: 0.78 Conformation dependent library (CDL) restraints added in 466.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 26 sheets defined 5.0% alpha, 43.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.002A 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: 3.836A 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: 3.987A pdb=" N ARG C 283 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'M' and resid 31 through 34 Processing helix chain 'M' and resid 65 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.056A pdb=" N PHE A 28 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 169 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 148 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 54 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN A 86 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 56 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN A 84 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 58 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE A 82 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 60 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.056A pdb=" N PHE A 28 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 169 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 128 " --> pdb=" O VAL A 143 " (cutoff:3.500A) 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: 4.309A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N LEU A 344 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N VAL A 320 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.028A pdb=" N PHE B 28 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS B 171 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N VAL B 143 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL B 54 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN B 86 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 56 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN B 84 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 58 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE B 82 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 60 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.028A pdb=" N PHE B 28 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS B 171 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N VAL B 143 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 128 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 190 Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.589A pdb=" N PHE B 342 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU B 344 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N VAL B 320 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 242 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLN B 249 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR B 247 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE C 76 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP C 79 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE C 62 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 81 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 54 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL C 143 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS C 171 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE C 28 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.589A pdb=" N PHE B 342 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU B 344 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N VAL B 320 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 242 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLN B 249 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR B 247 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE C 76 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP C 79 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE C 62 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 81 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 54 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL C 128 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.700A pdb=" N ARG V 337 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 184 through 187 Processing sheet with id=AB5, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.528A pdb=" N PHE C 342 " --> pdb=" O TYR C 322 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N LEU C 344 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N VAL C 320 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE C 232 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU C 258 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C 234 " --> pdb=" O GLN C 256 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN C 256 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C 236 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.682A pdb=" N GLN D 6 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 28 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.854A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR D 62 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AB9, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.686A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN E 39 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.577A pdb=" N SER H 24 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 60 through 63 removed outlier: 3.652A pdb=" N TYR H 62 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER H 53 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AC4, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.835A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN L 39 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 14 through 15 removed outlier: 6.799A pdb=" N ILE M 37 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER M 53 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TRP M 39 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR M 62 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR M 60 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 23 through 26 Processing sheet with id=AC7, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AC8, first strand: chain 'N' and resid 54 through 55 removed outlier: 6.882A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR N 50 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN N 39 " --> pdb=" O THR N 86 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1305 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: 1.91 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4237 1.34 - 1.47: 3295 1.47 - 1.59: 5854 1.59 - 1.71: 40 1.71 - 1.83: 33 Bond restraints: 13459 Sorted by residual: bond pdb=" OG1 TPO V 342 " pdb=" P TPO V 342 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.78e+01 bond pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" OG1 TPO G 339 " pdb=" P TPO G 339 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 1.717 1.613 0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 13454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 17789 2.22 - 4.44: 469 4.44 - 6.67: 64 6.67 - 8.89: 14 8.89 - 11.11: 10 Bond angle restraints: 18346 Sorted by residual: angle pdb=" N GLY D 12 " pdb=" CA GLY D 12 " pdb=" C GLY D 12 " ideal model delta sigma weight residual 111.42 120.68 -9.26 1.51e+00 4.39e-01 3.76e+01 angle pdb=" C PHE H 105 " pdb=" N TRP H 106 " pdb=" CA TRP H 106 " ideal model delta sigma weight residual 121.70 129.23 -7.53 1.80e+00 3.09e-01 1.75e+01 angle pdb=" N GLU A 314 " pdb=" CA GLU A 314 " pdb=" CB GLU A 314 " ideal model delta sigma weight residual 114.17 109.67 4.50 1.14e+00 7.69e-01 1.56e+01 angle pdb=" C PHE D 105 " pdb=" N TRP D 106 " pdb=" CA TRP D 106 " ideal model delta sigma weight residual 121.70 128.77 -7.07 1.80e+00 3.09e-01 1.54e+01 angle pdb=" C PHE M 105 " pdb=" N TRP M 106 " pdb=" CA TRP M 106 " ideal model delta sigma weight residual 121.70 128.75 -7.05 1.80e+00 3.09e-01 1.53e+01 ... (remaining 18341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7454 17.96 - 35.93: 463 35.93 - 53.89: 68 53.89 - 71.85: 15 71.85 - 89.82: 10 Dihedral angle restraints: 8010 sinusoidal: 2988 harmonic: 5022 Sorted by residual: dihedral pdb=" CB CYS D 25 " pdb=" SG CYS D 25 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 40.30 52.70 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CA MET H 86 " pdb=" C MET H 86 " pdb=" N ASN H 87 " pdb=" CA ASN H 87 " ideal model delta harmonic sigma weight residual -180.00 -150.18 -29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA MET D 86 " pdb=" C MET D 86 " pdb=" N ASN D 87 " pdb=" CA ASN D 87 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 8007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1371 0.038 - 0.076: 461 0.076 - 0.115: 190 0.115 - 0.153: 65 0.153 - 0.191: 9 Chirality restraints: 2096 Sorted by residual: chirality pdb=" CG LEU M 7 " pdb=" CB LEU M 7 " pdb=" CD1 LEU M 7 " pdb=" CD2 LEU M 7 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CB ILE L 107 " pdb=" CA ILE L 107 " pdb=" CG1 ILE L 107 " pdb=" CG2 ILE L 107 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CB ILE E 76 " pdb=" CA ILE E 76 " pdb=" CG1 ILE E 76 " pdb=" CG2 ILE E 76 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 2093 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE N 107 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ILE N 107 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE N 107 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS N 108 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 340 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 341 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 124 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO C 125 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.025 5.00e-02 4.00e+02 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 157 2.63 - 3.20: 12543 3.20 - 3.77: 19192 3.77 - 4.33: 25591 4.33 - 4.90: 42448 Nonbonded interactions: 99931 Sorted by model distance: nonbonded pdb=" NE2 GLN E 39 " pdb=" O LYS E 40 " model vdw 2.066 3.120 nonbonded pdb=" NE2 GLN L 39 " pdb=" O LYS L 40 " model vdw 2.095 3.120 nonbonded pdb=" NE2 GLN N 39 " pdb=" O LYS N 40 " model vdw 2.109 3.120 nonbonded pdb=" OD1 ASP N 18 " pdb=" N ARG N 19 " model vdw 2.149 3.120 nonbonded pdb=" OD1 ASP E 18 " pdb=" N ARG E 19 " model vdw 2.254 3.120 ... (remaining 99926 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 8 through 119 or (resid 120 and (name N or name CA or name \ C or name O or name CB )) or resid 121 through 188 or (resid 189 and (name N or \ name CA or name C or name O or name CB )) or resid 190 through 229 or (resid 23 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 231 through \ 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) or re \ sid 261 through 314 or (resid 315 through 316 and (name N or name CA or name C o \ r name O or name CB )) or resid 317 through 324 or (resid 325 and (name N or nam \ e CA or name C or name O or name CB )) or resid 326 through 338 or (resid 339 an \ d (name N or name CA or name C or name O or name CB )) or resid 340 through 350) \ ) selection = (chain 'B' and (resid 8 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 or (resid 158 and (name N o \ r name CA or name C or name O or name CB )) or resid 159 through 188 or (resid 1 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 190 through \ 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) or r \ esid 196 through 229 or (resid 230 and (name N or name CA or name C or name O or \ name CB )) or resid 231 through 315 or (resid 316 and (name N or name CA or nam \ e C or name O or name CB )) or resid 317 through 324 or (resid 325 and (name N o \ r name CA or name C or name O or name CB )) or resid 326 through 338 or (resid 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 350)) selection = (chain 'C' and (resid 8 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 350)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 5 through 122) selection = (chain 'M' and (resid 5 through 41 or (resid 42 through 43 and (name N or name C \ A or name C or name O or name CB )) or resid 44 through 122)) } ncs_group { reference = (chain 'E' and (resid 2 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 107)) selection = (chain 'L' and (resid 2 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 107)) selection = (chain 'N' and (resid 2 through 92 or (resid 93 and (name N or name CA or name C \ or name O or name CB )) or resid 94 through 107)) } ncs_group { reference = (chain 'G' and resid 334 through 342) selection = (chain 'U' and resid 334 through 342) 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: 3.680 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.950 Find NCS groups from input model: 0.260 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 0.007 0.107 13465 Z= 0.326 Angle : 0.916 11.110 18358 Z= 0.472 Chirality : 0.049 0.191 2096 Planarity : 0.006 0.059 2340 Dihedral : 12.708 89.817 4764 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.29 % Allowed : 0.58 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -1.50 (0.20), residues: 1672 helix: -2.36 (0.59), residues: 42 sheet: -0.64 (0.20), residues: 658 loop : -1.16 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 62 TYR 0.028 0.002 TYR M 33 PHE 0.020 0.002 PHE L 99 TRP 0.016 0.002 TRP E 36 HIS 0.006 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00670 (13459) covalent geometry : angle 0.91449 (18346) SS BOND : bond 0.01188 ( 6) SS BOND : angle 1.92889 ( 12) hydrogen bonds : bond 0.19212 ( 453) hydrogen bonds : angle 8.84797 ( 1305) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: B 295 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7744 (ptpp) REVERT: E 36 TRP cc_start: 0.7569 (m100) cc_final: 0.7248 (m100) REVERT: E 107 ILE cc_start: 0.6561 (mp) cc_final: 0.6308 (pt) outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.0802 time to fit residues: 12.5515 Evaluate side-chains 58 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.080590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.070148 restraints weight = 74408.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.072847 restraints weight = 79742.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.072626 restraints weight = 38058.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.073115 restraints weight = 34586.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.073909 restraints weight = 25937.386| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 13465 Z= 0.248 Angle : 0.783 9.550 18358 Z= 0.410 Chirality : 0.050 0.360 2096 Planarity : 0.005 0.046 2340 Dihedral : 7.338 48.003 1898 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.29 % Allowed : 5.76 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -1.36 (0.20), residues: 1672 helix: -0.31 (0.83), residues: 36 sheet: -0.61 (0.18), residues: 757 loop : -1.13 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 70 TYR 0.015 0.002 TYR L 37 PHE 0.020 0.002 PHE B 145 TRP 0.007 0.002 TRP H 106 HIS 0.005 0.002 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00546 (13459) covalent geometry : angle 0.78103 (18346) SS BOND : bond 0.01846 ( 6) SS BOND : angle 2.48219 ( 12) hydrogen bonds : bond 0.04474 ( 453) hydrogen bonds : angle 6.62156 ( 1305) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 0.0954 time to fit residues: 11.2389 Evaluate side-chains 49 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 26 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 164 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 238 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.079949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.069342 restraints weight = 76181.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.072064 restraints weight = 81922.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.071756 restraints weight = 37762.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.072123 restraints weight = 38286.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.072761 restraints weight = 28631.076| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 13465 Z= 0.218 Angle : 0.714 8.786 18358 Z= 0.372 Chirality : 0.047 0.351 2096 Planarity : 0.005 0.041 2340 Dihedral : 6.672 44.933 1898 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -1.28 (0.20), residues: 1672 helix: 0.81 (0.93), residues: 36 sheet: -0.40 (0.18), residues: 768 loop : -1.31 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 101 TYR 0.017 0.002 TYR M 33 PHE 0.018 0.002 PHE N 84 TRP 0.007 0.002 TRP H 39 HIS 0.006 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00476 (13459) covalent geometry : angle 0.70973 (18346) SS BOND : bond 0.01342 ( 6) SS BOND : angle 3.01336 ( 12) hydrogen bonds : bond 0.03771 ( 453) hydrogen bonds : angle 6.28066 ( 1305) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.502 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0729 time to fit residues: 9.1133 Evaluate side-chains 45 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 112 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.078703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.067700 restraints weight = 74934.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.070741 restraints weight = 82134.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.070295 restraints weight = 36534.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.070789 restraints weight = 36988.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.071565 restraints weight = 27769.630| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 13465 Z= 0.265 Angle : 0.747 10.026 18358 Z= 0.390 Chirality : 0.048 0.387 2096 Planarity : 0.005 0.040 2340 Dihedral : 6.677 44.438 1898 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -1.41 (0.20), residues: 1672 helix: 0.90 (1.00), residues: 36 sheet: -0.49 (0.18), residues: 771 loop : -1.41 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 41 TYR 0.016 0.002 TYR D 33 PHE 0.022 0.002 PHE L 99 TRP 0.008 0.002 TRP H 39 HIS 0.005 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00586 (13459) covalent geometry : angle 0.74417 (18346) SS BOND : bond 0.01532 ( 6) SS BOND : angle 2.64930 ( 12) hydrogen bonds : bond 0.03798 ( 453) hydrogen bonds : angle 6.22840 ( 1305) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: N 20 VAL cc_start: 0.6620 (t) cc_final: 0.6226 (t) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0730 time to fit residues: 8.2486 Evaluate side-chains 42 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 18 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 182 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.079684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.068558 restraints weight = 74978.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.071405 restraints weight = 81714.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.071166 restraints weight = 36681.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.071525 restraints weight = 37803.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.072359 restraints weight = 28389.300| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 13465 Z= 0.207 Angle : 0.687 7.648 18358 Z= 0.355 Chirality : 0.047 0.318 2096 Planarity : 0.004 0.038 2340 Dihedral : 6.355 43.270 1898 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -1.44 (0.20), residues: 1672 helix: 0.75 (0.95), residues: 36 sheet: -0.59 (0.19), residues: 773 loop : -1.34 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 101 TYR 0.013 0.002 TYR L 37 PHE 0.021 0.002 PHE L 99 TRP 0.007 0.001 TRP H 39 HIS 0.004 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00460 (13459) covalent geometry : angle 0.68472 (18346) SS BOND : bond 0.01294 ( 6) SS BOND : angle 2.19332 ( 12) hydrogen bonds : bond 0.03430 ( 453) hydrogen bonds : angle 6.02074 ( 1305) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.453 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0781 time to fit residues: 8.9108 Evaluate side-chains 42 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 112 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS B 300 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN L 7 GLN N 7 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.081216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.070467 restraints weight = 73866.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.072846 restraints weight = 82528.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.073433 restraints weight = 35262.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.073810 restraints weight = 29089.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.074125 restraints weight = 23585.428| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13465 Z= 0.129 Angle : 0.612 6.594 18358 Z= 0.311 Chirality : 0.045 0.213 2096 Planarity : 0.004 0.037 2340 Dihedral : 5.793 41.312 1898 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -1.18 (0.20), residues: 1672 helix: 0.81 (0.87), residues: 36 sheet: -0.24 (0.19), residues: 755 loop : -1.32 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 101 TYR 0.010 0.001 TYR C 250 PHE 0.015 0.001 PHE E 99 TRP 0.006 0.001 TRP H 39 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00287 (13459) covalent geometry : angle 0.61131 (18346) SS BOND : bond 0.00984 ( 6) SS BOND : angle 1.54473 ( 12) hydrogen bonds : bond 0.02944 ( 453) hydrogen bonds : angle 5.57418 ( 1305) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.465 Fit side-chains REVERT: B 300 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8415 (p0) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.0668 time to fit residues: 8.6891 Evaluate side-chains 49 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 28 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 0.0470 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 overall best weight: 1.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS C 182 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.080379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.069532 restraints weight = 74049.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.072559 restraints weight = 77483.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.072286 restraints weight = 30681.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.072652 restraints weight = 32905.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.073370 restraints weight = 24681.667| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13465 Z= 0.178 Angle : 0.648 7.455 18358 Z= 0.332 Chirality : 0.045 0.271 2096 Planarity : 0.004 0.037 2340 Dihedral : 5.895 40.687 1898 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -1.16 (0.20), residues: 1672 helix: 0.89 (0.89), residues: 36 sheet: -0.20 (0.19), residues: 753 loop : -1.35 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 90 TYR 0.012 0.001 TYR M 33 PHE 0.021 0.002 PHE L 99 TRP 0.007 0.001 TRP E 36 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00398 (13459) covalent geometry : angle 0.64496 (18346) SS BOND : bond 0.01189 ( 6) SS BOND : angle 2.50609 ( 12) hydrogen bonds : bond 0.03097 ( 453) hydrogen bonds : angle 5.56491 ( 1305) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.413 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0695 time to fit residues: 8.4533 Evaluate side-chains 46 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 23 optimal weight: 9.9990 chunk 87 optimal weight: 0.0000 chunk 106 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN L 7 GLN N 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.082126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.072503 restraints weight = 73399.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.074873 restraints weight = 68929.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.074600 restraints weight = 29656.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.075044 restraints weight = 27185.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.075435 restraints weight = 21954.122| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13465 Z= 0.114 Angle : 0.590 6.761 18358 Z= 0.297 Chirality : 0.044 0.186 2096 Planarity : 0.004 0.034 2340 Dihedral : 5.466 38.866 1898 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.97 (0.21), residues: 1672 helix: 0.91 (0.83), residues: 36 sheet: -0.04 (0.20), residues: 779 loop : -1.29 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 101 TYR 0.011 0.001 TYR C 250 PHE 0.019 0.001 PHE L 99 TRP 0.006 0.001 TRP M 39 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00256 (13459) covalent geometry : angle 0.58877 (18346) SS BOND : bond 0.00714 ( 6) SS BOND : angle 1.73683 ( 12) hydrogen bonds : bond 0.02730 ( 453) hydrogen bonds : angle 5.25714 ( 1305) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.366 Fit side-chains REVERT: E 49 ILE cc_start: 0.8195 (tt) cc_final: 0.7947 (tt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0729 time to fit residues: 9.3116 Evaluate side-chains 47 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 127 optimal weight: 0.2980 chunk 120 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.080412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.069426 restraints weight = 74605.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.071966 restraints weight = 81375.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.071966 restraints weight = 38268.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.072180 restraints weight = 41187.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.072834 restraints weight = 30156.936| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13465 Z= 0.154 Angle : 0.625 7.590 18358 Z= 0.317 Chirality : 0.045 0.307 2096 Planarity : 0.004 0.032 2340 Dihedral : 5.530 38.505 1898 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.98 (0.21), residues: 1672 helix: 1.01 (0.85), residues: 36 sheet: -0.07 (0.19), residues: 784 loop : -1.27 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 101 TYR 0.012 0.001 TYR N 88 PHE 0.020 0.001 PHE L 99 TRP 0.044 0.002 TRP E 36 HIS 0.006 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00344 (13459) covalent geometry : angle 0.62358 (18346) SS BOND : bond 0.01113 ( 6) SS BOND : angle 1.97349 ( 12) hydrogen bonds : bond 0.02923 ( 453) hydrogen bonds : angle 5.30945 ( 1305) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.399 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0624 time to fit residues: 8.3179 Evaluate side-chains 52 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 165 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 75 optimal weight: 0.0170 chunk 2 optimal weight: 1.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.082509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.071258 restraints weight = 74099.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.074109 restraints weight = 80432.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.074525 restraints weight = 36429.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.075016 restraints weight = 30366.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.075358 restraints weight = 24318.006| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13465 Z= 0.111 Angle : 0.591 7.001 18358 Z= 0.298 Chirality : 0.044 0.166 2096 Planarity : 0.004 0.034 2340 Dihedral : 5.335 37.550 1898 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: -0.85 (0.21), residues: 1672 helix: 1.04 (0.80), residues: 36 sheet: 0.10 (0.19), residues: 773 loop : -1.26 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 101 TYR 0.011 0.001 TYR C 250 PHE 0.020 0.001 PHE L 99 TRP 0.027 0.001 TRP E 36 HIS 0.003 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00248 (13459) covalent geometry : angle 0.58952 (18346) SS BOND : bond 0.00878 ( 6) SS BOND : angle 1.50517 ( 12) hydrogen bonds : bond 0.02704 ( 453) hydrogen bonds : angle 5.14118 ( 1305) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.502 Fit side-chains REVERT: M 54 ILE cc_start: 0.9239 (tp) cc_final: 0.9033 (tt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0728 time to fit residues: 9.7672 Evaluate side-chains 50 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 73 optimal weight: 0.0050 chunk 86 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 chunk 108 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS E 7 GLN L 7 GLN N 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.083215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.071793 restraints weight = 74032.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.074721 restraints weight = 84022.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.075343 restraints weight = 38045.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.075778 restraints weight = 29752.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.076167 restraints weight = 24953.177| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13465 Z= 0.099 Angle : 0.576 9.280 18358 Z= 0.286 Chirality : 0.044 0.171 2096 Planarity : 0.004 0.033 2340 Dihedral : 5.025 35.568 1898 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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 (0.21), residues: 1672 helix: 1.24 (0.81), residues: 36 sheet: 0.15 (0.19), residues: 780 loop : -1.11 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 101 TYR 0.012 0.001 TYR C 250 PHE 0.018 0.001 PHE L 99 TRP 0.021 0.001 TRP E 36 HIS 0.003 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00221 (13459) covalent geometry : angle 0.57561 (18346) SS BOND : bond 0.00694 ( 6) SS BOND : angle 1.10063 ( 12) hydrogen bonds : bond 0.02600 ( 453) hydrogen bonds : angle 4.90174 ( 1305) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1488.29 seconds wall clock time: 26 minutes 46.92 seconds (1606.92 seconds total)