Starting phenix.real_space_refine on Fri Jun 13 07:41:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kca_62247/06_2025/9kca_62247.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kca_62247/06_2025/9kca_62247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kca_62247/06_2025/9kca_62247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kca_62247/06_2025/9kca_62247.map" model { file = "/net/cci-nas-00/data/ceres_data/9kca_62247/06_2025/9kca_62247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kca_62247/06_2025/9kca_62247.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.240 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 80 5.16 5 Cl 10 4.86 5 C 9840 2.51 5 N 2480 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15005 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2998 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 348} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2998 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 348} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2998 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 348} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2998 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 348} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2998 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 348} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.11, per 1000 atoms: 0.61 Number of scatterers: 15005 At special positions: 0 Unit cell: (97.44, 96.57, 113.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 Cl 10 17.00 S 80 16.00 O 2590 8.00 N 2480 7.00 C 9840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3450 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 0 sheets defined 68.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.754A pdb=" N LEU A 22 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 33 through 53 removed outlier: 4.005A pdb=" N LEU A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.644A pdb=" N LEU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 removed outlier: 4.636A pdb=" N GLY A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.563A pdb=" N TYR A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.828A pdb=" N ILE A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 142 removed outlier: 4.058A pdb=" N ALA A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 135 " --> pdb=" O TYR A 131 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 removed outlier: 3.500A pdb=" N ARG A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.805A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.528A pdb=" N GLN A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.707A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 189 " --> pdb=" O TRP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.599A pdb=" N THR A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 removed outlier: 3.824A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.721A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.729A pdb=" N GLN A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.113A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.965A pdb=" N ILE A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 355 removed outlier: 3.808A pdb=" N ALA A 352 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG A 353 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 354 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.755A pdb=" N LEU B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.996A pdb=" N LEU B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 69 removed outlier: 3.664A pdb=" N LEU B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.525A pdb=" N VAL B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 99 removed outlier: 3.528A pdb=" N TYR B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.802A pdb=" N ILE B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 142 removed outlier: 4.074A pdb=" N ALA B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 135 " --> pdb=" O TYR B 131 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.791A pdb=" N LEU B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.669A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 189 " --> pdb=" O TRP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.585A pdb=" N THR B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 removed outlier: 3.805A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 removed outlier: 3.707A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.810A pdb=" N GLN B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 4.104A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 removed outlier: 3.951A pdb=" N ILE B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 311 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 removed outlier: 3.775A pdb=" N ALA B 352 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG B 353 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 354 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 355 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.514A pdb=" N LEU C 21 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 18 through 23' Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 33 through 53 removed outlier: 4.014A pdb=" N LEU C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 69 removed outlier: 3.654A pdb=" N LEU C 60 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 99 removed outlier: 3.528A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.726A pdb=" N ILE C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 142 removed outlier: 4.068A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 133 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.794A pdb=" N LEU C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.691A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.564A pdb=" N THR C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.831A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.702A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.804A pdb=" N GLN C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.117A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 removed outlier: 3.963A pdb=" N ILE C 310 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 311 " --> pdb=" O THR C 307 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 355 removed outlier: 3.804A pdb=" N ALA C 352 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ARG C 353 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 354 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 355 " --> pdb=" O ALA C 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.758A pdb=" N LEU D 22 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 33 through 53 removed outlier: 3.991A pdb=" N LEU D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 69 removed outlier: 3.660A pdb=" N LEU D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 85 removed outlier: 3.558A pdb=" N VAL D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.537A pdb=" N TYR D 97 " --> pdb=" O TRP D 93 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.888A pdb=" N ILE D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 142 removed outlier: 4.067A pdb=" N ALA D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.795A pdb=" N LEU D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.705A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 189 " --> pdb=" O TRP D 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN D 190 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.579A pdb=" N THR D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 244 removed outlier: 3.785A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.695A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 removed outlier: 3.783A pdb=" N GLN D 280 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP D 287 " --> pdb=" O PHE D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 removed outlier: 4.093A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 removed outlier: 3.956A pdb=" N ILE D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE D 311 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU D 315 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 355 removed outlier: 3.809A pdb=" N ALA D 352 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ARG D 353 " --> pdb=" O ALA D 350 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 354 " --> pdb=" O SER D 351 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG D 355 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.525A pdb=" N LEU E 20 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 21 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU E 22 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 17 through 23' Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 33 through 53 removed outlier: 4.004A pdb=" N LEU E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.674A pdb=" N LEU E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 85 removed outlier: 4.640A pdb=" N GLY E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 99 removed outlier: 3.542A pdb=" N TYR E 97 " --> pdb=" O TRP E 93 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.724A pdb=" N ILE E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 142 removed outlier: 4.071A pdb=" N ALA E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE E 133 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY E 135 " --> pdb=" O TYR E 131 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.808A pdb=" N LEU E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 158 " --> pdb=" O LEU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 172 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.714A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA E 189 " --> pdb=" O TRP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.566A pdb=" N THR E 216 " --> pdb=" O ASN E 212 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 241 removed outlier: 3.837A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 253 removed outlier: 3.692A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 287 removed outlier: 3.774A pdb=" N GLN E 280 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP E 287 " --> pdb=" O PHE E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 4.109A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 removed outlier: 3.959A pdb=" N ILE E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E 311 " --> pdb=" O THR E 307 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP E 312 " --> pdb=" O ASN E 308 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 315 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 355 removed outlier: 3.764A pdb=" N ALA E 352 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG E 353 " --> pdb=" O ALA E 350 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER E 354 " --> pdb=" O SER E 351 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG E 355 " --> pdb=" O ALA E 352 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2265 1.28 - 1.41: 4387 1.41 - 1.54: 8625 1.54 - 1.67: 18 1.67 - 1.81: 135 Bond restraints: 15430 Sorted by residual: bond pdb=" C ALA C 243 " pdb=" O ALA C 243 " ideal model delta sigma weight residual 1.235 1.147 0.088 1.25e-02 6.40e+03 4.97e+01 bond pdb=" C ALA B 243 " pdb=" O ALA B 243 " ideal model delta sigma weight residual 1.236 1.154 0.083 1.26e-02 6.30e+03 4.31e+01 bond pdb=" C THR E 241 " pdb=" O THR E 241 " ideal model delta sigma weight residual 1.235 1.148 0.087 1.38e-02 5.25e+03 3.99e+01 bond pdb=" C THR C 241 " pdb=" O THR C 241 " ideal model delta sigma weight residual 1.236 1.151 0.085 1.38e-02 5.25e+03 3.79e+01 bond pdb=" C VAL E 242 " pdb=" O VAL E 242 " ideal model delta sigma weight residual 1.236 1.151 0.085 1.47e-02 4.63e+03 3.34e+01 ... (remaining 15425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 20736 2.25 - 4.50: 214 4.50 - 6.75: 43 6.75 - 9.00: 12 9.00 - 11.25: 5 Bond angle restraints: 21010 Sorted by residual: angle pdb=" N ALA E 243 " pdb=" CA ALA E 243 " pdb=" C ALA E 243 " ideal model delta sigma weight residual 114.04 103.31 10.73 1.24e+00 6.50e-01 7.49e+01 angle pdb=" CA ALA B 243 " pdb=" C ALA B 243 " pdb=" O ALA B 243 " ideal model delta sigma weight residual 119.97 111.74 8.23 1.15e+00 7.56e-01 5.13e+01 angle pdb=" CA ALA C 243 " pdb=" C ALA C 243 " pdb=" O ALA C 243 " ideal model delta sigma weight residual 118.97 111.55 7.42 1.07e+00 8.73e-01 4.81e+01 angle pdb=" C VAL C 242 " pdb=" N ALA C 243 " pdb=" CA ALA C 243 " ideal model delta sigma weight residual 122.11 133.36 -11.25 1.64e+00 3.72e-01 4.71e+01 angle pdb=" C VAL E 242 " pdb=" CA VAL E 242 " pdb=" CB VAL E 242 " ideal model delta sigma weight residual 111.85 103.50 8.35 1.27e+00 6.20e-01 4.32e+01 ... (remaining 21005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7566 17.95 - 35.91: 1021 35.91 - 53.86: 315 53.86 - 71.81: 46 71.81 - 89.77: 12 Dihedral angle restraints: 8960 sinusoidal: 3585 harmonic: 5375 Sorted by residual: dihedral pdb=" CA VAL C 86 " pdb=" C VAL C 86 " pdb=" N THR C 87 " pdb=" CA THR C 87 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA VAL D 86 " pdb=" C VAL D 86 " pdb=" N THR D 87 " pdb=" CA THR D 87 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA VAL E 86 " pdb=" C VAL E 86 " pdb=" N THR E 87 " pdb=" CA THR E 87 " ideal model delta harmonic sigma weight residual 180.00 154.99 25.01 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 8957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2185 0.080 - 0.160: 123 0.160 - 0.241: 1 0.241 - 0.321: 0 0.321 - 0.401: 1 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CB VAL C 242 " pdb=" CA VAL C 242 " pdb=" CG1 VAL C 242 " pdb=" CG2 VAL C 242 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA ALA E 243 " pdb=" N ALA E 243 " pdb=" C ALA E 243 " pdb=" CB ALA E 243 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA THR E 241 " pdb=" N THR E 241 " pdb=" C THR E 241 " pdb=" CB THR E 241 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 2307 not shown) Planarity restraints: 2615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 241 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C THR C 241 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 241 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL C 242 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 242 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C VAL E 242 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL E 242 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA E 243 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 97 " 0.000 2.00e-02 2.50e+03 1.15e-02 2.64e+00 pdb=" CG TYR A 97 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 97 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 97 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 97 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 97 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 97 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 97 " -0.003 2.00e-02 2.50e+03 ... (remaining 2612 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2961 2.77 - 3.30: 12725 3.30 - 3.84: 23219 3.84 - 4.37: 27097 4.37 - 4.90: 49919 Nonbonded interactions: 115921 Sorted by model distance: nonbonded pdb=" O ALA A 160 " pdb=" OH TYR B 337 " model vdw 2.238 3.040 nonbonded pdb=" O ALA D 160 " pdb=" OH TYR E 337 " model vdw 2.251 3.040 nonbonded pdb=" O ALA B 160 " pdb=" OH TYR C 337 " model vdw 2.258 3.040 nonbonded pdb=" O ALA C 160 " pdb=" OH TYR D 337 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR A 337 " pdb=" O ALA E 160 " model vdw 2.279 3.040 ... (remaining 115916 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 366 or resid 703)) selection = (chain 'B' and (resid 2 through 366 or resid 703)) selection = (chain 'C' and (resid 2 through 366 or resid 703)) selection = (chain 'D' and (resid 2 through 366 or resid 703)) selection = (chain 'E' and (resid 2 through 366 or resid 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.820 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: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 33.270 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 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 : 0.005 0.088 15430 Z= 0.237 Angle : 0.648 11.254 21010 Z= 0.388 Chirality : 0.040 0.401 2310 Planarity : 0.004 0.036 2615 Dihedral : 17.726 89.768 5510 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.24 % Allowed : 25.87 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1815 helix: 0.04 (0.16), residues: 1135 sheet: None (None), residues: 0 loop : -1.58 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 102 HIS 0.004 0.001 HIS C 178 PHE 0.015 0.002 PHE A 247 TYR 0.023 0.001 TYR A 97 ARG 0.004 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.17276 ( 650) hydrogen bonds : angle 5.52294 ( 1896) covalent geometry : bond 0.00469 (15430) covalent geometry : angle 0.64848 (21010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 271 time to evaluate : 1.704 Fit side-chains REVERT: A 13 ARG cc_start: 0.7368 (ptp-170) cc_final: 0.7060 (ptp90) REVERT: A 70 ASP cc_start: 0.8530 (t0) cc_final: 0.8281 (t0) REVERT: C 51 ARG cc_start: 0.6795 (mmt90) cc_final: 0.6494 (mtt-85) outliers start: 4 outliers final: 1 residues processed: 274 average time/residue: 0.3520 time to fit residues: 132.9811 Evaluate side-chains 265 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 241 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 0.0770 chunk 141 optimal weight: 0.9990 chunk 54 optimal weight: 0.0070 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.126342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.092251 restraints weight = 16139.339| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.89 r_work: 0.2744 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15430 Z= 0.094 Angle : 0.464 6.590 21010 Z= 0.244 Chirality : 0.036 0.137 2310 Planarity : 0.004 0.038 2615 Dihedral : 4.083 31.517 2031 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.96 % Allowed : 25.20 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1815 helix: 0.80 (0.17), residues: 1095 sheet: None (None), residues: 0 loop : -1.46 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 102 HIS 0.001 0.000 HIS E 168 PHE 0.008 0.001 PHE D 247 TYR 0.012 0.001 TYR E 97 ARG 0.003 0.000 ARG D 25 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 650) hydrogen bonds : angle 3.77893 ( 1896) covalent geometry : bond 0.00220 (15430) covalent geometry : angle 0.46423 (21010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 1.554 Fit side-chains REVERT: A 325 MET cc_start: 0.9033 (mtp) cc_final: 0.8796 (mtm) REVERT: C 51 ARG cc_start: 0.6569 (mmt90) cc_final: 0.6337 (mmt90) REVERT: D 75 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6643 (mt) outliers start: 32 outliers final: 17 residues processed: 283 average time/residue: 0.3333 time to fit residues: 129.8966 Evaluate side-chains 261 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.123574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.090574 restraints weight = 16227.907| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.75 r_work: 0.2721 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15430 Z= 0.126 Angle : 0.487 6.750 21010 Z= 0.255 Chirality : 0.037 0.135 2310 Planarity : 0.004 0.042 2615 Dihedral : 4.026 27.809 2030 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.63 % Allowed : 23.49 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1815 helix: 0.79 (0.17), residues: 1105 sheet: None (None), residues: 0 loop : -1.40 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 93 HIS 0.003 0.000 HIS A 178 PHE 0.011 0.001 PHE D 247 TYR 0.018 0.001 TYR C 97 ARG 0.002 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 650) hydrogen bonds : angle 3.71876 ( 1896) covalent geometry : bond 0.00312 (15430) covalent geometry : angle 0.48693 (21010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 1.695 Fit side-chains REVERT: A 70 ASP cc_start: 0.8483 (t0) cc_final: 0.8241 (t0) REVERT: B 332 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8505 (ttp) REVERT: D 75 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6892 (mt) outliers start: 43 outliers final: 23 residues processed: 276 average time/residue: 0.3479 time to fit residues: 132.0049 Evaluate side-chains 261 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 117 optimal weight: 0.0270 chunk 111 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.130118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.098750 restraints weight = 16015.987| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.61 r_work: 0.2809 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15430 Z= 0.092 Angle : 0.445 7.505 21010 Z= 0.232 Chirality : 0.035 0.140 2310 Planarity : 0.003 0.042 2615 Dihedral : 3.864 30.299 2030 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.14 % Allowed : 23.91 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1815 helix: 0.92 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.29 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 102 HIS 0.001 0.000 HIS A 178 PHE 0.009 0.001 PHE D 247 TYR 0.016 0.001 TYR C 97 ARG 0.003 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 650) hydrogen bonds : angle 3.60341 ( 1896) covalent geometry : bond 0.00225 (15430) covalent geometry : angle 0.44496 (21010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 1.507 Fit side-chains REVERT: B 332 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8455 (ttp) REVERT: D 75 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6855 (mt) outliers start: 35 outliers final: 25 residues processed: 273 average time/residue: 0.3431 time to fit residues: 128.1995 Evaluate side-chains 266 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 140 optimal weight: 0.0370 chunk 77 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.123902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.089618 restraints weight = 16467.936| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.90 r_work: 0.2706 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15430 Z= 0.119 Angle : 0.472 6.809 21010 Z= 0.247 Chirality : 0.036 0.136 2310 Planarity : 0.004 0.043 2615 Dihedral : 3.921 28.838 2030 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.57 % Allowed : 23.67 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1815 helix: 0.96 (0.17), residues: 1100 sheet: None (None), residues: 0 loop : -1.31 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 93 HIS 0.002 0.000 HIS A 178 PHE 0.011 0.001 PHE D 247 TYR 0.018 0.001 TYR C 97 ARG 0.003 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 650) hydrogen bonds : angle 3.64134 ( 1896) covalent geometry : bond 0.00295 (15430) covalent geometry : angle 0.47250 (21010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 1.658 Fit side-chains REVERT: A 70 ASP cc_start: 0.8521 (t0) cc_final: 0.8268 (t0) REVERT: B 332 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8474 (ttp) REVERT: D 75 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6937 (mt) outliers start: 42 outliers final: 36 residues processed: 279 average time/residue: 0.3858 time to fit residues: 150.3504 Evaluate side-chains 276 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 365 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.120643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.087345 restraints weight = 16391.637| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.75 r_work: 0.2690 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15430 Z= 0.184 Angle : 0.541 6.898 21010 Z= 0.282 Chirality : 0.039 0.133 2310 Planarity : 0.004 0.045 2615 Dihedral : 4.205 26.387 2030 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.30 % Allowed : 23.24 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1815 helix: 0.75 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -1.40 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 93 HIS 0.004 0.001 HIS E 178 PHE 0.014 0.002 PHE D 247 TYR 0.025 0.001 TYR C 97 ARG 0.003 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.05737 ( 650) hydrogen bonds : angle 3.79534 ( 1896) covalent geometry : bond 0.00461 (15430) covalent geometry : angle 0.54117 (21010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 1.858 Fit side-chains REVERT: A 13 ARG cc_start: 0.7346 (ptp-170) cc_final: 0.7057 (ptp90) REVERT: A 70 ASP cc_start: 0.8561 (t0) cc_final: 0.8355 (t0) REVERT: B 171 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8158 (tt) REVERT: B 332 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8499 (ttp) REVERT: C 88 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8401 (tp) REVERT: D 75 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7050 (mt) REVERT: D 171 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8162 (tt) outliers start: 54 outliers final: 32 residues processed: 290 average time/residue: 0.4212 time to fit residues: 169.8097 Evaluate side-chains 273 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 365 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 136 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 82 optimal weight: 0.0030 chunk 85 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.125149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.090754 restraints weight = 16388.445| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.90 r_work: 0.2731 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15430 Z= 0.094 Angle : 0.452 7.941 21010 Z= 0.235 Chirality : 0.035 0.140 2310 Planarity : 0.003 0.042 2615 Dihedral : 3.946 30.984 2030 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.96 % Allowed : 24.95 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1815 helix: 0.93 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.33 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 93 HIS 0.001 0.000 HIS E 178 PHE 0.009 0.001 PHE D 247 TYR 0.019 0.001 TYR C 97 ARG 0.003 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 650) hydrogen bonds : angle 3.63043 ( 1896) covalent geometry : bond 0.00234 (15430) covalent geometry : angle 0.45169 (21010) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 2.064 Fit side-chains REVERT: A 70 ASP cc_start: 0.8459 (t0) cc_final: 0.8226 (t0) REVERT: B 332 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8505 (ttp) REVERT: D 75 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6863 (mt) REVERT: D 171 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8098 (tt) outliers start: 32 outliers final: 26 residues processed: 269 average time/residue: 0.4169 time to fit residues: 154.5413 Evaluate side-chains 267 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 83 optimal weight: 0.2980 chunk 144 optimal weight: 1.9990 chunk 161 optimal weight: 0.0980 chunk 121 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 177 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.126570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.092044 restraints weight = 16237.524| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.91 r_work: 0.2744 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15430 Z= 0.093 Angle : 0.447 7.876 21010 Z= 0.230 Chirality : 0.035 0.139 2310 Planarity : 0.003 0.043 2615 Dihedral : 3.795 30.595 2030 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.20 % Allowed : 24.28 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1815 helix: 1.07 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.25 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 102 HIS 0.001 0.000 HIS A 178 PHE 0.008 0.001 PHE D 247 TYR 0.017 0.001 TYR C 97 ARG 0.004 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 650) hydrogen bonds : angle 3.54317 ( 1896) covalent geometry : bond 0.00232 (15430) covalent geometry : angle 0.44725 (21010) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 2.735 Fit side-chains REVERT: A 13 ARG cc_start: 0.7129 (ptp-170) cc_final: 0.6611 (ptp90) REVERT: B 332 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8452 (ttp) REVERT: C 88 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7849 (tp) REVERT: D 75 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6848 (mt) outliers start: 36 outliers final: 30 residues processed: 279 average time/residue: 0.4299 time to fit residues: 166.6957 Evaluate side-chains 275 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 365 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 0.0770 chunk 137 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 50 optimal weight: 0.1980 chunk 37 optimal weight: 10.0000 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.124792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.090461 restraints weight = 16202.664| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.89 r_work: 0.2717 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15430 Z= 0.109 Angle : 0.464 7.289 21010 Z= 0.240 Chirality : 0.036 0.136 2310 Planarity : 0.004 0.043 2615 Dihedral : 3.848 28.035 2030 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.20 % Allowed : 24.34 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1815 helix: 1.06 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 93 HIS 0.002 0.000 HIS E 178 PHE 0.010 0.001 PHE D 247 TYR 0.022 0.001 TYR C 97 ARG 0.004 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 650) hydrogen bonds : angle 3.56503 ( 1896) covalent geometry : bond 0.00270 (15430) covalent geometry : angle 0.46441 (21010) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 1.561 Fit side-chains REVERT: A 13 ARG cc_start: 0.7207 (ptp-170) cc_final: 0.6696 (ptp90) REVERT: B 332 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8479 (ttp) REVERT: C 88 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8064 (tp) REVERT: C 333 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7834 (mm-30) REVERT: D 75 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6955 (mt) REVERT: E 115 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7846 (mm-30) outliers start: 36 outliers final: 32 residues processed: 273 average time/residue: 0.3504 time to fit residues: 130.9425 Evaluate side-chains 274 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 365 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 12 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 70 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.127502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.094205 restraints weight = 16321.685| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.78 r_work: 0.2771 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15430 Z= 0.089 Angle : 0.438 7.213 21010 Z= 0.227 Chirality : 0.035 0.145 2310 Planarity : 0.003 0.043 2615 Dihedral : 3.733 29.343 2030 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.02 % Allowed : 24.65 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1815 helix: 1.18 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.23 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 102 HIS 0.001 0.000 HIS E 178 PHE 0.007 0.001 PHE D 247 TYR 0.017 0.001 TYR C 97 ARG 0.004 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 650) hydrogen bonds : angle 3.49267 ( 1896) covalent geometry : bond 0.00222 (15430) covalent geometry : angle 0.43849 (21010) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3630 Ramachandran restraints generated. 1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 1.538 Fit side-chains REVERT: A 13 ARG cc_start: 0.7088 (ptp-170) cc_final: 0.6578 (ptp90) REVERT: C 333 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7793 (mm-30) REVERT: D 75 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6841 (mt) REVERT: D 171 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7945 (tt) REVERT: D 285 MET cc_start: 0.8309 (tpt) cc_final: 0.8086 (mmt) outliers start: 33 outliers final: 29 residues processed: 267 average time/residue: 0.3594 time to fit residues: 131.5133 Evaluate side-chains 266 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 365 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 88 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.127001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.093705 restraints weight = 16208.408| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.77 r_work: 0.2765 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15430 Z= 0.093 Angle : 0.444 6.988 21010 Z= 0.229 Chirality : 0.035 0.143 2310 Planarity : 0.004 0.044 2615 Dihedral : 3.718 28.876 2030 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.14 % Allowed : 24.59 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1815 helix: 1.21 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.20 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 102 HIS 0.001 0.000 HIS A 178 PHE 0.010 0.001 PHE C 62 TYR 0.017 0.001 TYR C 97 ARG 0.004 0.000 ARG C 51 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 650) hydrogen bonds : angle 3.47478 ( 1896) covalent geometry : bond 0.00232 (15430) covalent geometry : angle 0.44372 (21010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7961.17 seconds wall clock time: 143 minutes 55.12 seconds (8635.12 seconds total)