Starting phenix.real_space_refine on Wed Mar 4 22:55:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8goc_34175/03_2026/8goc_34175.cif Found real_map, /net/cci-nas-00/data/ceres_data/8goc_34175/03_2026/8goc_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 { model { file = "/net/cci-nas-00/data/ceres_data/8goc_34175/03_2026/8goc_34175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8goc_34175/03_2026/8goc_34175.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8goc_34175/03_2026/8goc_34175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8goc_34175/03_2026/8goc_34175.map" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLU: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: {'ASN:plan1': 1, 'GLU:plan': 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, 'ASP:plan': 3, 'HIS:plan': 1} 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: {'ASN:plan1': 1, 'GLU:plan': 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, 'ASP:plan': 3, 'HIS:plan': 1} 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: {'ASN:plan1': 1, 'GLU:plan': 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, 'ASP:plan': 3, 'HIS:plan': 1} 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: 3.36, per 1000 atoms: 0.20 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: 1.18 Conformation dependent library (CDL) restraints added in 731.5 milliseconds 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: 0.69 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: 2.89 Time building geometry restraints manager: 1.63 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: 9.630 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: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.120 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.140 ------------------------------------------------------------------------------- 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 : 13.07 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.023 0.001 ARG E 143 TYR 0.019 0.001 TYR E 174 PHE 0.016 0.001 PHE E 140 TRP 0.050 0.002 TRP H 39 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00440 (17338) covalent geometry : angle 0.74596 (23634) SS BOND : bond 0.00327 ( 9) SS BOND : angle 0.74940 ( 18) hydrogen bonds : bond 0.27246 ( 573) hydrogen bonds : angle 9.92617 ( 1566) *********************** 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 : 0.721 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: 0.1140 time to fit residues: 35.0244 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 : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.0040 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.0040 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 overall best weight: 2.1808 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** N 167 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.100057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072281 restraints weight = 63128.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072411 restraints weight = 45541.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073205 restraints weight = 38348.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073188 restraints weight = 34352.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.073491 restraints weight = 33040.673| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17347 Z= 0.241 Angle : 0.686 9.799 23652 Z= 0.349 Chirality : 0.046 0.158 2688 Planarity : 0.005 0.055 3026 Dihedral : 6.325 79.278 2430 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.03 % Favored : 92.83 % Rotamer: Outliers : 0.22 % Allowed : 6.05 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.19), residues: 2163 helix: 1.26 (0.61), residues: 75 sheet: 0.49 (0.17), residues: 963 loop : -1.02 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 8 TYR 0.014 0.002 TYR L 92 PHE 0.019 0.002 PHE A 28 TRP 0.042 0.002 TRP H 39 HIS 0.007 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00544 (17338) covalent geometry : angle 0.68548 (23634) SS BOND : bond 0.00585 ( 9) SS BOND : angle 1.07603 ( 18) hydrogen bonds : bond 0.05001 ( 573) hydrogen bonds : angle 7.17044 ( 1566) *********************** 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 177 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 0.634 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: 0.8595 (tt) cc_final: 0.8392 (tt) REVERT: A 345 MET cc_start: 0.8302 (ppp) cc_final: 0.7893 (ppp) REVERT: B 120 ILE cc_start: 0.8587 (mm) cc_final: 0.8289 (mt) REVERT: B 275 ILE cc_start: 0.8680 (tt) cc_final: 0.8479 (tt) REVERT: B 345 MET cc_start: 0.8327 (ppp) cc_final: 0.7603 (ppp) REVERT: D 86 MET cc_start: 0.7810 (mmp) cc_final: 0.7604 (mmp) REVERT: E 143 ARG cc_start: 0.7797 (mmt-90) cc_final: 0.7471 (mmt180) REVERT: L 137 LEU cc_start: 0.9292 (mm) cc_final: 0.9086 (mp) REVERT: L 162 GLU cc_start: 0.9287 (pm20) cc_final: 0.9083 (pm20) REVERT: L 180 LEU cc_start: 0.8129 (tp) cc_final: 0.7719 (tp) REVERT: N 137 LEU cc_start: 0.9247 (mm) cc_final: 0.9030 (mp) REVERT: N 162 GLU cc_start: 0.8802 (pp20) cc_final: 0.8469 (tm-30) REVERT: N 182 LEU cc_start: 0.7766 (mm) cc_final: 0.7552 (mm) outliers start: 4 outliers final: 1 residues processed: 177 average time/residue: 0.1147 time to fit residues: 32.6273 Evaluate side-chains 120 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 53 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** 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 ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN C 199 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.098744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070847 restraints weight = 64113.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071026 restraints weight = 46427.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.071814 restraints weight = 39424.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071775 restraints weight = 35290.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071934 restraints weight = 33301.920| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17347 Z= 0.277 Angle : 0.702 9.745 23652 Z= 0.359 Chirality : 0.047 0.192 2688 Planarity : 0.005 0.048 3026 Dihedral : 6.566 81.791 2430 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.00 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 2163 helix: 1.02 (0.60), residues: 78 sheet: 0.14 (0.17), residues: 969 loop : -1.06 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 8 TYR 0.026 0.002 TYR E 56 PHE 0.022 0.002 PHE B 28 TRP 0.030 0.002 TRP H 39 HIS 0.006 0.002 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00629 (17338) covalent geometry : angle 0.70157 (23634) SS BOND : bond 0.00545 ( 9) SS BOND : angle 0.96036 ( 18) hydrogen bonds : bond 0.04265 ( 573) hydrogen bonds : angle 6.58594 ( 1566) *********************** 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 170 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.8421 (ppp) cc_final: 0.7751 (ppp) REVERT: B 120 ILE cc_start: 0.8605 (mm) cc_final: 0.8293 (mt) REVERT: B 345 MET cc_start: 0.8441 (ppp) cc_final: 0.8222 (ppp) REVERT: C 273 TYR cc_start: 0.8759 (m-80) cc_final: 0.8347 (m-10) REVERT: E 92 TYR cc_start: 0.9103 (p90) cc_final: 0.8850 (p90) REVERT: E 174 TYR cc_start: 0.8399 (m-80) cc_final: 0.7770 (m-10) REVERT: L 137 LEU cc_start: 0.9244 (mm) cc_final: 0.9043 (mp) REVERT: L 162 GLU cc_start: 0.9332 (pm20) cc_final: 0.8887 (tm-30) REVERT: L 180 LEU cc_start: 0.8203 (tp) cc_final: 0.7806 (tp) REVERT: M 39 TRP cc_start: 0.8170 (m100) cc_final: 0.7485 (m100) REVERT: M 49 GLU cc_start: 0.8655 (tp30) cc_final: 0.8303 (tp30) REVERT: N 144 GLU cc_start: 0.9065 (pp20) cc_final: 0.8597 (tp30) REVERT: N 162 GLU cc_start: 0.8829 (pp20) cc_final: 0.8486 (tm-30) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1108 time to fit residues: 30.4858 Evaluate side-chains 116 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 132 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 172 optimal weight: 20.0000 chunk 211 optimal weight: 20.0000 chunk 153 optimal weight: 30.0000 chunk 198 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN B 31 HIS B 163 ASN B 262 GLN B 282 ASN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.095739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068339 restraints weight = 64154.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.067361 restraints weight = 48980.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068049 restraints weight = 41906.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068277 restraints weight = 39120.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.068238 restraints weight = 36910.350| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.097 17347 Z= 0.427 Angle : 0.828 10.295 23652 Z= 0.427 Chirality : 0.050 0.272 2688 Planarity : 0.006 0.049 3026 Dihedral : 7.113 82.714 2430 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.85 % Favored : 90.01 % Rotamer: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2163 helix: 0.95 (0.59), residues: 75 sheet: -0.16 (0.17), residues: 942 loop : -1.47 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 62 TYR 0.032 0.003 TYR N 92 PHE 0.030 0.003 PHE B 28 TRP 0.031 0.003 TRP H 39 HIS 0.008 0.002 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00967 (17338) covalent geometry : angle 0.82805 (23634) SS BOND : bond 0.00760 ( 9) SS BOND : angle 1.13715 ( 18) hydrogen bonds : bond 0.04759 ( 573) hydrogen bonds : angle 6.80264 ( 1566) *********************** 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 142 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.8516 (ppp) cc_final: 0.7212 (ppp) REVERT: B 345 MET cc_start: 0.8392 (ppp) cc_final: 0.7992 (ppp) REVERT: E 174 TYR cc_start: 0.8417 (m-80) cc_final: 0.7657 (m-80) REVERT: L 28 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7882 (tm-30) REVERT: L 137 LEU cc_start: 0.9182 (mm) cc_final: 0.8945 (mp) REVERT: L 162 GLU cc_start: 0.9289 (pm20) cc_final: 0.9042 (pm20) REVERT: L 180 LEU cc_start: 0.8132 (tp) cc_final: 0.7726 (tp) REVERT: M 39 TRP cc_start: 0.8256 (m100) cc_final: 0.7617 (m100) REVERT: M 49 GLU cc_start: 0.8670 (tp30) cc_final: 0.8307 (tp30) REVERT: N 162 GLU cc_start: 0.8807 (pp20) cc_final: 0.8493 (tm-30) outliers start: 2 outliers final: 1 residues processed: 142 average time/residue: 0.1190 time to fit residues: 27.0079 Evaluate side-chains 105 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 2 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 262 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS B 262 GLN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN H 31 ASN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 31 ASN ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.101058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074414 restraints weight = 64836.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073818 restraints weight = 47457.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.075025 restraints weight = 39861.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074827 restraints weight = 34446.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075236 restraints weight = 33351.498| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17347 Z= 0.138 Angle : 0.660 10.610 23652 Z= 0.327 Chirality : 0.047 0.194 2688 Planarity : 0.004 0.046 3026 Dihedral : 6.344 78.300 2430 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.92 % Favored : 93.99 % Rotamer: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 2163 helix: 1.36 (0.59), residues: 75 sheet: 0.18 (0.17), residues: 948 loop : -1.28 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 143 TYR 0.023 0.001 TYR E 88 PHE 0.016 0.002 PHE L 72 TRP 0.033 0.002 TRP H 39 HIS 0.006 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00317 (17338) covalent geometry : angle 0.66056 (23634) SS BOND : bond 0.00547 ( 9) SS BOND : angle 0.57095 ( 18) hydrogen bonds : bond 0.03297 ( 573) hydrogen bonds : angle 6.08170 ( 1566) *********************** 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 174 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.699 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: 0.8560 (tt) cc_final: 0.8324 (tt) REVERT: B 120 ILE cc_start: 0.8570 (mm) cc_final: 0.8325 (mt) REVERT: B 345 MET cc_start: 0.8281 (ppp) cc_final: 0.7556 (ppp) REVERT: C 273 TYR cc_start: 0.8771 (m-80) cc_final: 0.8317 (m-10) REVERT: E 92 TYR cc_start: 0.8933 (p90) cc_final: 0.8685 (p90) REVERT: E 174 TYR cc_start: 0.8429 (m-80) cc_final: 0.7656 (m-80) REVERT: L 56 TYR cc_start: 0.8599 (t80) cc_final: 0.8325 (t80) REVERT: L 92 TYR cc_start: 0.9017 (p90) cc_final: 0.8743 (p90) REVERT: L 137 LEU cc_start: 0.9202 (mm) cc_final: 0.8993 (mp) REVERT: L 162 GLU cc_start: 0.9349 (pm20) cc_final: 0.9076 (pm20) REVERT: L 180 LEU cc_start: 0.8315 (tp) cc_final: 0.7846 (tp) REVERT: M 39 TRP cc_start: 0.8010 (m100) cc_final: 0.7158 (m100) REVERT: M 49 GLU cc_start: 0.8569 (tp30) cc_final: 0.8241 (tp30) REVERT: N 162 GLU cc_start: 0.8842 (pp20) cc_final: 0.8470 (tm-30) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1152 time to fit residues: 32.1168 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 : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 2.9990 chunk 75 optimal weight: 0.0020 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- 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** D 31 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3745 r_free = 0.3745 target = 0.100409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073460 restraints weight = 64668.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.073004 restraints weight = 46042.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.073939 restraints weight = 38900.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.074158 restraints weight = 33552.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074363 restraints weight = 31505.612| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2494 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= 0.168 Angle : 0.641 9.415 23652 Z= 0.320 Chirality : 0.046 0.164 2688 Planarity : 0.004 0.049 3026 Dihedral : 6.291 79.338 2430 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.44 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 2163 helix: 1.65 (0.61), residues: 75 sheet: 0.07 (0.17), residues: 972 loop : -1.16 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.024 0.002 TYR E 88 PHE 0.026 0.002 PHE A 28 TRP 0.052 0.002 TRP H 39 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00389 (17338) covalent geometry : angle 0.64044 (23634) SS BOND : bond 0.00528 ( 9) SS BOND : angle 0.90368 ( 18) hydrogen bonds : bond 0.03287 ( 573) hydrogen bonds : angle 5.88406 ( 1566) *********************** 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 169 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.651 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: 0.8643 (tt) cc_final: 0.8427 (tt) REVERT: A 345 MET cc_start: 0.8206 (ppp) cc_final: 0.7950 (ppp) REVERT: B 120 ILE cc_start: 0.8601 (mm) cc_final: 0.8339 (mt) REVERT: C 273 TYR cc_start: 0.8772 (m-80) cc_final: 0.8288 (m-10) REVERT: E 56 TYR cc_start: 0.8541 (t80) cc_final: 0.8316 (t80) REVERT: E 92 TYR cc_start: 0.8902 (p90) cc_final: 0.8653 (p90) REVERT: E 174 TYR cc_start: 0.8401 (m-80) cc_final: 0.7555 (m-80) REVERT: E 180 LEU cc_start: 0.8159 (tp) cc_final: 0.7763 (tp) REVERT: L 162 GLU cc_start: 0.9326 (pm20) cc_final: 0.9065 (pm20) REVERT: L 180 LEU cc_start: 0.8276 (tp) cc_final: 0.7837 (tp) REVERT: M 39 TRP cc_start: 0.8029 (m100) cc_final: 0.7337 (m100) REVERT: M 49 GLU cc_start: 0.8538 (tp30) cc_final: 0.8170 (tp30) REVERT: N 137 LEU cc_start: 0.9404 (mp) cc_final: 0.9199 (mm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1210 time to fit residues: 32.4633 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 : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** D 31 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.101692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074525 restraints weight = 64520.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074541 restraints weight = 47269.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.075547 restraints weight = 39093.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.075459 restraints weight = 34053.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075636 restraints weight = 32914.692| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2579 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= 0.134 Angle : 0.635 8.795 23652 Z= 0.312 Chirality : 0.046 0.166 2688 Planarity : 0.004 0.047 3026 Dihedral : 6.107 77.174 2430 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 2163 helix: 1.72 (0.62), residues: 75 sheet: 0.15 (0.18), residues: 942 loop : -1.03 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 96 TYR 0.019 0.001 TYR E 88 PHE 0.017 0.001 PHE C 28 TRP 0.043 0.002 TRP H 39 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00311 (17338) covalent geometry : angle 0.63480 (23634) SS BOND : bond 0.00480 ( 9) SS BOND : angle 0.70635 ( 18) hydrogen bonds : bond 0.03073 ( 573) hydrogen bonds : angle 5.63574 ( 1566) *********************** 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 176 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.685 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 345 MET cc_start: 0.8263 (ppp) cc_final: 0.7991 (ppp) REVERT: B 120 ILE cc_start: 0.8595 (mm) cc_final: 0.8321 (mt) REVERT: B 345 MET cc_start: 0.8102 (ppp) cc_final: 0.7183 (ppp) REVERT: C 273 TYR cc_start: 0.8714 (m-80) cc_final: 0.8206 (m-10) REVERT: D 115 GLN cc_start: 0.8566 (tm-30) cc_final: 0.7903 (tm-30) REVERT: E 56 TYR cc_start: 0.8575 (t80) cc_final: 0.8365 (t80) REVERT: E 174 TYR cc_start: 0.8389 (m-80) cc_final: 0.7558 (m-10) REVERT: L 47 LEU cc_start: 0.8074 (pt) cc_final: 0.7804 (pt) REVERT: L 137 LEU cc_start: 0.9409 (mp) cc_final: 0.9177 (mm) REVERT: L 162 GLU cc_start: 0.9378 (pm20) cc_final: 0.9107 (pm20) REVERT: L 180 LEU cc_start: 0.8382 (tp) cc_final: 0.7968 (tp) REVERT: M 39 TRP cc_start: 0.7961 (m100) cc_final: 0.7015 (m100) REVERT: M 49 GLU cc_start: 0.8520 (tp30) cc_final: 0.8138 (tp30) REVERT: N 137 LEU cc_start: 0.9428 (mp) cc_final: 0.9210 (mm) REVERT: N 144 GLU cc_start: 0.9093 (pp20) cc_final: 0.8709 (tp30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1160 time to fit residues: 32.9415 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 : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 56 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 195 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 112 HIS D 31 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.099030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071514 restraints weight = 65092.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071411 restraints weight = 46761.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.071967 restraints weight = 39787.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.072087 restraints weight = 37694.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072139 restraints weight = 33902.061| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17347 Z= 0.245 Angle : 0.701 9.263 23652 Z= 0.351 Chirality : 0.048 0.240 2688 Planarity : 0.005 0.051 3026 Dihedral : 6.515 85.007 2430 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.19), residues: 2163 helix: 1.77 (0.62), residues: 75 sheet: 0.02 (0.17), residues: 975 loop : -1.14 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 96 TYR 0.017 0.002 TYR C 209 PHE 0.026 0.002 PHE B 28 TRP 0.037 0.002 TRP H 39 HIS 0.006 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00562 (17338) covalent geometry : angle 0.70088 (23634) SS BOND : bond 0.00573 ( 9) SS BOND : angle 0.91286 ( 18) hydrogen bonds : bond 0.03523 ( 573) hydrogen bonds : angle 5.88497 ( 1566) *********************** 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 156 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.8413 (ppp) cc_final: 0.8007 (ppp) REVERT: B 345 MET cc_start: 0.8353 (ppp) cc_final: 0.7731 (ppp) REVERT: C 273 TYR cc_start: 0.8759 (m-80) cc_final: 0.8220 (m-10) REVERT: D 39 TRP cc_start: 0.8042 (m100) cc_final: 0.7763 (m100) REVERT: E 174 TYR cc_start: 0.8367 (m-80) cc_final: 0.7474 (m-80) REVERT: L 137 LEU cc_start: 0.9424 (mp) cc_final: 0.9190 (mm) REVERT: L 162 GLU cc_start: 0.9348 (pm20) cc_final: 0.9071 (pm20) REVERT: L 180 LEU cc_start: 0.8301 (tp) cc_final: 0.7878 (tp) REVERT: M 39 TRP cc_start: 0.8088 (m100) cc_final: 0.7490 (m100) REVERT: M 49 GLU cc_start: 0.8533 (tp30) cc_final: 0.8121 (tp30) REVERT: N 143 ARG cc_start: 0.8403 (ttm110) cc_final: 0.8176 (ttm110) REVERT: N 144 GLU cc_start: 0.9104 (pp20) cc_final: 0.8672 (tp30) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1138 time to fit residues: 28.5827 Evaluate side-chains 109 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 117 optimal weight: 20.0000 chunk 43 optimal weight: 0.2980 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** D 31 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 31 ASN ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.101525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.074289 restraints weight = 64178.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.074378 restraints weight = 45707.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.075521 restraints weight = 38097.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.075303 restraints weight = 32494.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.075441 restraints weight = 31227.784| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17347 Z= 0.139 Angle : 0.660 10.901 23652 Z= 0.322 Chirality : 0.046 0.172 2688 Planarity : 0.004 0.051 3026 Dihedral : 6.197 81.048 2430 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 2163 helix: 2.16 (0.64), residues: 72 sheet: 0.09 (0.17), residues: 975 loop : -1.07 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 96 TYR 0.013 0.001 TYR N 37 PHE 0.017 0.001 PHE B 145 TRP 0.037 0.002 TRP H 39 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00325 (17338) covalent geometry : angle 0.65954 (23634) SS BOND : bond 0.00459 ( 9) SS BOND : angle 0.78728 ( 18) hydrogen bonds : bond 0.03016 ( 573) hydrogen bonds : angle 5.62270 ( 1566) *********************** 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 : 0.501 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: 0.8380 (ppp) cc_final: 0.8144 (ppp) REVERT: B 120 ILE cc_start: 0.8606 (mm) cc_final: 0.8326 (mt) REVERT: C 273 TYR cc_start: 0.8728 (m-80) cc_final: 0.8185 (m-10) REVERT: D 39 TRP cc_start: 0.7871 (m100) cc_final: 0.7514 (m100) REVERT: D 115 GLN cc_start: 0.8599 (tm-30) cc_final: 0.7935 (tm-30) REVERT: E 56 TYR cc_start: 0.8571 (t80) cc_final: 0.8351 (t80) REVERT: E 174 TYR cc_start: 0.8328 (m-80) cc_final: 0.7415 (m-10) REVERT: L 162 GLU cc_start: 0.9367 (pm20) cc_final: 0.9078 (pm20) REVERT: L 182 LEU cc_start: 0.7640 (mm) cc_final: 0.7438 (mm) REVERT: M 39 TRP cc_start: 0.7932 (m100) cc_final: 0.6960 (m100) REVERT: M 49 GLU cc_start: 0.8436 (tp30) cc_final: 0.8067 (tp30) REVERT: N 91 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8755 (tm-30) REVERT: N 144 GLU cc_start: 0.9093 (pp20) cc_final: 0.8660 (tp30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1096 time to fit residues: 29.5739 Evaluate side-chains 118 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 59 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 262 GLN ** 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 = 0.3732 r_free = 0.3732 target = 0.099632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071962 restraints weight = 64272.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072347 restraints weight = 46100.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073189 restraints weight = 38133.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073062 restraints weight = 33793.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073145 restraints weight = 31966.745| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17347 Z= 0.227 Angle : 0.697 10.508 23652 Z= 0.346 Chirality : 0.047 0.184 2688 Planarity : 0.005 0.054 3026 Dihedral : 6.417 83.879 2430 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.19), residues: 2163 helix: 2.09 (0.63), residues: 72 sheet: 0.05 (0.17), residues: 975 loop : -1.16 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 96 TYR 0.018 0.002 TYR L 92 PHE 0.024 0.002 PHE C 28 TRP 0.035 0.002 TRP H 39 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00521 (17338) covalent geometry : angle 0.69724 (23634) SS BOND : bond 0.00542 ( 9) SS BOND : angle 0.86488 ( 18) hydrogen bonds : bond 0.03411 ( 573) hydrogen bonds : angle 5.78180 ( 1566) ********************** 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 150 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.8462 (ppp) cc_final: 0.8083 (ppp) REVERT: B 120 ILE cc_start: 0.8607 (mm) cc_final: 0.8352 (mt) REVERT: B 345 MET cc_start: 0.8225 (ppp) cc_final: 0.7640 (ppp) REVERT: C 273 TYR cc_start: 0.8704 (m-80) cc_final: 0.8167 (m-10) REVERT: D 39 TRP cc_start: 0.8003 (m100) cc_final: 0.7762 (m100) REVERT: E 174 TYR cc_start: 0.8308 (m-80) cc_final: 0.7346 (m-10) REVERT: L 162 GLU cc_start: 0.9378 (pm20) cc_final: 0.9079 (pm20) REVERT: M 39 TRP cc_start: 0.8063 (m100) cc_final: 0.7577 (m100) REVERT: M 49 GLU cc_start: 0.8445 (tp30) cc_final: 0.8031 (tp30) REVERT: N 143 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8193 (ttm110) REVERT: N 144 GLU cc_start: 0.9085 (pp20) cc_final: 0.8514 (tp30) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1132 time to fit residues: 27.8129 Evaluate side-chains 105 residues out of total 1935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 175 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 chunk 133 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 184 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** 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 L 101 GLN M 31 ASN ** M 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.099628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072187 restraints weight = 64485.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071941 restraints weight = 43790.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072814 restraints weight = 36571.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073130 restraints weight = 32197.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073242 restraints weight = 30230.949| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17347 Z= 0.215 Angle : 0.695 10.427 23652 Z= 0.345 Chirality : 0.047 0.198 2688 Planarity : 0.004 0.052 3026 Dihedral : 6.433 83.151 2430 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.19), residues: 2163 helix: 2.03 (0.63), residues: 72 sheet: 0.13 (0.18), residues: 945 loop : -1.29 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.013 0.002 TYR N 92 PHE 0.022 0.002 PHE B 28 TRP 0.035 0.002 TRP H 39 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00495 (17338) covalent geometry : angle 0.69524 (23634) SS BOND : bond 0.00548 ( 9) SS BOND : angle 0.82841 ( 18) hydrogen bonds : bond 0.03363 ( 573) hydrogen bonds : angle 5.79916 ( 1566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2818.21 seconds wall clock time: 49 minutes 46.50 seconds (2986.50 seconds total)