Starting phenix.real_space_refine on Wed Jun 11 22:21:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i0z_35114/06_2025/8i0z_35114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i0z_35114/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8i0z_35114/06_2025/8i0z_35114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i0z_35114/06_2025/8i0z_35114.map" model { file = "/net/cci-nas-00/data/ceres_data/8i0z_35114/06_2025/8i0z_35114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i0z_35114/06_2025/8i0z_35114.cif" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 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: {'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 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: {'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} 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: 8.97, per 1000 atoms: 0.68 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 2.22 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: 4.17 Time building geometry restraints manager: 3.61 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.910 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.520 ------------------------------------------------------------------------------- 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 : 6.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (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 TRP 0.016 0.002 TRP E 36 HIS 0.006 0.001 HIS C 114 PHE 0.020 0.002 PHE L 99 TYR 0.028 0.002 TYR M 33 ARG 0.007 0.001 ARG E 62 Details of bonding type rmsd hydrogen bonds : bond 0.19212 ( 453) hydrogen bonds : angle 8.84797 ( 1305) SS BOND : bond 0.01188 ( 6) SS BOND : angle 1.92889 ( 12) covalent geometry : bond 0.00670 (13459) covalent geometry : angle 0.91449 (18346) *********************** 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 : 1.645 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: 0.2301 time to fit residues: 35.4090 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 : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.081022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.069934 restraints weight = 74400.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.072318 restraints weight = 84371.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.072908 restraints weight = 38390.668| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13465 Z= 0.204 Angle : 0.742 8.029 18358 Z= 0.385 Chirality : 0.049 0.315 2096 Planarity : 0.005 0.045 2340 Dihedral : 7.067 47.568 1898 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.29 % Allowed : 5.48 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1672 helix: -0.29 (0.81), residues: 36 sheet: -0.57 (0.18), residues: 772 loop : -1.07 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 106 HIS 0.005 0.001 HIS D 38 PHE 0.020 0.002 PHE B 145 TYR 0.016 0.002 TYR D 63 ARG 0.004 0.001 ARG H 70 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 453) hydrogen bonds : angle 6.41513 ( 1305) SS BOND : bond 0.01590 ( 6) SS BOND : angle 2.24490 ( 12) covalent geometry : bond 0.00447 (13459) covalent geometry : angle 0.73953 (18346) *********************** 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 77 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.2182 time to fit residues: 27.4690 Evaluate side-chains 49 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 148 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 41 optimal weight: 0.3980 chunk 128 optimal weight: 0.2980 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 238 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.079345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.068897 restraints weight = 75588.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.071322 restraints weight = 82598.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.071525 restraints weight = 35307.977| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 13465 Z= 0.309 Angle : 0.825 10.905 18358 Z= 0.433 Chirality : 0.050 0.362 2096 Planarity : 0.006 0.047 2340 Dihedral : 7.110 45.167 1898 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.07 % Allowed : 5.98 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.20), residues: 1672 helix: 0.61 (0.99), residues: 36 sheet: -0.59 (0.18), residues: 765 loop : -1.48 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 106 HIS 0.008 0.002 HIS C 296 PHE 0.024 0.003 PHE N 84 TYR 0.020 0.002 TYR M 33 ARG 0.004 0.001 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 453) hydrogen bonds : angle 6.60283 ( 1305) SS BOND : bond 0.01821 ( 6) SS BOND : angle 3.63029 ( 12) covalent geometry : bond 0.00677 (13459) covalent geometry : angle 0.81955 (18346) *********************** 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 63 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 1.611 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.1866 time to fit residues: 20.5615 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 : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 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 ** 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 = 0.3615 r_free = 0.3615 target = 0.079548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.068968 restraints weight = 73481.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.071623 restraints weight = 79581.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.071283 restraints weight = 36118.670| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 13465 Z= 0.218 Angle : 0.705 9.460 18358 Z= 0.366 Chirality : 0.047 0.334 2096 Planarity : 0.004 0.041 2340 Dihedral : 6.598 44.340 1898 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.07 % Allowed : 4.83 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.20), residues: 1672 helix: 0.84 (0.98), residues: 36 sheet: -0.63 (0.19), residues: 763 loop : -1.37 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 39 HIS 0.006 0.001 HIS H 38 PHE 0.020 0.002 PHE E 99 TYR 0.017 0.002 TYR D 33 ARG 0.003 0.000 ARG M 101 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 453) hydrogen bonds : angle 6.23690 ( 1305) SS BOND : bond 0.01504 ( 6) SS BOND : angle 2.80944 ( 12) covalent geometry : bond 0.00483 (13459) covalent geometry : angle 0.70109 (18346) *********************** 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: 1 poor density : 65 time to evaluate : 1.779 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.1980 time to fit residues: 22.7946 Evaluate side-chains 41 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 100 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 238 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** 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** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.079766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.068911 restraints weight = 74113.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.071390 restraints weight = 79838.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.071538 restraints weight = 38615.858| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13465 Z= 0.176 Angle : 0.661 7.524 18358 Z= 0.338 Chirality : 0.046 0.290 2096 Planarity : 0.004 0.039 2340 Dihedral : 6.136 42.463 1898 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.20), residues: 1672 helix: 0.74 (0.93), residues: 36 sheet: -0.41 (0.19), residues: 765 loop : -1.42 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 39 HIS 0.004 0.001 HIS C 296 PHE 0.017 0.002 PHE L 99 TYR 0.013 0.001 TYR L 37 ARG 0.003 0.000 ARG M 101 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 453) hydrogen bonds : angle 5.91431 ( 1305) SS BOND : bond 0.01043 ( 6) SS BOND : angle 1.82743 ( 12) covalent geometry : bond 0.00393 (13459) covalent geometry : angle 0.66003 (18346) *********************** 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 : 1.654 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2126 time to fit residues: 25.1295 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 : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 2 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 102 optimal weight: 0.0020 chunk 140 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 overall best weight: 4.3996 ------------------------------------------------------------------------------- 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 31 HIS B 114 HIS ** 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 ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.078046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.067710 restraints weight = 75824.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.070235 restraints weight = 83728.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.070141 restraints weight = 38303.544| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.155 13465 Z= 0.360 Angle : 0.848 11.521 18358 Z= 0.443 Chirality : 0.052 0.479 2096 Planarity : 0.005 0.044 2340 Dihedral : 6.943 43.486 1898 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.20), residues: 1672 helix: 0.56 (1.00), residues: 36 sheet: -0.77 (0.19), residues: 791 loop : -1.62 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 106 HIS 0.008 0.002 HIS C 114 PHE 0.039 0.003 PHE L 99 TYR 0.019 0.002 TYR L 37 ARG 0.008 0.001 ARG D 90 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 453) hydrogen bonds : angle 6.49533 ( 1305) SS BOND : bond 0.01882 ( 6) SS BOND : angle 3.73195 ( 12) covalent geometry : bond 0.00797 (13459) covalent geometry : angle 0.84275 (18346) *********************** 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 57 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.910 Fit side-chains REVERT: N 38 GLN cc_start: 0.8220 (pp30) cc_final: 0.7997 (pp30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1750 time to fit residues: 18.3790 Evaluate side-chains 36 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.080720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.069517 restraints weight = 73497.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.071982 restraints weight = 85432.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.072613 restraints weight = 36838.232| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13465 Z= 0.170 Angle : 0.666 10.575 18358 Z= 0.342 Chirality : 0.046 0.255 2096 Planarity : 0.004 0.042 2340 Dihedral : 6.239 42.420 1898 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1672 helix: 0.67 (0.93), residues: 36 sheet: -0.39 (0.19), residues: 767 loop : -1.58 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 39 HIS 0.004 0.001 HIS A 211 PHE 0.027 0.002 PHE L 99 TYR 0.014 0.001 TYR M 33 ARG 0.004 0.000 ARG M 101 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 453) hydrogen bonds : angle 6.00946 ( 1305) SS BOND : bond 0.01512 ( 6) SS BOND : angle 2.79578 ( 12) covalent geometry : bond 0.00377 (13459) covalent geometry : angle 0.66265 (18346) *********************** 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 64 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.499 Fit side-chains REVERT: N 38 GLN cc_start: 0.8312 (pp30) cc_final: 0.8035 (tm-30) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1988 time to fit residues: 21.7163 Evaluate side-chains 40 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 120 optimal weight: 0.0050 chunk 127 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** 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 = 0.3652 r_free = 0.3652 target = 0.081569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.070411 restraints weight = 74455.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.073024 restraints weight = 83586.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.073694 restraints weight = 37724.131| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13465 Z= 0.128 Angle : 0.614 9.350 18358 Z= 0.309 Chirality : 0.044 0.234 2096 Planarity : 0.004 0.037 2340 Dihedral : 5.708 39.798 1898 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.20), residues: 1672 helix: 0.74 (0.85), residues: 36 sheet: -0.08 (0.19), residues: 763 loop : -1.50 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 39 HIS 0.003 0.001 HIS B 211 PHE 0.031 0.001 PHE L 99 TYR 0.010 0.001 TYR C 250 ARG 0.005 0.000 ARG D 103 Details of bonding type rmsd hydrogen bonds : bond 0.02846 ( 453) hydrogen bonds : angle 5.51996 ( 1305) SS BOND : bond 0.00922 ( 6) SS BOND : angle 1.67268 ( 12) covalent geometry : bond 0.00286 (13459) covalent geometry : angle 0.61225 (18346) *********************** 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 59 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.544 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1734 time to fit residues: 18.6971 Evaluate side-chains 40 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 77 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 112 HIS E 7 GLN L 7 GLN N 7 GLN N 28 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.082539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.072412 restraints weight = 73389.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.074703 restraints weight = 76655.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.074982 restraints weight = 31990.793| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13465 Z= 0.104 Angle : 0.592 7.717 18358 Z= 0.295 Chirality : 0.044 0.163 2096 Planarity : 0.004 0.032 2340 Dihedral : 5.370 37.707 1898 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.07 % Allowed : 0.86 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1672 helix: 1.04 (0.82), residues: 36 sheet: 0.05 (0.19), residues: 778 loop : -1.36 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 36 HIS 0.003 0.001 HIS B 211 PHE 0.024 0.001 PHE L 99 TYR 0.010 0.001 TYR H 98 ARG 0.007 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.02684 ( 453) hydrogen bonds : angle 5.23406 ( 1305) SS BOND : bond 0.00818 ( 6) SS BOND : angle 1.51447 ( 12) covalent geometry : bond 0.00232 (13459) covalent geometry : angle 0.59060 (18346) *********************** 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 65 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 2.006 Fit side-chains REVERT: B 300 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8416 (p0) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.2201 time to fit residues: 25.9665 Evaluate side-chains 47 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 126 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 135 optimal weight: 0.0470 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS C 111 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.081758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.070594 restraints weight = 73563.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.073265 restraints weight = 82367.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.073667 restraints weight = 34618.642| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13465 Z= 0.117 Angle : 0.590 7.831 18358 Z= 0.295 Chirality : 0.044 0.186 2096 Planarity : 0.004 0.031 2340 Dihedral : 5.277 36.494 1898 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.07 % Allowed : 0.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1672 helix: 1.07 (0.82), residues: 36 sheet: 0.10 (0.20), residues: 780 loop : -1.34 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 39 HIS 0.004 0.001 HIS B 346 PHE 0.021 0.001 PHE L 99 TYR 0.010 0.001 TYR C 250 ARG 0.003 0.000 ARG M 101 Details of bonding type rmsd hydrogen bonds : bond 0.02691 ( 453) hydrogen bonds : angle 5.13092 ( 1305) SS BOND : bond 0.00871 ( 6) SS BOND : angle 1.91999 ( 12) covalent geometry : bond 0.00261 (13459) covalent geometry : angle 0.58793 (18346) ********************** 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 68 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 1.863 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.2137 time to fit residues: 26.5060 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 : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 25 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** 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 ** N 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.079349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.068135 restraints weight = 74803.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.071380 restraints weight = 79723.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.070974 restraints weight = 31263.604| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3855 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= 0.217 Angle : 0.682 10.785 18358 Z= 0.348 Chirality : 0.046 0.370 2096 Planarity : 0.004 0.034 2340 Dihedral : 5.757 37.416 1898 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.21), residues: 1672 helix: 0.74 (0.90), residues: 36 sheet: -0.01 (0.20), residues: 780 loop : -1.41 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 50 HIS 0.005 0.001 HIS C 114 PHE 0.027 0.002 PHE L 99 TYR 0.012 0.001 TYR N 88 ARG 0.003 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 453) hydrogen bonds : angle 5.51824 ( 1305) SS BOND : bond 0.01262 ( 6) SS BOND : angle 2.79195 ( 12) covalent geometry : bond 0.00486 (13459) covalent geometry : angle 0.67867 (18346) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4079.99 seconds wall clock time: 75 minutes 37.12 seconds (4537.12 seconds total)