Starting phenix.real_space_refine on Thu Sep 18 06:50:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kca_62247/09_2025/9kca_62247.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kca_62247/09_2025/9kca_62247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kca_62247/09_2025/9kca_62247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kca_62247/09_2025/9kca_62247.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kca_62247/09_2025/9kca_62247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kca_62247/09_2025/9kca_62247.map" } 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-2.0-5805/lib/python3.9/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, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.18, per 1000 atoms: 0.28 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: 1.26 Conformation dependent library (CDL) restraints added in 788.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.44 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: 2.41 Time building geometry restraints manager: 1.73 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.090 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 15430 Z= 0.237 Angle : 0.648 11.254 21010 Z= 0.388 Chirality : 0.040 0.401 2310 Planarity : 0.004 0.036 2615 Dihedral : 17.726 89.768 5510 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.01 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 aren 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 covalent geometry : bond 0.00469 (15430) covalent geometry : angle 0.64848 (21010) hydrogen bonds : bond 0.17276 ( 650) hydrogen bonds : angle 5.52294 ( 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 : 0.578 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: 0.1601 time to fit residues: 60.0411 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 : 0.565 ------------------------------------------------------------------------------- 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: 0.7980 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: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.123714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.090688 restraints weight = 16286.302| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.76 r_work: 0.2734 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15430 Z= 0.119 Angle : 0.495 6.780 21010 Z= 0.260 Chirality : 0.037 0.134 2310 Planarity : 0.004 0.039 2615 Dihedral : 4.195 29.745 2031 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.26 % Allowed : 24.65 % 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 aren not related in a simple way. whole: -0.30 (0.20), residues: 1815 helix: 0.63 (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 0.010 0.001 PHE D 247 TRP 0.009 0.001 TRP D 102 HIS 0.002 0.000 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00288 (15430) covalent geometry : angle 0.49540 (21010) hydrogen bonds : bond 0.04737 ( 650) hydrogen bonds : angle 3.83017 ( 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 291 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.491 Fit side-chains REVERT: A 13 ARG cc_start: 0.7317 (ptp-170) cc_final: 0.7015 (ptp90) REVERT: A 70 ASP cc_start: 0.8459 (t0) cc_final: 0.8189 (t0) REVERT: B 88 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7856 (tp) REVERT: D 75 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6780 (mt) outliers start: 37 outliers final: 17 residues processed: 284 average time/residue: 0.1517 time to fit residues: 59.6224 Evaluate side-chains 262 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 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 335 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 282 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: 3.9990 chunk 161 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.122752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.089600 restraints weight = 16470.224| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.76 r_work: 0.2717 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0741 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= 0.132 Angle : 0.495 6.970 21010 Z= 0.260 Chirality : 0.037 0.137 2310 Planarity : 0.004 0.044 2615 Dihedral : 4.119 29.483 2030 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.00 % Allowed : 23.49 % Favored : 73.52 % 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 aren not related in a simple way. whole: -0.19 (0.20), residues: 1815 helix: 0.71 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -1.45 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 B 93 HIS 0.003 0.000 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00327 (15430) covalent geometry : angle 0.49534 (21010) hydrogen bonds : bond 0.04880 ( 650) hydrogen bonds : angle 3.75881 ( 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 291 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 0.570 Fit side-chains REVERT: A 13 ARG cc_start: 0.7327 (ptp-170) cc_final: 0.7026 (ptp90) REVERT: A 70 ASP cc_start: 0.8493 (t0) cc_final: 0.8240 (t0) REVERT: B 88 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7862 (tp) REVERT: B 332 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8478 (ttp) REVERT: D 75 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6896 (mt) outliers start: 49 outliers final: 31 residues processed: 284 average time/residue: 0.1532 time to fit residues: 60.0206 Evaluate side-chains 276 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain 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 312 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 175 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.123453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.090287 restraints weight = 16437.918| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.77 r_work: 0.2737 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.0856 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= 0.119 Angle : 0.480 7.268 21010 Z= 0.250 Chirality : 0.036 0.139 2310 Planarity : 0.004 0.044 2615 Dihedral : 4.045 27.986 2030 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.81 % Allowed : 23.85 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.20), residues: 1815 helix: 0.86 (0.17), residues: 1095 sheet: None (None), residues: 0 loop : -1.33 (0.21), residues: 720 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 0.011 0.001 PHE D 247 TRP 0.009 0.001 TRP D 93 HIS 0.002 0.000 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00295 (15430) covalent geometry : angle 0.48002 (21010) hydrogen bonds : bond 0.04543 ( 650) hydrogen bonds : angle 3.70531 ( 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 292 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 0.586 Fit side-chains REVERT: A 13 ARG cc_start: 0.7285 (ptp-170) cc_final: 0.6987 (ptp90) REVERT: A 70 ASP cc_start: 0.8489 (t0) cc_final: 0.8265 (t0) REVERT: B 88 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7784 (tp) REVERT: B 332 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8499 (ttp) REVERT: D 75 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6929 (mt) outliers start: 46 outliers final: 34 residues processed: 283 average time/residue: 0.1532 time to fit residues: 59.6774 Evaluate side-chains 272 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 B residue 81 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 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 335 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 335 ASP 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: 1.9990 chunk 139 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.121064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.087836 restraints weight = 16446.135| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.75 r_work: 0.2689 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15430 Z= 0.165 Angle : 0.526 6.780 21010 Z= 0.274 Chirality : 0.038 0.135 2310 Planarity : 0.004 0.045 2615 Dihedral : 4.198 26.122 2030 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.43 % Allowed : 23.67 % Favored : 72.91 % 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 aren not related in a simple way. whole: -0.17 (0.20), residues: 1815 helix: 0.72 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -1.42 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.023 0.001 TYR C 97 PHE 0.013 0.001 PHE D 247 TRP 0.011 0.001 TRP B 93 HIS 0.003 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00413 (15430) covalent geometry : angle 0.52645 (21010) hydrogen bonds : bond 0.05464 ( 650) hydrogen bonds : angle 3.79321 ( 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 298 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 0.469 Fit side-chains REVERT: A 13 ARG cc_start: 0.7358 (ptp-170) cc_final: 0.7051 (ptp90) REVERT: B 88 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7930 (tp) REVERT: B 171 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8109 (tt) REVERT: B 332 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8472 (ttp) REVERT: C 88 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8371 (tp) REVERT: D 75 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7047 (mt) REVERT: D 171 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8136 (tt) outliers start: 56 outliers final: 38 residues processed: 291 average time/residue: 0.1479 time to fit residues: 59.4947 Evaluate side-chains 285 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 88 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain C residue 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 205 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 312 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 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: 0.9980 chunk 6 optimal weight: 7.9990 chunk 62 optimal weight: 0.1980 chunk 141 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.123268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.090067 restraints weight = 16311.221| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.77 r_work: 0.2726 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0966 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= 0.120 Angle : 0.482 7.599 21010 Z= 0.252 Chirality : 0.036 0.140 2310 Planarity : 0.004 0.045 2615 Dihedral : 4.077 28.506 2030 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.36 % Allowed : 23.91 % Favored : 72.72 % 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 aren not related in a simple way. whole: 0.01 (0.20), residues: 1815 helix: 0.88 (0.17), residues: 1095 sheet: None (None), residues: 0 loop : -1.35 (0.21), residues: 720 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 0.011 0.001 PHE D 247 TRP 0.010 0.001 TRP B 93 HIS 0.002 0.000 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00299 (15430) covalent geometry : angle 0.48229 (21010) hydrogen bonds : bond 0.04574 ( 650) hydrogen bonds : angle 3.71878 ( 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 299 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.613 Fit side-chains REVERT: A 13 ARG cc_start: 0.7346 (ptp-170) cc_final: 0.7051 (ptp90) REVERT: B 88 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7805 (tp) REVERT: B 171 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8177 (tt) REVERT: B 332 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8535 (ttp) REVERT: C 88 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8280 (tp) REVERT: D 75 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6971 (mt) REVERT: D 171 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8187 (tt) outliers start: 55 outliers final: 38 residues processed: 291 average time/residue: 0.1480 time to fit residues: 59.3806 Evaluate side-chains 286 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 88 LEU 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 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain D residue 70 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 129 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 171 optimal weight: 0.0870 chunk 76 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.122138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.088827 restraints weight = 16255.766| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.76 r_work: 0.2710 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15430 Z= 0.144 Angle : 0.508 7.616 21010 Z= 0.265 Chirality : 0.037 0.136 2310 Planarity : 0.004 0.045 2615 Dihedral : 4.121 27.476 2030 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.24 % Allowed : 23.73 % Favored : 73.03 % 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 aren not related in a simple way. whole: -0.09 (0.20), residues: 1815 helix: 0.79 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -1.38 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.024 0.001 TYR C 97 PHE 0.012 0.001 PHE D 247 TRP 0.010 0.001 TRP E 93 HIS 0.003 0.000 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00359 (15430) covalent geometry : angle 0.50830 (21010) hydrogen bonds : bond 0.05019 ( 650) hydrogen bonds : angle 3.75478 ( 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 295 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 0.603 Fit side-chains REVERT: A 13 ARG cc_start: 0.7385 (ptp-170) cc_final: 0.7090 (ptp90) REVERT: B 88 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7880 (tp) REVERT: B 165 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7616 (m-70) REVERT: B 171 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8162 (tt) REVERT: B 332 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8512 (ttp) REVERT: C 88 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8329 (tp) REVERT: D 75 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7030 (mt) REVERT: D 171 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8217 (tt) outliers start: 53 outliers final: 41 residues processed: 290 average time/residue: 0.1529 time to fit residues: 61.0291 Evaluate side-chains 289 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 88 LEU Chi-restraints excluded: chain B residue 146 SER 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 329 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 146 SER 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 70 ASP 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 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 146 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 70 optimal weight: 0.0010 chunk 171 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 overall best weight: 1.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.087051 restraints weight = 16432.604| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.76 r_work: 0.2684 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15430 Z= 0.170 Angle : 0.535 7.341 21010 Z= 0.278 Chirality : 0.039 0.134 2310 Planarity : 0.004 0.046 2615 Dihedral : 4.242 26.698 2030 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.06 % Allowed : 24.28 % Favored : 72.66 % 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 aren not related in a simple way. whole: -0.20 (0.20), residues: 1815 helix: 0.72 (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 0.027 0.001 TYR C 97 PHE 0.014 0.001 PHE D 247 TRP 0.011 0.001 TRP E 93 HIS 0.003 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00426 (15430) covalent geometry : angle 0.53452 (21010) hydrogen bonds : bond 0.05566 ( 650) hydrogen bonds : angle 3.81860 ( 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 300 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 250 time to evaluate : 0.616 Fit side-chains REVERT: A 13 ARG cc_start: 0.7458 (ptp-170) cc_final: 0.7158 (ptp90) REVERT: B 88 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7974 (tp) REVERT: B 165 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7638 (m-70) REVERT: B 171 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8256 (tt) REVERT: B 332 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8499 (ttp) REVERT: C 88 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8426 (tp) REVERT: D 75 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7072 (mt) REVERT: D 171 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8272 (tt) REVERT: D 333 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8072 (mt-10) outliers start: 50 outliers final: 37 residues processed: 294 average time/residue: 0.1528 time to fit residues: 62.2171 Evaluate side-chains 291 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 88 LEU Chi-restraints excluded: chain B residue 146 SER 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 329 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 0.8980 chunk 172 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.124586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.091363 restraints weight = 16189.946| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.76 r_work: 0.2732 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15430 Z= 0.102 Angle : 0.461 6.745 21010 Z= 0.241 Chirality : 0.036 0.141 2310 Planarity : 0.004 0.045 2615 Dihedral : 3.998 30.309 2030 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.45 % Allowed : 24.95 % Favored : 72.60 % 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 aren not related in a simple way. whole: 0.14 (0.20), residues: 1815 helix: 1.00 (0.17), residues: 1095 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.021 0.001 TYR C 97 PHE 0.010 0.001 PHE E 62 TRP 0.010 0.001 TRP B 93 HIS 0.001 0.000 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00253 (15430) covalent geometry : angle 0.46143 (21010) hydrogen bonds : bond 0.04044 ( 650) hydrogen bonds : angle 3.67515 ( 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 286 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 0.572 Fit side-chains REVERT: A 75 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7058 (mt) REVERT: B 88 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7688 (tp) REVERT: B 165 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7530 (m-70) REVERT: C 88 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8131 (tp) REVERT: D 75 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6904 (mt) REVERT: D 171 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8124 (tt) outliers start: 40 outliers final: 29 residues processed: 282 average time/residue: 0.1603 time to fit residues: 62.1079 Evaluate side-chains 277 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 153 THR 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 88 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 165 HIS 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 348 THR 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 146 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 VAL 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: 1.9990 chunk 160 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 178 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.124903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.090567 restraints weight = 16293.320| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.90 r_work: 0.2732 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1202 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= 0.100 Angle : 0.461 6.907 21010 Z= 0.240 Chirality : 0.036 0.139 2310 Planarity : 0.004 0.046 2615 Dihedral : 3.908 29.900 2030 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.20 % Allowed : 25.02 % Favored : 72.78 % 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 aren not related in a simple way. whole: 0.27 (0.20), residues: 1815 helix: 1.03 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -1.23 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.022 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 178 Details of bonding type rmsd covalent geometry : bond 0.00248 (15430) covalent geometry : angle 0.46120 (21010) hydrogen bonds : bond 0.03943 ( 650) hydrogen bonds : angle 3.62665 ( 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 282 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.552 Fit side-chains REVERT: A 75 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7100 (mt) REVERT: B 88 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7435 (tp) REVERT: B 165 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.7481 (m-70) REVERT: C 88 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8045 (tp) REVERT: D 75 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6920 (mt) outliers start: 36 outliers final: 28 residues processed: 279 average time/residue: 0.1628 time to fit residues: 62.1009 Evaluate side-chains 273 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 153 THR 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 88 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 165 HIS 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 348 THR 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 205 VAL Chi-restraints excluded: chain D residue 303 ASP 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: 4.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.124275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.092383 restraints weight = 16223.885| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.62 r_work: 0.2737 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15430 Z= 0.173 Angle : 0.538 6.799 21010 Z= 0.279 Chirality : 0.039 0.133 2310 Planarity : 0.004 0.047 2615 Dihedral : 4.179 26.625 2030 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.26 % Allowed : 24.83 % Favored : 72.91 % 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 aren not related in a simple way. whole: -0.02 (0.20), residues: 1815 helix: 0.86 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -1.39 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 51 TYR 0.029 0.001 TYR C 97 PHE 0.014 0.001 PHE B 62 TRP 0.010 0.001 TRP D 102 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00433 (15430) covalent geometry : angle 0.53809 (21010) hydrogen bonds : bond 0.05516 ( 650) hydrogen bonds : angle 3.77554 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3471.54 seconds wall clock time: 60 minutes 18.48 seconds (3618.48 seconds total)