Starting phenix.real_space_refine on Sun Jun 15 07:21:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8goc_34175/06_2025/8goc_34175.cif Found real_map, /net/cci-nas-00/data/ceres_data/8goc_34175/06_2025/8goc_34175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8goc_34175/06_2025/8goc_34175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8goc_34175/06_2025/8goc_34175.map" model { file = "/net/cci-nas-00/data/ceres_data/8goc_34175/06_2025/8goc_34175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8goc_34175/06_2025/8goc_34175.cif" } resolution = 4.18 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= 0.010 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 36 5.16 5 C 10723 2.51 5 N 2888 2.21 5 O 3280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16942 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2725 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2725 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2717 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "M" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "U" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "V" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 12.73, per 1000 atoms: 0.75 Number of scatterers: 16942 At special positions: 0 Unit cell: (187.78, 178.76, 96.76, 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 36 16.00 P 15 15.00 O 3280 8.00 N 2888 7.00 C 10723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 99 " distance=2.04 Simple disulfide: pdb=" SG CYS M 150 " - pdb=" SG CYS M 206 " distance=2.03 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 89 " distance=2.03 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: 4.86 Conformation dependent library (CDL) restraints added in 2.7 seconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4182 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 46 sheets defined 5.4% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.181A pdb=" N LEU A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'B' and resid 45 through 50 removed outlier: 4.351A pdb=" N LEU B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'C' and resid 46 through 49 Processing helix chain 'C' and resid 99 through 110 Processing helix chain 'D' and resid 65 through 68 Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.838A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.823A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.576A pdb=" N GLY L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'M' and resid 65 through 68 Processing helix chain 'M' and resid 90 through 94 removed outlier: 3.856A pdb=" N THR M 94 " --> pdb=" O ALA M 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 129 removed outlier: 3.577A pdb=" N GLY N 129 " --> pdb=" O GLN N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 117 removed outlier: 3.738A pdb=" N PHE A 10 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.118A pdb=" N PHE A 28 " --> pdb=" O VAL A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 88 removed outlier: 5.966A pdb=" N ILE A 82 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL A 60 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN A 84 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLN A 86 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 56 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.639A pdb=" N TYR A 209 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU A 344 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N VAL A 320 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 232 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 259 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 255 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 113 through 118 removed outlier: 3.613A pdb=" N GLY B 40 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 10 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.023A pdb=" N PHE B 28 " --> pdb=" O VAL B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 79 through 88 removed outlier: 5.909A pdb=" N ILE B 82 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL B 60 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 58 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLN B 86 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 56 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 190 Processing sheet with id=AB3, first strand: chain 'B' and resid 247 through 259 removed outlier: 4.879A pdb=" N GLN B 249 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE B 242 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 255 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 259 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 232 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 336 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 113 through 118 removed outlier: 3.698A pdb=" N GLY C 40 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 10 " --> pdb=" O LEU C 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AB6, first strand: chain 'C' and resid 79 through 88 removed outlier: 5.845A pdb=" N ILE C 82 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL C 60 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN C 84 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU C 58 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLN C 86 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 56 " --> pdb=" O GLN C 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AB8, first strand: chain 'C' and resid 184 through 190 Processing sheet with id=AB9, first strand: chain 'C' and resid 247 through 249 removed outlier: 3.810A pdb=" N ILE C 232 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN C 259 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA C 255 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN C 238 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 247 through 249 removed outlier: 3.955A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 336 " --> pdb=" O LEU C 328 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.679A pdb=" N SER D 28 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 82 " --> pdb=" O CYS D 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.061A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N SER D 35 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER D 55 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.061A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR D 112 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 130 through 134 removed outlier: 3.785A pdb=" N SER D 130 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D 153 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER D 189 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL D 191 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N THR D 175 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AC7, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.575A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.596A pdb=" N THR E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.627A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.554A pdb=" N SER E 115 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.744A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 84 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS H 25 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA H 82 " --> pdb=" O CYS H 25 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.116A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL H 40 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.116A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.671A pdb=" N SER H 130 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER H 189 " --> pdb=" O PRO H 177 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL H 191 " --> pdb=" O THR H 175 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N THR H 175 " --> pdb=" O VAL H 191 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 161 through 163 Processing sheet with id=AD7, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.554A pdb=" N THR L 23 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.520A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.520A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.652A pdb=" N SER L 115 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 6 through 10 removed outlier: 3.750A pdb=" N SER M 28 " --> pdb=" O GLN M 6 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.152A pdb=" N GLY M 13 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N SER M 35 " --> pdb=" O SER M 55 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER M 55 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE M 37 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER M 53 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TRP M 39 " --> pdb=" O VAL M 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.152A pdb=" N GLY M 13 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR M 112 " --> pdb=" O ARG M 101 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 130 through 134 removed outlier: 3.657A pdb=" N SER M 130 " --> pdb=" O LYS M 153 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER M 187 " --> pdb=" O ALA M 178 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA M 178 " --> pdb=" O SER M 187 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER M 189 " --> pdb=" O PHE M 176 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 161 through 163 Processing sheet with id=AE7, first strand: chain 'N' and resid 5 through 8 removed outlier: 3.518A pdb=" N THR N 23 " --> pdb=" O SER N 8 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 11 through 14 Processing sheet with id=AE9, first strand: chain 'N' and resid 54 through 55 removed outlier: 6.671A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR N 50 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 115 through 119 removed outlier: 3.709A pdb=" N SER N 115 " --> pdb=" O ASN N 138 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN N 138 " --> pdb=" O SER N 115 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR N 174 " --> pdb=" O ASN N 139 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1566 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: 6.13 Time building geometry restraints manager: 5.27 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: 5430 1.34 - 1.46: 3951 1.46 - 1.58: 7858 1.58 - 1.70: 51 1.70 - 1.82: 48 Bond restraints: 17338 Sorted by residual: bond pdb=" OG1 TPO G 359 " pdb=" P TPO G 359 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" OG1 TPO U 359 " pdb=" P TPO U 359 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO G 360 " pdb=" P TPO G 360 " ideal model delta sigma weight residual 1.717 1.618 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.717 1.618 0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 17333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 23304 2.59 - 5.18: 260 5.18 - 7.78: 52 7.78 - 10.37: 13 10.37 - 12.96: 5 Bond angle restraints: 23634 Sorted by residual: angle pdb=" CB TPO V 359 " pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 119.31 106.35 12.96 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CB TPO U 359 " pdb=" OG1 TPO U 359 " pdb=" P TPO U 359 " ideal model delta sigma weight residual 119.31 106.36 12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CB TPO G 359 " pdb=" OG1 TPO G 359 " pdb=" P TPO G 359 " ideal model delta sigma weight residual 119.31 106.37 12.94 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C LEU C 49 " pdb=" N LYS C 50 " pdb=" CA LYS C 50 " ideal model delta sigma weight residual 121.54 129.44 -7.90 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C LEU B 49 " pdb=" N LYS B 50 " pdb=" CA LYS B 50 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 ... (remaining 23629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9513 17.98 - 35.97: 752 35.97 - 53.95: 98 53.95 - 71.94: 20 71.94 - 89.92: 20 Dihedral angle restraints: 10403 sinusoidal: 3920 harmonic: 6483 Sorted by residual: dihedral pdb=" CA PRO B 95 " pdb=" C PRO B 95 " pdb=" N ARG B 96 " pdb=" CA ARG B 96 " ideal model delta harmonic sigma weight residual 0.00 -38.65 38.65 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA PRO C 95 " pdb=" C PRO C 95 " pdb=" N ARG C 96 " pdb=" CA ARG C 96 " ideal model delta harmonic sigma weight residual 0.00 -36.09 36.09 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" CA PRO A 95 " pdb=" C PRO A 95 " pdb=" N ARG A 96 " pdb=" CA ARG A 96 " ideal model delta harmonic sigma weight residual 0.00 -35.56 35.56 0 5.00e+00 4.00e-02 5.06e+01 ... (remaining 10400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1762 0.036 - 0.072: 567 0.072 - 0.108: 268 0.108 - 0.144: 79 0.144 - 0.179: 12 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA LYS C 295 " pdb=" N LYS C 295 " pdb=" C LYS C 295 " pdb=" CB LYS C 295 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CB TPO U 360 " pdb=" CA TPO U 360 " pdb=" OG1 TPO U 360 " pdb=" CG2 TPO U 360 " both_signs ideal model delta sigma weight residual False 2.48 2.31 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB TPO V 360 " pdb=" CA TPO V 360 " pdb=" OG1 TPO V 360 " pdb=" CG2 TPO V 360 " both_signs ideal model delta sigma weight residual False 2.48 2.31 0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 2685 not shown) Planarity restraints: 3026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 39 " -0.021 2.00e-02 2.50e+03 1.99e-02 9.94e+00 pdb=" CG TRP H 39 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP H 39 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 39 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 39 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 39 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 39 " -0.012 2.00e-02 2.50e+03 1.41e-02 5.00e+00 pdb=" CG TRP M 39 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP M 39 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP M 39 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP M 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP M 39 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP M 39 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 39 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 39 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP M 39 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 143 " 0.148 9.50e-02 1.11e+02 6.74e-02 4.46e+00 pdb=" NE ARG E 143 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG E 143 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG E 143 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG E 143 " -0.002 2.00e-02 2.50e+03 ... (remaining 3023 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3278 2.78 - 3.31: 16047 3.31 - 3.84: 27014 3.84 - 4.37: 29513 4.37 - 4.90: 52345 Nonbonded interactions: 128197 Sorted by model distance: nonbonded pdb=" O ASN M 31 " pdb=" OG SER M 35 " model vdw 2.249 3.040 nonbonded pdb=" O TYR L 50 " pdb=" OG SER L 54 " model vdw 2.249 3.040 nonbonded pdb=" NZ LYS B 12 " pdb=" O3P TPO U 360 " model vdw 2.253 3.120 nonbonded pdb=" N CYS H 206 " pdb=" O LYS H 219 " model vdw 2.253 3.120 nonbonded pdb=" N CYS M 206 " pdb=" O LYS M 219 " model vdw 2.253 3.120 ... (remaining 128192 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 350)) selection = (chain 'B' and (resid 7 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 350)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 15.340 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 44.850 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.004 0.109 17347 Z= 0.221 Angle : 0.746 12.961 23652 Z= 0.367 Chirality : 0.046 0.179 2688 Planarity : 0.004 0.067 3026 Dihedral : 13.289 89.922 6194 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.76 % Favored : 95.05 % Rotamer: Outliers : 0.05 % Allowed : 0.49 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.10 (0.19), residues: 2163 helix: 1.74 (0.62), residues: 75 sheet: 0.67 (0.17), residues: 945 loop : -0.84 (0.20), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 39 HIS 0.004 0.001 HIS B 211 PHE 0.016 0.001 PHE E 140 TYR 0.019 0.001 TYR E 174 ARG 0.023 0.001 ARG E 143 Details of bonding type rmsd hydrogen bonds : bond 0.27246 ( 573) hydrogen bonds : angle 9.92617 ( 1566) SS BOND : bond 0.00327 ( 9) SS BOND : angle 0.74940 ( 18) covalent geometry : bond 0.00440 (17338) covalent geometry : angle 0.74596 (23634) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8623 (mm) cc_final: 0.8394 (mt) REVERT: E 74 LEU cc_start: 0.8662 (tp) cc_final: 0.8452 (tp) REVERT: E 174 TYR cc_start: 0.8188 (m-80) cc_final: 0.7653 (m-10) REVERT: E 180 LEU cc_start: 0.8428 (tp) cc_final: 0.8177 (tp) REVERT: E 182 LEU cc_start: 0.7721 (mm) cc_final: 0.7501 (mm) REVERT: L 180 LEU cc_start: 0.8348 (tp) cc_final: 0.8021 (tp) REVERT: L 182 LEU cc_start: 0.7942 (mm) cc_final: 0.7736 (mm) REVERT: N 92 TYR cc_start: 0.8813 (p90) cc_final: 0.8548 (p90) REVERT: N 137 LEU cc_start: 0.9105 (mm) cc_final: 0.8780 (mp) REVERT: N 180 LEU cc_start: 0.8535 (tp) cc_final: 0.8318 (tp) REVERT: N 182 LEU cc_start: 0.7938 (mm) cc_final: 0.7723 (mm) outliers start: 1 outliers final: 1 residues processed: 192 average time/residue: 0.2796 time to fit residues: 85.6939 Evaluate side-chains 122 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 198 optimal weight: 30.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 199 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN M 181 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 167 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.101565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.074940 restraints weight = 64238.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074490 restraints weight = 46996.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075592 restraints weight = 39489.684| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17347 Z= 0.178 Angle : 0.652 10.181 23652 Z= 0.329 Chirality : 0.045 0.152 2688 Planarity : 0.004 0.054 3026 Dihedral : 6.151 77.888 2430 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.59 % Favored : 94.27 % Rotamer: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.26 (0.19), residues: 2163 helix: 1.24 (0.60), residues: 75 sheet: 0.56 (0.17), residues: 963 loop : -0.93 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 39 HIS 0.006 0.001 HIS A 112 PHE 0.014 0.001 PHE E 72 TYR 0.014 0.002 TYR A 22 ARG 0.004 0.001 ARG D 101 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 573) hydrogen bonds : angle 6.95793 ( 1566) SS BOND : bond 0.00542 ( 9) SS BOND : angle 0.92426 ( 18) covalent geometry : bond 0.00402 (17338) covalent geometry : angle 0.65169 (23634) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8589 (tt) cc_final: 0.8388 (tt) REVERT: A 345 MET cc_start: 0.8309 (ppp) cc_final: 0.7916 (ppp) REVERT: B 120 ILE cc_start: 0.8541 (mm) cc_final: 0.8248 (mt) REVERT: B 345 MET cc_start: 0.8296 (ppp) cc_final: 0.7871 (ppp) REVERT: C 273 TYR cc_start: 0.8609 (m-80) cc_final: 0.8235 (m-10) REVERT: D 86 MET cc_start: 0.7887 (mmp) cc_final: 0.7598 (mmp) REVERT: E 143 ARG cc_start: 0.7776 (mmt-90) cc_final: 0.7439 (mmt180) REVERT: L 162 GLU cc_start: 0.9312 (pm20) cc_final: 0.9108 (pm20) REVERT: L 180 LEU cc_start: 0.8139 (tp) cc_final: 0.7731 (tp) REVERT: M 49 GLU cc_start: 0.8617 (tp30) cc_final: 0.8393 (tp30) REVERT: N 162 GLU cc_start: 0.8826 (pp20) cc_final: 0.8469 (tm-30) REVERT: N 182 LEU cc_start: 0.7839 (mm) cc_final: 0.7616 (mm) outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.2534 time to fit residues: 72.9154 Evaluate side-chains 124 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 149 optimal weight: 2.9990 chunk 211 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 193 optimal weight: 0.3980 chunk 216 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN M 181 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.100752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.073685 restraints weight = 63293.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073174 restraints weight = 46828.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074350 restraints weight = 38771.744| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17347 Z= 0.192 Angle : 0.643 9.048 23652 Z= 0.324 Chirality : 0.045 0.179 2688 Planarity : 0.004 0.049 3026 Dihedral : 6.207 79.191 2430 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.61 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 2163 helix: 1.16 (0.61), residues: 78 sheet: 0.48 (0.17), residues: 981 loop : -1.02 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 39 HIS 0.005 0.001 HIS B 211 PHE 0.021 0.002 PHE L 72 TYR 0.025 0.002 TYR L 56 ARG 0.003 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 573) hydrogen bonds : angle 6.31369 ( 1566) SS BOND : bond 0.00634 ( 9) SS BOND : angle 0.82053 ( 18) covalent geometry : bond 0.00440 (17338) covalent geometry : angle 0.64313 (23634) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.8444 (ppp) cc_final: 0.7841 (ppp) REVERT: B 120 ILE cc_start: 0.8564 (mm) cc_final: 0.8252 (mt) REVERT: B 345 MET cc_start: 0.8368 (ppp) cc_final: 0.7445 (ppp) REVERT: C 273 TYR cc_start: 0.8593 (m-80) cc_final: 0.8167 (m-10) REVERT: E 47 LEU cc_start: 0.7961 (pt) cc_final: 0.7723 (pp) REVERT: E 174 TYR cc_start: 0.8438 (m-80) cc_final: 0.7846 (m-10) REVERT: E 180 LEU cc_start: 0.8097 (tp) cc_final: 0.7718 (tp) REVERT: E 182 LEU cc_start: 0.7713 (mm) cc_final: 0.7471 (mm) REVERT: H 86 MET cc_start: 0.7771 (mmp) cc_final: 0.7534 (mmp) REVERT: L 162 GLU cc_start: 0.9348 (pm20) cc_final: 0.8886 (tm-30) REVERT: L 180 LEU cc_start: 0.8203 (tp) cc_final: 0.7759 (tp) REVERT: N 28 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7845 (tm-30) REVERT: N 92 TYR cc_start: 0.8913 (p90) cc_final: 0.8689 (p90) REVERT: N 162 GLU cc_start: 0.8820 (pp20) cc_final: 0.8451 (tm-30) REVERT: N 180 LEU cc_start: 0.8511 (pp) cc_final: 0.7695 (tp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2489 time to fit residues: 74.5095 Evaluate side-chains 127 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 135 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 128 optimal weight: 0.5980 chunk 197 optimal weight: 30.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.101930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.074414 restraints weight = 62905.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074652 restraints weight = 42655.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075517 restraints weight = 34576.204| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17347 Z= 0.139 Angle : 0.616 9.419 23652 Z= 0.307 Chirality : 0.045 0.180 2688 Planarity : 0.005 0.070 3026 Dihedral : 6.024 78.772 2430 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.59 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.32 (0.19), residues: 2163 helix: 1.30 (0.60), residues: 78 sheet: 0.46 (0.17), residues: 999 loop : -0.96 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 39 HIS 0.004 0.001 HIS B 211 PHE 0.018 0.001 PHE B 145 TYR 0.029 0.001 TYR L 56 ARG 0.004 0.000 ARG L 143 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 573) hydrogen bonds : angle 5.87345 ( 1566) SS BOND : bond 0.00451 ( 9) SS BOND : angle 0.64125 ( 18) covalent geometry : bond 0.00321 (17338) covalent geometry : angle 0.61631 (23634) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8550 (mm) cc_final: 0.8260 (mt) REVERT: B 146 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7236 (tm-30) REVERT: C 273 TYR cc_start: 0.8597 (m-80) cc_final: 0.8166 (m-10) REVERT: D 115 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7732 (tm-30) REVERT: E 162 GLU cc_start: 0.9228 (pm20) cc_final: 0.8773 (tm-30) REVERT: E 174 TYR cc_start: 0.8380 (m-80) cc_final: 0.7670 (m-10) REVERT: L 28 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7733 (tm-30) REVERT: L 137 LEU cc_start: 0.9401 (mp) cc_final: 0.9186 (mm) REVERT: L 162 GLU cc_start: 0.9278 (pm20) cc_final: 0.8833 (tm-30) REVERT: L 180 LEU cc_start: 0.8196 (tp) cc_final: 0.7708 (tp) REVERT: M 49 GLU cc_start: 0.8557 (tp30) cc_final: 0.8255 (tp30) REVERT: N 56 TYR cc_start: 0.8312 (t80) cc_final: 0.8101 (t80) REVERT: N 137 LEU cc_start: 0.9402 (mp) cc_final: 0.9195 (mm) REVERT: N 144 GLU cc_start: 0.9079 (pp20) cc_final: 0.8658 (tp30) REVERT: N 162 GLU cc_start: 0.8754 (pp20) cc_final: 0.8336 (tm-30) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2474 time to fit residues: 76.7972 Evaluate side-chains 135 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 31 ASN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.101313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074525 restraints weight = 65415.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073981 restraints weight = 47629.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.075183 restraints weight = 39222.609| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17347 Z= 0.153 Angle : 0.621 9.545 23652 Z= 0.308 Chirality : 0.045 0.162 2688 Planarity : 0.004 0.060 3026 Dihedral : 6.035 78.573 2430 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.56 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.32 (0.19), residues: 2163 helix: 1.55 (0.61), residues: 78 sheet: 0.46 (0.17), residues: 996 loop : -0.98 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 39 HIS 0.004 0.001 HIS B 211 PHE 0.016 0.001 PHE E 72 TYR 0.025 0.001 TYR L 56 ARG 0.002 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 573) hydrogen bonds : angle 5.66663 ( 1566) SS BOND : bond 0.00491 ( 9) SS BOND : angle 0.75571 ( 18) covalent geometry : bond 0.00353 (17338) covalent geometry : angle 0.62123 (23634) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8530 (tt) cc_final: 0.8325 (tt) REVERT: B 120 ILE cc_start: 0.8528 (mm) cc_final: 0.8220 (mt) REVERT: C 23 LEU cc_start: 0.8973 (tp) cc_final: 0.8503 (mp) REVERT: C 273 TYR cc_start: 0.8601 (m-80) cc_final: 0.8141 (m-10) REVERT: D 115 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7752 (tm-30) REVERT: E 162 GLU cc_start: 0.9294 (pm20) cc_final: 0.8856 (tm-30) REVERT: E 174 TYR cc_start: 0.8458 (m-80) cc_final: 0.7811 (m-80) REVERT: E 180 LEU cc_start: 0.8142 (tp) cc_final: 0.7791 (tp) REVERT: E 182 LEU cc_start: 0.7712 (mm) cc_final: 0.7474 (mm) REVERT: L 137 LEU cc_start: 0.9405 (mp) cc_final: 0.9180 (mm) REVERT: L 162 GLU cc_start: 0.9311 (pm20) cc_final: 0.8833 (tm-30) REVERT: L 180 LEU cc_start: 0.8251 (tp) cc_final: 0.7800 (tp) REVERT: M 49 GLU cc_start: 0.8547 (tp30) cc_final: 0.8179 (tp30) REVERT: N 56 TYR cc_start: 0.8333 (t80) cc_final: 0.8113 (t80) REVERT: N 137 LEU cc_start: 0.9422 (mp) cc_final: 0.9212 (mm) REVERT: N 162 GLU cc_start: 0.8789 (pp20) cc_final: 0.8366 (tm-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2450 time to fit residues: 73.0907 Evaluate side-chains 133 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 77 optimal weight: 0.0020 chunk 191 optimal weight: 3.9990 chunk 185 optimal weight: 0.5980 chunk 211 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 31 ASN ** N 7 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 = 0.3795 r_free = 0.3795 target = 0.102970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075289 restraints weight = 63300.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.076037 restraints weight = 42210.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076928 restraints weight = 33125.316| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17347 Z= 0.118 Angle : 0.610 9.578 23652 Z= 0.301 Chirality : 0.045 0.168 2688 Planarity : 0.004 0.049 3026 Dihedral : 5.913 78.140 2430 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.26 (0.19), residues: 2163 helix: 1.70 (0.62), residues: 78 sheet: 0.51 (0.17), residues: 996 loop : -0.96 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 39 HIS 0.003 0.001 HIS B 211 PHE 0.015 0.001 PHE C 28 TYR 0.025 0.001 TYR L 56 ARG 0.001 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.02984 ( 573) hydrogen bonds : angle 5.49550 ( 1566) SS BOND : bond 0.00457 ( 9) SS BOND : angle 0.66883 ( 18) covalent geometry : bond 0.00275 (17338) covalent geometry : angle 0.61029 (23634) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 TYR cc_start: 0.8643 (m-10) cc_final: 0.8421 (m-10) REVERT: A 275 ILE cc_start: 0.8465 (tt) cc_final: 0.8242 (tt) REVERT: B 120 ILE cc_start: 0.8537 (mm) cc_final: 0.8242 (mt) REVERT: C 23 LEU cc_start: 0.8891 (tp) cc_final: 0.8464 (mp) REVERT: C 273 TYR cc_start: 0.8543 (m-80) cc_final: 0.8095 (m-10) REVERT: D 115 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7733 (tm-30) REVERT: E 56 TYR cc_start: 0.8527 (t80) cc_final: 0.8312 (t80) REVERT: E 162 GLU cc_start: 0.9294 (pm20) cc_final: 0.8841 (tm-30) REVERT: E 174 TYR cc_start: 0.8437 (m-80) cc_final: 0.7719 (m-10) REVERT: E 180 LEU cc_start: 0.8176 (tp) cc_final: 0.7823 (tp) REVERT: E 182 LEU cc_start: 0.7632 (mm) cc_final: 0.7418 (mm) REVERT: L 137 LEU cc_start: 0.9412 (mp) cc_final: 0.9186 (mm) REVERT: L 162 GLU cc_start: 0.9302 (pm20) cc_final: 0.9020 (pm20) REVERT: L 180 LEU cc_start: 0.8336 (tp) cc_final: 0.7787 (tp) REVERT: M 49 GLU cc_start: 0.8541 (tp30) cc_final: 0.8205 (tp30) REVERT: N 137 LEU cc_start: 0.9428 (mp) cc_final: 0.9201 (mm) REVERT: N 144 GLU cc_start: 0.9086 (pp20) cc_final: 0.8684 (tp30) REVERT: N 162 GLU cc_start: 0.8804 (pp20) cc_final: 0.8336 (tm-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2452 time to fit residues: 76.4428 Evaluate side-chains 138 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 211 optimal weight: 0.4980 chunk 76 optimal weight: 0.9980 chunk 167 optimal weight: 0.0770 chunk 92 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 31 ASN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.102014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.074412 restraints weight = 62947.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074695 restraints weight = 44713.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.075501 restraints weight = 37156.651| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17347 Z= 0.146 Angle : 0.622 8.593 23652 Z= 0.307 Chirality : 0.045 0.161 2688 Planarity : 0.004 0.050 3026 Dihedral : 5.961 78.131 2430 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.26 (0.19), residues: 2163 helix: 1.70 (0.62), residues: 78 sheet: 0.49 (0.17), residues: 996 loop : -0.94 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 39 HIS 0.004 0.001 HIS B 211 PHE 0.018 0.001 PHE C 28 TYR 0.032 0.001 TYR N 56 ARG 0.007 0.000 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 573) hydrogen bonds : angle 5.44876 ( 1566) SS BOND : bond 0.00445 ( 9) SS BOND : angle 0.74926 ( 18) covalent geometry : bond 0.00340 (17338) covalent geometry : angle 0.62165 (23634) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 TYR cc_start: 0.8667 (m-10) cc_final: 0.8437 (m-10) REVERT: B 120 ILE cc_start: 0.8509 (mm) cc_final: 0.8224 (mt) REVERT: C 23 LEU cc_start: 0.8934 (tp) cc_final: 0.8471 (mp) REVERT: C 273 TYR cc_start: 0.8589 (m-80) cc_final: 0.8114 (m-10) REVERT: D 115 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7812 (tm-30) REVERT: E 56 TYR cc_start: 0.8585 (t80) cc_final: 0.8348 (t80) REVERT: E 162 GLU cc_start: 0.9343 (pm20) cc_final: 0.9085 (pm20) REVERT: E 174 TYR cc_start: 0.8446 (m-80) cc_final: 0.7659 (m-10) REVERT: E 180 LEU cc_start: 0.8111 (tp) cc_final: 0.7763 (tp) REVERT: E 182 LEU cc_start: 0.7609 (mm) cc_final: 0.7399 (mm) REVERT: L 137 LEU cc_start: 0.9404 (mp) cc_final: 0.9154 (mm) REVERT: L 162 GLU cc_start: 0.9370 (pm20) cc_final: 0.9080 (pm20) REVERT: L 180 LEU cc_start: 0.8369 (tp) cc_final: 0.7949 (tp) REVERT: M 49 GLU cc_start: 0.8518 (tp30) cc_final: 0.8137 (tp30) REVERT: N 144 GLU cc_start: 0.9088 (pp20) cc_final: 0.8639 (tp30) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2650 time to fit residues: 78.8954 Evaluate side-chains 130 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 218 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 31 ASN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.100728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072561 restraints weight = 62446.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072977 restraints weight = 44259.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073714 restraints weight = 35569.501| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17347 Z= 0.176 Angle : 0.637 9.400 23652 Z= 0.316 Chirality : 0.045 0.162 2688 Planarity : 0.004 0.049 3026 Dihedral : 6.059 78.389 2430 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.29 (0.19), residues: 2163 helix: 1.76 (0.63), residues: 78 sheet: 0.43 (0.17), residues: 996 loop : -0.92 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 39 HIS 0.004 0.001 HIS A 199 PHE 0.021 0.001 PHE C 28 TYR 0.026 0.001 TYR L 56 ARG 0.007 0.000 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 573) hydrogen bonds : angle 5.45767 ( 1566) SS BOND : bond 0.00499 ( 9) SS BOND : angle 0.72391 ( 18) covalent geometry : bond 0.00405 (17338) covalent geometry : angle 0.63669 (23634) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8504 (mm) cc_final: 0.8258 (mt) REVERT: C 23 LEU cc_start: 0.8920 (tp) cc_final: 0.8460 (mp) REVERT: C 273 TYR cc_start: 0.8633 (m-80) cc_final: 0.8127 (m-10) REVERT: D 115 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7877 (tm-30) REVERT: E 56 TYR cc_start: 0.8664 (t80) cc_final: 0.8452 (t80) REVERT: E 92 TYR cc_start: 0.8913 (p90) cc_final: 0.8655 (p90) REVERT: E 162 GLU cc_start: 0.9403 (pm20) cc_final: 0.9130 (pm20) REVERT: E 174 TYR cc_start: 0.8457 (m-80) cc_final: 0.7660 (m-10) REVERT: E 180 LEU cc_start: 0.8155 (tp) cc_final: 0.7802 (tp) REVERT: E 182 LEU cc_start: 0.7643 (mm) cc_final: 0.7436 (mm) REVERT: L 137 LEU cc_start: 0.9401 (mp) cc_final: 0.9152 (mm) REVERT: L 162 GLU cc_start: 0.9373 (pm20) cc_final: 0.9061 (pm20) REVERT: L 180 LEU cc_start: 0.8326 (tp) cc_final: 0.7916 (tp) REVERT: M 49 GLU cc_start: 0.8548 (tp30) cc_final: 0.8147 (tp30) REVERT: N 137 LEU cc_start: 0.9404 (mp) cc_final: 0.9148 (mm) REVERT: N 144 GLU cc_start: 0.9113 (pp20) cc_final: 0.8660 (tp30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2445 time to fit residues: 73.3713 Evaluate side-chains 125 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 106 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 31 ASN N 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.099323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071512 restraints weight = 63165.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071225 restraints weight = 46048.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071814 restraints weight = 38114.201| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17347 Z= 0.238 Angle : 0.696 9.521 23652 Z= 0.347 Chirality : 0.047 0.187 2688 Planarity : 0.005 0.049 3026 Dihedral : 6.363 81.215 2430 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.54 (0.19), residues: 2163 helix: 1.97 (0.64), residues: 75 sheet: 0.20 (0.17), residues: 1002 loop : -1.04 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 39 HIS 0.005 0.001 HIS A 199 PHE 0.021 0.002 PHE A 28 TYR 0.029 0.002 TYR L 56 ARG 0.006 0.000 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 573) hydrogen bonds : angle 5.73083 ( 1566) SS BOND : bond 0.00589 ( 9) SS BOND : angle 0.84561 ( 18) covalent geometry : bond 0.00545 (17338) covalent geometry : angle 0.69580 (23634) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 MET cc_start: 0.8217 (ppp) cc_final: 0.7702 (ppp) REVERT: C 273 TYR cc_start: 0.8641 (m-80) cc_final: 0.8115 (m-10) REVERT: D 39 TRP cc_start: 0.8083 (m100) cc_final: 0.7791 (m100) REVERT: D 115 GLN cc_start: 0.8561 (tm-30) cc_final: 0.7961 (tm-30) REVERT: E 56 TYR cc_start: 0.8678 (t80) cc_final: 0.8438 (t80) REVERT: E 162 GLU cc_start: 0.9359 (pm20) cc_final: 0.9102 (pm20) REVERT: E 174 TYR cc_start: 0.8430 (m-80) cc_final: 0.7507 (m-10) REVERT: E 180 LEU cc_start: 0.8130 (tp) cc_final: 0.7761 (tp) REVERT: L 162 GLU cc_start: 0.9318 (pm20) cc_final: 0.9025 (pm20) REVERT: M 49 GLU cc_start: 0.8486 (tp30) cc_final: 0.8042 (tp30) REVERT: N 144 GLU cc_start: 0.9109 (pp20) cc_final: 0.8613 (tp30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2412 time to fit residues: 66.8903 Evaluate side-chains 115 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 161 optimal weight: 5.9990 chunk 197 optimal weight: 0.0670 chunk 215 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 164 optimal weight: 0.8980 chunk 210 optimal weight: 8.9990 chunk 211 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 31 ASN N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.101113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073557 restraints weight = 63076.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073260 restraints weight = 44373.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.074228 restraints weight = 36385.087| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17347 Z= 0.145 Angle : 0.656 10.485 23652 Z= 0.320 Chirality : 0.047 0.177 2688 Planarity : 0.004 0.052 3026 Dihedral : 6.105 77.420 2430 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.45 (0.19), residues: 2163 helix: 1.97 (0.65), residues: 75 sheet: 0.26 (0.17), residues: 1002 loop : -0.98 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 39 HIS 0.004 0.001 HIS C 211 PHE 0.015 0.001 PHE N 99 TYR 0.027 0.001 TYR L 56 ARG 0.006 0.000 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 573) hydrogen bonds : angle 5.49967 ( 1566) SS BOND : bond 0.00506 ( 9) SS BOND : angle 0.79765 ( 18) covalent geometry : bond 0.00337 (17338) covalent geometry : angle 0.65571 (23634) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8520 (tt) cc_final: 0.8307 (tt) REVERT: B 28 PHE cc_start: 0.8547 (m-80) cc_final: 0.8332 (m-80) REVERT: B 120 ILE cc_start: 0.8567 (mm) cc_final: 0.8329 (mt) REVERT: B 345 MET cc_start: 0.8097 (ppp) cc_final: 0.7505 (ppp) REVERT: C 273 TYR cc_start: 0.8607 (m-80) cc_final: 0.8082 (m-10) REVERT: D 39 TRP cc_start: 0.7907 (m100) cc_final: 0.7487 (m100) REVERT: D 115 GLN cc_start: 0.8507 (tm-30) cc_final: 0.7911 (tm-30) REVERT: E 56 TYR cc_start: 0.8639 (t80) cc_final: 0.8431 (t80) REVERT: E 162 GLU cc_start: 0.9390 (pm20) cc_final: 0.9108 (pm20) REVERT: E 174 TYR cc_start: 0.8387 (m-80) cc_final: 0.7481 (m-10) REVERT: E 180 LEU cc_start: 0.8237 (tp) cc_final: 0.7863 (tp) REVERT: L 137 LEU cc_start: 0.9411 (mp) cc_final: 0.9159 (mm) REVERT: L 162 GLU cc_start: 0.9370 (pm20) cc_final: 0.9054 (pm20) REVERT: L 182 LEU cc_start: 0.7687 (mm) cc_final: 0.7480 (mm) REVERT: M 49 GLU cc_start: 0.8457 (tp30) cc_final: 0.8043 (tp30) REVERT: N 91 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8627 (tm-30) REVERT: N 144 GLU cc_start: 0.9125 (pp20) cc_final: 0.8707 (tp30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2383 time to fit residues: 68.6460 Evaluate side-chains 126 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 68 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 31 ASN N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.099099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071732 restraints weight = 63290.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.071112 restraints weight = 46819.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071806 restraints weight = 40444.050| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17347 Z= 0.259 Angle : 0.729 10.096 23652 Z= 0.363 Chirality : 0.048 0.262 2688 Planarity : 0.005 0.052 3026 Dihedral : 6.488 82.508 2430 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.67 (0.19), residues: 2163 helix: 1.91 (0.64), residues: 75 sheet: 0.10 (0.17), residues: 1002 loop : -1.13 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP H 39 HIS 0.005 0.001 HIS B 211 PHE 0.029 0.002 PHE C 28 TYR 0.031 0.002 TYR L 56 ARG 0.005 0.001 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 573) hydrogen bonds : angle 5.80252 ( 1566) SS BOND : bond 0.00660 ( 9) SS BOND : angle 1.20172 ( 18) covalent geometry : bond 0.00593 (17338) covalent geometry : angle 0.72872 (23634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7096.27 seconds wall clock time: 127 minutes 2.92 seconds (7622.92 seconds total)