Starting phenix.real_space_refine on Fri Jul 3 15:26:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kca_62247/07_2026/9kca_62247.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kca_62247/07_2026/9kca_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_62247/07_2026/9kca_62247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kca_62247/07_2026/9kca_62247.map" model { file = "/net/cci-nas-00/data/ceres_data/9kca_62247/07_2026/9kca_62247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kca_62247/07_2026/9kca_62247.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.240 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 0 Ad-hoc single atom residues: {' CA': 1, ' CL': 2} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 2, ' CA': 1} Chain breaks: 3 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 2, ' CA': 1} Chain breaks: 3 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 2, ' CA': 1} Chain breaks: 3 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 2, ' CA': 1} Chain breaks: 3 Time building chain proxies: 3.83, per 1000 atoms: 0.26 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: 1.22 Conformation dependent library (CDL) restraints added in 632.6 milliseconds 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: 0.39 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: 2.21 Time building geometry restraints manager: 1.65 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: 0.01 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.720 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 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 : 4.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (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 ARG 0.004 0.000 ARG E 25 TYR 0.023 0.001 TYR A 97 PHE 0.015 0.002 PHE A 247 TRP 0.011 0.001 TRP B 102 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.24 (15430) covalent geometry : angle 0.64848 / 0.39 (21010) hydrogen bonds : bond 0.17276 / 11.32 ( 650) hydrogen bonds : angle 5.52294 / 3.89 ( 1896) *********************** 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 : 0.709 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: 0.1644 time to fit residues: 62.4976 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 : 0.658 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.122736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.088582 restraints weight = 16333.054| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.89 r_work: 0.2696 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.0605 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= 0.133 Angle : 0.508 6.905 21010 Z= 0.267 Chirality : 0.037 0.133 2310 Planarity : 0.004 0.040 2615 Dihedral : 4.223 29.134 2031 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.32 % Allowed : 24.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1815 helix: 0.58 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -1.50 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 25 TYR 0.014 0.001 TYR E 97 PHE 0.011 0.001 PHE D 247 TRP 0.010 0.001 TRP D 102 HIS 0.002 0.000 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (15430) covalent geometry : angle 0.50789 / 0.27 (21010) hydrogen bonds : bond 0.05063 / 3.26 ( 650) hydrogen bonds : angle 3.86821 / 2.69 ( 1896) *********************** 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 283 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.638 Fit side-chains REVERT: A 13 ARG cc_start: 0.7342 (ptp-170) cc_final: 0.7037 (ptp90) REVERT: A 70 ASP cc_start: 0.8464 (t0) cc_final: 0.8259 (t0) REVERT: B 88 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7918 (tp) REVERT: C 51 ARG cc_start: 0.6781 (mmt90) cc_final: 0.6566 (mmt90) REVERT: D 75 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6819 (mt) outliers start: 38 outliers final: 18 residues processed: 280 average time/residue: 0.1626 time to fit residues: 63.3691 Evaluate side-chains 262 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 88 LEU 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 81 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 D residue 75 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 302 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 171 optimal weight: 2.9990 chunk 161 optimal weight: 0.0010 chunk 167 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.125042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.091862 restraints weight = 16420.535| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.78 r_work: 0.2750 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.0866 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= 0.105 Angle : 0.463 6.883 21010 Z= 0.243 Chirality : 0.036 0.139 2310 Planarity : 0.004 0.041 2615 Dihedral : 4.004 30.922 2030 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.63 % Allowed : 24.16 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1815 helix: 0.76 (0.16), residues: 1130 sheet: None (None), residues: 0 loop : -1.39 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 51 TYR 0.016 0.001 TYR C 97 PHE 0.010 0.001 PHE D 247 TRP 0.008 0.001 TRP B 93 HIS 0.002 0.000 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (15430) covalent geometry : angle 0.46338 / 0.24 (21010) hydrogen bonds : bond 0.04201 / 2.70 ( 650) hydrogen bonds : angle 3.69843 / 2.57 ( 1896) *********************** 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 284 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.606 Fit side-chains REVERT: D 75 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6847 (mt) outliers start: 43 outliers final: 25 residues processed: 279 average time/residue: 0.1609 time to fit residues: 62.0810 Evaluate side-chains 265 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 81 VAL 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 175 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 144 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.123122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.089814 restraints weight = 16454.477| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.77 r_work: 0.2721 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.0861 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= 0.130 Angle : 0.492 7.462 21010 Z= 0.256 Chirality : 0.037 0.135 2310 Planarity : 0.004 0.044 2615 Dihedral : 4.031 27.348 2030 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.00 % Allowed : 23.79 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.20), residues: 1815 helix: 0.82 (0.17), residues: 1100 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 51 TYR 0.019 0.001 TYR C 97 PHE 0.012 0.001 PHE D 247 TRP 0.009 0.001 TRP E 93 HIS 0.003 0.000 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (15430) covalent geometry : angle 0.49187 / 0.26 (21010) hydrogen bonds : bond 0.04781 / 3.07 ( 650) hydrogen bonds : angle 3.72241 / 2.58 ( 1896) *********************** 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 286 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 0.584 Fit side-chains REVERT: A 70 ASP cc_start: 0.8503 (t0) cc_final: 0.8293 (t0) REVERT: D 75 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6975 (mt) outliers start: 49 outliers final: 39 residues processed: 282 average time/residue: 0.1584 time to fit residues: 62.3636 Evaluate side-chains 273 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 205 VAL 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 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 205 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 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 302 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 96 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.125262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.091932 restraints weight = 16327.185| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.78 r_work: 0.2749 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15430 Z= 0.103 Angle : 0.458 6.592 21010 Z= 0.239 Chirality : 0.036 0.139 2310 Planarity : 0.003 0.043 2615 Dihedral : 3.916 29.343 2030 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.00 % Allowed : 23.91 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.20), residues: 1815 helix: 0.89 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 51 TYR 0.017 0.001 TYR C 97 PHE 0.010 0.001 PHE D 247 TRP 0.008 0.001 TRP E 93 HIS 0.002 0.000 HIS E 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.10 (15430) covalent geometry : angle 0.45777 / 0.24 (21010) hydrogen bonds : bond 0.04072 / 2.61 ( 650) hydrogen bonds : angle 3.64280 / 2.52 ( 1896) *********************** 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 290 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.517 Fit side-chains REVERT: A 70 ASP cc_start: 0.8465 (t0) cc_final: 0.8237 (t0) REVERT: B 171 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8021 (tt) REVERT: C 88 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8089 (tp) REVERT: D 75 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6920 (mt) outliers start: 49 outliers final: 38 residues processed: 285 average time/residue: 0.1439 time to fit residues: 57.0411 Evaluate side-chains 282 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 171 LEU 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 335 ASP Chi-restraints excluded: chain B residue 348 THR 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 88 LEU 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 C residue 365 ASN Chi-restraints excluded: chain D residue 70 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 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 130 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.118752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.084502 restraints weight = 16488.097| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.88 r_work: 0.2644 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 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 : 0.006 0.045 15430 Z= 0.229 Angle : 0.589 8.883 21010 Z= 0.305 Chirality : 0.041 0.131 2310 Planarity : 0.004 0.046 2615 Dihedral : 4.318 24.293 2030 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.30 % Allowed : 23.30 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1815 helix: 0.60 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -1.46 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.029 0.002 TYR C 97 PHE 0.016 0.002 PHE D 247 TRP 0.011 0.002 TRP E 93 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.23 (15430) covalent geometry : angle 0.58898 / 0.30 (21010) hydrogen bonds : bond 0.06338 / 4.08 ( 650) hydrogen bonds : angle 3.88810 / 2.69 ( 1896) *********************** 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 298 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 0.560 Fit side-chains REVERT: A 13 ARG cc_start: 0.7364 (ptp-170) cc_final: 0.7086 (ptp90) REVERT: B 171 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8050 (tt) REVERT: C 88 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8388 (tp) REVERT: D 75 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7006 (mt) REVERT: D 171 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8073 (tt) outliers start: 54 outliers final: 39 residues processed: 293 average time/residue: 0.1312 time to fit residues: 53.4819 Evaluate side-chains 279 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 236 TYR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 312 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 146 SER 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 329 LEU 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 146 SER 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 146 SER 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 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 146 SER Chi-restraints excluded: chain E residue 163 MET 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 129 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 171 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.124431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.091147 restraints weight = 16173.254| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.77 r_work: 0.2739 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15430 Z= 0.102 Angle : 0.466 7.612 21010 Z= 0.242 Chirality : 0.036 0.140 2310 Planarity : 0.004 0.044 2615 Dihedral : 4.026 30.112 2030 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.26 % Allowed : 24.53 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1815 helix: 0.83 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -1.34 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.016 0.001 TYR C 97 PHE 0.010 0.001 PHE D 247 TRP 0.010 0.001 TRP B 93 HIS 0.001 0.000 HIS E 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.10 (15430) covalent geometry : angle 0.46624 / 0.24 (21010) hydrogen bonds : bond 0.04136 / 2.65 ( 650) hydrogen bonds : angle 3.68633 / 2.55 ( 1896) *********************** 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 277 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.483 Fit side-chains REVERT: A 13 ARG cc_start: 0.7235 (ptp-170) cc_final: 0.6972 (ptp90) REVERT: B 171 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8151 (tt) REVERT: C 88 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8212 (tp) REVERT: D 75 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6892 (mt) REVERT: D 171 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8142 (tt) outliers start: 37 outliers final: 32 residues processed: 273 average time/residue: 0.1375 time to fit residues: 51.9520 Evaluate side-chains 273 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 348 THR 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 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 88 LEU 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 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 163 MET Chi-restraints excluded: chain E residue 282 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 161 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.118212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.083960 restraints weight = 16498.067| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.88 r_work: 0.2624 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15430 Z= 0.226 Angle : 0.585 7.424 21010 Z= 0.303 Chirality : 0.041 0.132 2310 Planarity : 0.004 0.046 2615 Dihedral : 4.357 24.661 2030 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.81 % Allowed : 24.04 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1815 helix: 0.61 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -1.50 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.030 0.002 TYR C 97 PHE 0.015 0.002 PHE D 247 TRP 0.011 0.002 TRP D 102 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.23 (15430) covalent geometry : angle 0.58531 / 0.30 (21010) hydrogen bonds : bond 0.06364 / 4.09 ( 650) hydrogen bonds : angle 3.88889 / 2.69 ( 1896) *********************** 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 289 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 0.584 Fit side-chains REVERT: A 13 ARG cc_start: 0.7417 (ptp-170) cc_final: 0.7143 (ptp90) REVERT: A 70 ASP cc_start: 0.8648 (t0) cc_final: 0.8441 (t0) REVERT: B 165 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7638 (m-70) REVERT: B 171 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8159 (tt) REVERT: C 88 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8443 (tp) REVERT: D 75 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7111 (mt) REVERT: D 171 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8235 (tt) outliers start: 46 outliers final: 32 residues processed: 285 average time/residue: 0.1357 time to fit residues: 53.7407 Evaluate side-chains 277 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 165 HIS 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 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 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 146 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 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 146 SER Chi-restraints excluded: chain E residue 163 MET 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 115 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 179 optimal weight: 9.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.095006 restraints weight = 16100.330| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.66 r_work: 0.2804 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15430 Z= 0.096 Angle : 0.456 6.707 21010 Z= 0.237 Chirality : 0.035 0.142 2310 Planarity : 0.003 0.044 2615 Dihedral : 3.990 31.251 2030 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.14 % Allowed : 25.20 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.20), residues: 1815 helix: 0.89 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -1.35 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.019 0.001 TYR C 97 PHE 0.009 0.001 PHE D 247 TRP 0.010 0.001 TRP B 93 HIS 0.001 0.000 HIS E 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (15430) covalent geometry : angle 0.45555 / 0.24 (21010) hydrogen bonds : bond 0.03833 / 2.45 ( 650) hydrogen bonds : angle 3.65896 / 2.53 ( 1896) *********************** 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 278 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 0.556 Fit side-chains REVERT: A 13 ARG cc_start: 0.7266 (ptp-170) cc_final: 0.7010 (ptp90) REVERT: A 70 ASP cc_start: 0.8429 (t0) cc_final: 0.8223 (t0) REVERT: A 75 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7069 (mt) REVERT: B 165 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7552 (m-70) REVERT: C 88 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8134 (tp) REVERT: D 75 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6917 (mt) REVERT: D 171 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8215 (tt) outliers start: 35 outliers final: 26 residues processed: 274 average time/residue: 0.1440 time to fit residues: 54.5382 Evaluate side-chains 268 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU 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 165 HIS 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 81 VAL Chi-restraints excluded: chain C residue 88 LEU 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 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 146 SER 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 154 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 178 optimal weight: 0.6980 chunk 147 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.125233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.090831 restraints weight = 16297.913| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.90 r_work: 0.2726 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1238 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= 0.098 Angle : 0.458 6.700 21010 Z= 0.237 Chirality : 0.036 0.138 2310 Planarity : 0.004 0.045 2615 Dihedral : 3.880 29.731 2030 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.02 % Allowed : 24.89 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.20), residues: 1815 helix: 1.01 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -1.25 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.021 0.001 TYR C 97 PHE 0.010 0.001 PHE C 62 TRP 0.010 0.001 TRP C 93 HIS 0.001 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (15430) covalent geometry : angle 0.45756 / 0.24 (21010) hydrogen bonds : bond 0.03885 / 2.49 ( 650) hydrogen bonds : angle 3.60511 / 2.50 ( 1896) ********************** 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 276 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.366 Fit side-chains REVERT: A 13 ARG cc_start: 0.7170 (ptp-170) cc_final: 0.6685 (ptp90) REVERT: B 165 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7425 (m-70) REVERT: C 88 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7945 (tp) REVERT: D 75 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6829 (mt) REVERT: D 171 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8025 (tt) outliers start: 33 outliers final: 29 residues processed: 274 average time/residue: 0.1369 time to fit residues: 52.0095 Evaluate side-chains 272 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 165 HIS 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 81 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 146 SER 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 205 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 146 SER 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 102 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.125772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.091433 restraints weight = 16241.437| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.90 r_work: 0.2734 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15430 Z= 0.097 Angle : 0.451 6.649 21010 Z= 0.234 Chirality : 0.036 0.138 2310 Planarity : 0.004 0.045 2615 Dihedral : 3.836 30.198 2030 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.14 % Allowed : 24.71 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1815 helix: 1.07 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -1.20 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.020 0.001 TYR C 97 PHE 0.010 0.001 PHE D 62 TRP 0.010 0.001 TRP E 102 HIS 0.001 0.000 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (15430) covalent geometry : angle 0.45104 / 0.23 (21010) hydrogen bonds : bond 0.03789 / 2.42 ( 650) hydrogen bonds : angle 3.56855 / 2.47 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3374.90 seconds wall clock time: 58 minutes 35.30 seconds (3515.30 seconds total)