Starting phenix.real_space_refine on Thu Mar 5 03:14:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0o_22605/03_2026/7k0o_22605.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0o_22605/03_2026/7k0o_22605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0o_22605/03_2026/7k0o_22605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0o_22605/03_2026/7k0o_22605.map" model { file = "/net/cci-nas-00/data/ceres_data/7k0o_22605/03_2026/7k0o_22605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0o_22605/03_2026/7k0o_22605.cif" } resolution = 3.1 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= 0.001 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 C 11986 2.51 5 N 3116 2.21 5 O 3352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18558 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3582 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3582 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-2': 3, 'POV:plan-3': 3, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'PLP': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 4.22, per 1000 atoms: 0.23 Number of scatterers: 18558 At special positions: 0 Unit cell: (149.745, 135.675, 118.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 4 15.00 O 3352 8.00 N 3116 7.00 C 11986 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 874.1 milliseconds 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 14 sheets defined 54.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.520A pdb=" N ALA A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.713A pdb=" N LEU A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.693A pdb=" N TRP A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.666A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.191A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.749A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 removed outlier: 3.535A pdb=" N HIS A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.678A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 360 through 378 removed outlier: 4.298A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.557A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 Processing helix chain 'B' and resid 67 through 94 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.742A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.708A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.887A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 4.057A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 55 Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'D' and resid 11 through 19 removed outlier: 4.704A pdb=" N MET D 17 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 Processing helix chain 'D' and resid 44 through 66 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 96 through 117 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 120 through 136 Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.567A pdb=" N GLY D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 150 " --> pdb=" O ILE D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 150' Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.520A pdb=" N ALA E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 removed outlier: 3.713A pdb=" N LEU E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 64 removed outlier: 3.694A pdb=" N TRP E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 142 through 156 removed outlier: 3.667A pdb=" N LEU E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 179 removed outlier: 4.191A pdb=" N ILE E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 213 through 231 removed outlier: 3.749A pdb=" N LEU E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 288 through 294 removed outlier: 3.535A pdb=" N HIS E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 332 removed outlier: 4.679A pdb=" N HIS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 359 Processing helix chain 'E' and resid 360 through 378 removed outlier: 4.298A pdb=" N ALA E 364 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 422 removed outlier: 3.557A pdb=" N ASP E 408 " --> pdb=" O SER E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 473 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 30 through 55 Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'H' and resid 11 through 19 removed outlier: 4.704A pdb=" N MET H 17 " --> pdb=" O THR H 14 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER H 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 39 Processing helix chain 'H' and resid 44 through 66 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'H' and resid 90 through 93 Processing helix chain 'H' and resid 96 through 117 Proline residue: H 106 - end of helix Processing helix chain 'H' and resid 120 through 136 Processing helix chain 'H' and resid 146 through 150 removed outlier: 3.567A pdb=" N GLY H 149 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 150 " --> pdb=" O ILE H 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 146 through 150' Processing helix chain 'F' and resid 67 through 94 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 116 through 119 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 130 through 134 Processing helix chain 'F' and resid 186 through 200 Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.741A pdb=" N GLU F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 250 removed outlier: 3.708A pdb=" N ASN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 263 through 273 Processing helix chain 'F' and resid 284 through 299 Processing helix chain 'F' and resid 326 through 338 Processing helix chain 'F' and resid 358 through 364 Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 391 through 402 Processing helix chain 'F' and resid 402 through 407 Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 433 through 455 removed outlier: 3.887A pdb=" N VAL F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 4.058A pdb=" N GLY F 480 " --> pdb=" O PRO F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 536 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.328A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 164 removed outlier: 7.057A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.208A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.986A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.646A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.820A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 94 through 95 Processing sheet with id=AA9, first strand: chain 'E' and resid 101 through 102 removed outlier: 6.329A pdb=" N ILE E 101 " --> pdb=" O ALA E 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 160 through 164 removed outlier: 7.058A pdb=" N ILE E 271 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N SER E 304 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU E 273 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ASN E 306 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG E 240 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE E 272 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE E 242 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLU E 274 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL E 244 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP E 188 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLU E 245 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE E 209 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL E 187 " --> pdb=" O PHE E 209 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 383 through 386 removed outlier: 4.207A pdb=" N THR E 427 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 145 through 152 removed outlier: 6.987A pdb=" N VAL F 146 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE F 167 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE F 148 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN F 165 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU F 150 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY F 492 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE F 171 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.646A pdb=" N ILE F 310 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR F 342 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE F 312 " --> pdb=" O TYR F 342 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP F 344 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL F 314 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.820A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2727 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: 2.60 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3566 1.33 - 1.45: 4454 1.45 - 1.57: 10754 1.57 - 1.69: 4 1.69 - 1.81: 168 Bond restraints: 18946 Sorted by residual: bond pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" O12 POV F 601 " pdb=" P POV F 601 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O12 POV B 602 " pdb=" P POV B 602 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CA PRO B 413 " pdb=" C PRO B 413 " ideal model delta sigma weight residual 1.517 1.547 -0.029 9.30e-03 1.16e+04 1.00e+01 ... (remaining 18941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 25475 3.54 - 7.09: 119 7.09 - 10.63: 6 10.63 - 14.17: 0 14.17 - 17.72: 4 Bond angle restraints: 25604 Sorted by residual: angle pdb=" C28 POV D 901 " pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 127.79 110.07 17.72 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C28 POV H 901 " pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 127.79 110.08 17.71 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C29 POV H 901 " pdb="C210 POV H 901 " pdb="C211 POV H 901 " ideal model delta sigma weight residual 127.67 110.03 17.64 3.00e+00 1.11e-01 3.46e+01 angle pdb=" C29 POV D 901 " pdb="C210 POV D 901 " pdb="C211 POV D 901 " ideal model delta sigma weight residual 127.67 110.05 17.62 3.00e+00 1.11e-01 3.45e+01 angle pdb=" CA PRO F 413 " pdb=" C PRO F 413 " pdb=" N PRO F 414 " ideal model delta sigma weight residual 117.93 124.26 -6.33 1.20e+00 6.94e-01 2.78e+01 ... (remaining 25599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10442 17.80 - 35.60: 746 35.60 - 53.40: 152 53.40 - 71.20: 12 71.20 - 88.99: 14 Dihedral angle restraints: 11366 sinusoidal: 4580 harmonic: 6786 Sorted by residual: dihedral pdb=" CA LYS D 79 " pdb=" C LYS D 79 " pdb=" N ALA D 80 " pdb=" CA ALA D 80 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LYS H 79 " pdb=" C LYS H 79 " pdb=" N ALA H 80 " pdb=" CA ALA H 80 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA VAL D 93 " pdb=" C VAL D 93 " pdb=" N GLN D 94 " pdb=" CA GLN D 94 " ideal model delta harmonic sigma weight residual 180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 11363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1882 0.038 - 0.076: 683 0.076 - 0.114: 227 0.114 - 0.152: 56 0.152 - 0.190: 6 Chirality restraints: 2854 Sorted by residual: chirality pdb=" CA THR H 105 " pdb=" N THR H 105 " pdb=" C THR H 105 " pdb=" CB THR H 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA THR D 105 " pdb=" N THR D 105 " pdb=" C THR D 105 " pdb=" CB THR D 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA PRO B 413 " pdb=" N PRO B 413 " pdb=" C PRO B 413 " pdb=" CB PRO B 413 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 2851 not shown) Planarity restraints: 3244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 469 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO F 470 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 470 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 470 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO B 470 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 502 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.027 5.00e-02 4.00e+02 ... (remaining 3241 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 516 2.71 - 3.26: 18077 3.26 - 3.80: 28687 3.80 - 4.35: 37141 4.35 - 4.90: 65235 Nonbonded interactions: 149656 Sorted by model distance: nonbonded pdb=" O VAL D 10 " pdb=" OG1 THR D 74 " model vdw 2.161 3.040 nonbonded pdb=" O VAL H 10 " pdb=" OG1 THR H 74 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR B 448 " pdb=" OD1 ASP B 522 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR F 448 " pdb=" OD1 ASP F 522 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.266 3.040 ... (remaining 149651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 53 through 544) selection = (chain 'F' and resid 53 through 544) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 1 through 902) } 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: 4.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.500 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.006 0.190 18948 Z= 0.261 Angle : 0.745 17.715 25604 Z= 0.411 Chirality : 0.045 0.190 2854 Planarity : 0.005 0.050 3244 Dihedral : 13.026 88.995 7022 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.21 % Allowed : 0.67 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2326 helix: 1.76 (0.15), residues: 1092 sheet: -0.25 (0.35), residues: 226 loop : -0.38 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 459 TYR 0.029 0.002 TYR E 166 PHE 0.022 0.002 PHE E 168 TRP 0.014 0.001 TRP G 32 HIS 0.007 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00560 (18946) covalent geometry : angle 0.74500 (25604) hydrogen bonds : bond 0.13470 ( 953) hydrogen bonds : angle 5.86448 ( 2727) Misc. bond : bond 0.02896 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 0.604 Fit side-chains REVERT: A 214 MET cc_start: 0.6571 (mmt) cc_final: 0.6189 (mmt) REVERT: B 285 MET cc_start: 0.8032 (mmt) cc_final: 0.7384 (mmt) REVERT: E 214 MET cc_start: 0.6508 (mmt) cc_final: 0.6166 (mmt) REVERT: F 285 MET cc_start: 0.7993 (mmt) cc_final: 0.7333 (mmt) outliers start: 4 outliers final: 0 residues processed: 233 average time/residue: 0.1464 time to fit residues: 50.7726 Evaluate side-chains 193 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.0570 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112763 restraints weight = 22485.945| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.71 r_work: 0.3124 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18948 Z= 0.128 Angle : 0.515 7.142 25604 Z= 0.277 Chirality : 0.042 0.179 2854 Planarity : 0.005 0.047 3244 Dihedral : 6.896 74.111 2710 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.72 % Allowed : 6.36 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.17), residues: 2326 helix: 1.98 (0.15), residues: 1134 sheet: -0.09 (0.35), residues: 226 loop : -0.21 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.014 0.001 TYR D 26 PHE 0.016 0.001 PHE E 168 TRP 0.013 0.001 TRP G 32 HIS 0.005 0.001 HIS H 143 Details of bonding type rmsd covalent geometry : bond 0.00289 (18946) covalent geometry : angle 0.51545 (25604) hydrogen bonds : bond 0.04599 ( 953) hydrogen bonds : angle 4.61027 ( 2727) Misc. bond : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.694 Fit side-chains REVERT: A 55 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8373 (pttp) REVERT: A 150 ASP cc_start: 0.7328 (m-30) cc_final: 0.7108 (m-30) REVERT: B 285 MET cc_start: 0.8198 (mmt) cc_final: 0.7661 (mmt) REVERT: B 423 MET cc_start: 0.8505 (ttm) cc_final: 0.8249 (mtt) REVERT: D 79 LYS cc_start: 0.8389 (mmmm) cc_final: 0.7879 (tppt) REVERT: D 89 MET cc_start: 0.8681 (ttm) cc_final: 0.8461 (ttm) REVERT: E 55 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8351 (pttp) REVERT: E 150 ASP cc_start: 0.7333 (m-30) cc_final: 0.7124 (m-30) REVERT: H 79 LYS cc_start: 0.8376 (mmmm) cc_final: 0.7812 (tppt) REVERT: H 89 MET cc_start: 0.8683 (ttm) cc_final: 0.8445 (ttm) REVERT: F 285 MET cc_start: 0.8198 (mmt) cc_final: 0.7641 (mmt) REVERT: F 423 MET cc_start: 0.8499 (ttm) cc_final: 0.8237 (mtt) outliers start: 14 outliers final: 8 residues processed: 215 average time/residue: 0.1518 time to fit residues: 48.2551 Evaluate side-chains 207 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 296 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111525 restraints weight = 22987.450| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.52 r_work: 0.3162 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18948 Z= 0.220 Angle : 0.584 6.963 25604 Z= 0.311 Chirality : 0.046 0.180 2854 Planarity : 0.005 0.051 3244 Dihedral : 6.804 72.229 2710 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.34 % Allowed : 8.58 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2326 helix: 1.75 (0.15), residues: 1124 sheet: -0.24 (0.35), residues: 224 loop : -0.47 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 136 TYR 0.016 0.002 TYR D 26 PHE 0.018 0.002 PHE E 209 TRP 0.015 0.002 TRP G 32 HIS 0.006 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00539 (18946) covalent geometry : angle 0.58446 (25604) hydrogen bonds : bond 0.05455 ( 953) hydrogen bonds : angle 4.60255 ( 2727) Misc. bond : bond 0.00110 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: B 281 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8557 (mptt) REVERT: B 285 MET cc_start: 0.8270 (mmt) cc_final: 0.7541 (mmt) REVERT: F 281 LYS cc_start: 0.9010 (mtpt) cc_final: 0.8547 (mptt) REVERT: F 285 MET cc_start: 0.8223 (mmt) cc_final: 0.7471 (mmt) outliers start: 26 outliers final: 15 residues processed: 218 average time/residue: 0.1427 time to fit residues: 46.8507 Evaluate side-chains 205 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 296 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 192 optimal weight: 0.0060 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 200 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN E 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110915 restraints weight = 22808.382| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.74 r_work: 0.3112 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18948 Z= 0.132 Angle : 0.498 7.077 25604 Z= 0.268 Chirality : 0.042 0.169 2854 Planarity : 0.005 0.050 3244 Dihedral : 6.422 73.854 2710 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.40 % Allowed : 9.98 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.17), residues: 2326 helix: 1.94 (0.15), residues: 1134 sheet: 0.04 (0.32), residues: 248 loop : -0.32 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 459 TYR 0.013 0.001 TYR D 26 PHE 0.014 0.001 PHE H 115 TRP 0.015 0.001 TRP C 32 HIS 0.004 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00310 (18946) covalent geometry : angle 0.49845 (25604) hydrogen bonds : bond 0.04319 ( 953) hydrogen bonds : angle 4.40034 ( 2727) Misc. bond : bond 0.00078 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7749 (tp40) cc_final: 0.7289 (tt0) REVERT: B 126 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8619 (tt) REVERT: D 79 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8341 (tttm) REVERT: D 113 THR cc_start: 0.8137 (t) cc_final: 0.7805 (p) REVERT: E 407 GLN cc_start: 0.7760 (tp40) cc_final: 0.7285 (tt0) REVERT: H 79 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8319 (tttm) REVERT: H 113 THR cc_start: 0.8038 (t) cc_final: 0.7725 (p) REVERT: F 126 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8610 (tt) outliers start: 27 outliers final: 16 residues processed: 214 average time/residue: 0.1372 time to fit residues: 44.4829 Evaluate side-chains 209 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 296 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 141 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 231 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110456 restraints weight = 22587.629| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.87 r_work: 0.3119 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18948 Z= 0.118 Angle : 0.482 7.584 25604 Z= 0.259 Chirality : 0.041 0.164 2854 Planarity : 0.004 0.048 3244 Dihedral : 6.180 72.823 2710 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.71 % Allowed : 10.75 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.17), residues: 2326 helix: 2.10 (0.15), residues: 1134 sheet: 0.26 (0.32), residues: 246 loop : -0.27 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 459 TYR 0.012 0.001 TYR H 26 PHE 0.013 0.001 PHE E 168 TRP 0.014 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00269 (18946) covalent geometry : angle 0.48186 (25604) hydrogen bonds : bond 0.04010 ( 953) hydrogen bonds : angle 4.30411 ( 2727) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.757 Fit side-chains REVERT: A 150 ASP cc_start: 0.7309 (m-30) cc_final: 0.7079 (m-30) REVERT: A 407 GLN cc_start: 0.7673 (tp40) cc_final: 0.7113 (tt0) REVERT: B 285 MET cc_start: 0.8086 (mmt) cc_final: 0.7610 (mmt) REVERT: D 79 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8347 (tttm) REVERT: D 89 MET cc_start: 0.8654 (ttm) cc_final: 0.8449 (ttm) REVERT: D 113 THR cc_start: 0.8100 (t) cc_final: 0.7773 (p) REVERT: D 119 TYR cc_start: 0.7216 (m-80) cc_final: 0.6688 (m-80) REVERT: E 407 GLN cc_start: 0.7674 (tp40) cc_final: 0.7130 (tt0) REVERT: H 79 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8337 (tttm) REVERT: H 113 THR cc_start: 0.8008 (t) cc_final: 0.7694 (p) REVERT: F 126 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8582 (tt) REVERT: F 285 MET cc_start: 0.8082 (mmt) cc_final: 0.7608 (mmt) outliers start: 33 outliers final: 19 residues processed: 225 average time/residue: 0.1418 time to fit residues: 48.4732 Evaluate side-chains 211 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 0.0370 chunk 223 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 211 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 441 GLN F 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111322 restraints weight = 22549.900| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.80 r_work: 0.3147 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18948 Z= 0.122 Angle : 0.487 8.358 25604 Z= 0.261 Chirality : 0.041 0.164 2854 Planarity : 0.004 0.049 3244 Dihedral : 6.144 74.292 2710 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.71 % Allowed : 11.58 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.17), residues: 2326 helix: 2.12 (0.15), residues: 1136 sheet: 0.07 (0.35), residues: 220 loop : -0.34 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 459 TYR 0.012 0.001 TYR D 26 PHE 0.017 0.001 PHE D 115 TRP 0.013 0.001 TRP G 32 HIS 0.005 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00283 (18946) covalent geometry : angle 0.48665 (25604) hydrogen bonds : bond 0.04010 ( 953) hydrogen bonds : angle 4.29374 ( 2727) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7627 (tp40) cc_final: 0.7128 (tt0) REVERT: B 126 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8584 (tt) REVERT: B 285 MET cc_start: 0.8109 (mmt) cc_final: 0.7667 (mmt) REVERT: D 79 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8410 (tttm) REVERT: D 89 MET cc_start: 0.8681 (ttm) cc_final: 0.8461 (ttm) REVERT: D 113 THR cc_start: 0.8116 (t) cc_final: 0.7784 (p) REVERT: E 407 GLN cc_start: 0.7678 (tp40) cc_final: 0.7174 (tt0) REVERT: H 79 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8398 (tttm) REVERT: H 113 THR cc_start: 0.8080 (t) cc_final: 0.7767 (p) REVERT: F 126 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8596 (tt) REVERT: F 285 MET cc_start: 0.8061 (mmt) cc_final: 0.7595 (mmt) outliers start: 33 outliers final: 21 residues processed: 223 average time/residue: 0.1443 time to fit residues: 48.4171 Evaluate side-chains 217 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 209 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 120 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 172 optimal weight: 0.0770 chunk 155 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 441 GLN F 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112223 restraints weight = 22770.868| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.83 r_work: 0.3145 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18948 Z= 0.114 Angle : 0.473 8.144 25604 Z= 0.254 Chirality : 0.041 0.163 2854 Planarity : 0.004 0.048 3244 Dihedral : 6.049 74.197 2710 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.76 % Allowed : 12.00 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.17), residues: 2326 helix: 2.17 (0.15), residues: 1138 sheet: 0.08 (0.35), residues: 220 loop : -0.31 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 459 TYR 0.012 0.001 TYR D 26 PHE 0.012 0.001 PHE A 168 TRP 0.013 0.001 TRP G 32 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00263 (18946) covalent geometry : angle 0.47340 (25604) hydrogen bonds : bond 0.03833 ( 953) hydrogen bonds : angle 4.23359 ( 2727) Misc. bond : bond 0.00067 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.594 Fit side-chains REVERT: B 126 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8561 (tt) REVERT: B 281 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8237 (mmtt) REVERT: B 285 MET cc_start: 0.8092 (mmt) cc_final: 0.7693 (mmt) REVERT: D 79 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8312 (tttm) REVERT: D 89 MET cc_start: 0.8652 (ttm) cc_final: 0.8435 (ttm) REVERT: D 113 THR cc_start: 0.8114 (t) cc_final: 0.7787 (p) REVERT: E 407 GLN cc_start: 0.7635 (tp40) cc_final: 0.7073 (tt0) REVERT: H 79 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8464 (tttm) REVERT: H 113 THR cc_start: 0.8077 (t) cc_final: 0.7761 (p) REVERT: F 126 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8571 (tt) REVERT: F 281 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8239 (mmtt) REVERT: F 285 MET cc_start: 0.8111 (mmt) cc_final: 0.7674 (mmt) outliers start: 34 outliers final: 21 residues processed: 221 average time/residue: 0.1480 time to fit residues: 48.9896 Evaluate side-chains 212 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 218 optimal weight: 0.0970 chunk 144 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 124 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 226 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 GLN F 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113279 restraints weight = 22509.686| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.86 r_work: 0.3157 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18948 Z= 0.102 Angle : 0.478 9.582 25604 Z= 0.254 Chirality : 0.041 0.187 2854 Planarity : 0.004 0.048 3244 Dihedral : 5.960 74.127 2710 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.65 % Allowed : 12.46 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.17), residues: 2326 helix: 2.26 (0.15), residues: 1138 sheet: 0.12 (0.35), residues: 220 loop : -0.28 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 459 TYR 0.011 0.001 TYR D 26 PHE 0.019 0.001 PHE D 115 TRP 0.013 0.001 TRP G 32 HIS 0.003 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00224 (18946) covalent geometry : angle 0.47828 (25604) hydrogen bonds : bond 0.03592 ( 953) hydrogen bonds : angle 4.23870 ( 2727) Misc. bond : bond 0.00058 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.624 Fit side-chains REVERT: A 150 ASP cc_start: 0.7265 (m-30) cc_final: 0.7038 (m-30) REVERT: A 407 GLN cc_start: 0.7573 (tp40) cc_final: 0.7168 (tt0) REVERT: B 126 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8546 (tt) REVERT: B 281 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8194 (mmtt) REVERT: B 285 MET cc_start: 0.8074 (mmt) cc_final: 0.7674 (mmt) REVERT: D 79 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8304 (tttm) REVERT: D 113 THR cc_start: 0.8066 (t) cc_final: 0.7756 (p) REVERT: E 150 ASP cc_start: 0.7259 (m-30) cc_final: 0.7030 (m-30) REVERT: E 407 GLN cc_start: 0.7679 (tp40) cc_final: 0.7095 (tt0) REVERT: G 13 MET cc_start: 0.6763 (tpt) cc_final: 0.5737 (mpp) REVERT: H 79 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8285 (tttm) REVERT: H 113 THR cc_start: 0.8023 (t) cc_final: 0.7726 (p) REVERT: F 281 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8196 (mmtt) REVERT: F 285 MET cc_start: 0.8075 (mmt) cc_final: 0.7673 (mmt) outliers start: 32 outliers final: 19 residues processed: 223 average time/residue: 0.1427 time to fit residues: 47.7934 Evaluate side-chains 213 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 0 optimal weight: 50.0000 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 168 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 chunk 213 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 GLN F 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118675 restraints weight = 22514.371| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.53 r_work: 0.3113 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18948 Z= 0.118 Angle : 0.496 13.272 25604 Z= 0.265 Chirality : 0.042 0.184 2854 Planarity : 0.004 0.056 3244 Dihedral : 5.988 75.513 2710 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.45 % Allowed : 12.56 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.17), residues: 2326 helix: 2.23 (0.15), residues: 1142 sheet: 0.13 (0.35), residues: 220 loop : -0.34 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 459 TYR 0.011 0.001 TYR D 26 PHE 0.014 0.001 PHE A 168 TRP 0.012 0.001 TRP G 32 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00269 (18946) covalent geometry : angle 0.49598 (25604) hydrogen bonds : bond 0.03797 ( 953) hydrogen bonds : angle 4.24211 ( 2727) Misc. bond : bond 0.00067 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.687 Fit side-chains REVERT: B 126 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8586 (tt) REVERT: B 281 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8409 (mmtt) REVERT: B 285 MET cc_start: 0.8092 (mmt) cc_final: 0.7723 (mmt) REVERT: D 79 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8283 (tttm) REVERT: D 113 THR cc_start: 0.8079 (t) cc_final: 0.7761 (p) REVERT: E 407 GLN cc_start: 0.7693 (tp40) cc_final: 0.7206 (tt0) REVERT: G 13 MET cc_start: 0.6867 (tpt) cc_final: 0.5856 (mpp) REVERT: H 79 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8310 (tttm) REVERT: H 113 THR cc_start: 0.8065 (t) cc_final: 0.7760 (p) REVERT: F 126 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8568 (tt) REVERT: F 281 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8409 (mmtt) REVERT: F 285 MET cc_start: 0.8044 (mmt) cc_final: 0.7662 (mmt) outliers start: 28 outliers final: 21 residues processed: 218 average time/residue: 0.1399 time to fit residues: 46.2828 Evaluate side-chains 215 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 188 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 159 optimal weight: 0.0170 chunk 114 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 chunk 171 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 GLN ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.146209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119814 restraints weight = 22470.035| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.52 r_work: 0.3144 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18948 Z= 0.106 Angle : 0.475 10.118 25604 Z= 0.254 Chirality : 0.041 0.186 2854 Planarity : 0.004 0.049 3244 Dihedral : 5.907 74.705 2710 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.40 % Allowed : 12.67 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.17), residues: 2326 helix: 2.26 (0.15), residues: 1146 sheet: 0.19 (0.33), residues: 250 loop : -0.25 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 459 TYR 0.011 0.001 TYR D 26 PHE 0.020 0.001 PHE H 115 TRP 0.013 0.001 TRP G 32 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00237 (18946) covalent geometry : angle 0.47460 (25604) hydrogen bonds : bond 0.03581 ( 953) hydrogen bonds : angle 4.21229 ( 2727) Misc. bond : bond 0.00060 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.691 Fit side-chains REVERT: A 25 LEU cc_start: 0.6862 (mm) cc_final: 0.6574 (mp) REVERT: B 126 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8548 (tt) REVERT: B 281 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8404 (mmtt) REVERT: B 285 MET cc_start: 0.8015 (mmt) cc_final: 0.7689 (mmt) REVERT: C 13 MET cc_start: 0.6891 (tpt) cc_final: 0.5864 (mpp) REVERT: D 79 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8098 (tttm) REVERT: D 113 THR cc_start: 0.8061 (t) cc_final: 0.7757 (p) REVERT: E 25 LEU cc_start: 0.6857 (mm) cc_final: 0.6574 (mp) REVERT: E 407 GLN cc_start: 0.7696 (tp40) cc_final: 0.7207 (tt0) REVERT: G 13 MET cc_start: 0.6889 (tpt) cc_final: 0.5919 (mpp) REVERT: H 79 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8088 (tttm) REVERT: H 113 THR cc_start: 0.8023 (t) cc_final: 0.7727 (p) REVERT: F 126 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8571 (tt) REVERT: F 281 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8415 (mmtt) REVERT: F 285 MET cc_start: 0.8064 (mmt) cc_final: 0.7723 (mmt) outliers start: 27 outliers final: 19 residues processed: 220 average time/residue: 0.1420 time to fit residues: 47.2019 Evaluate side-chains 214 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 101 optimal weight: 4.9990 chunk 94 optimal weight: 0.2980 chunk 169 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 217 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119445 restraints weight = 22585.294| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.59 r_work: 0.3139 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18948 Z= 0.109 Angle : 0.477 9.854 25604 Z= 0.257 Chirality : 0.041 0.189 2854 Planarity : 0.004 0.056 3244 Dihedral : 5.904 75.076 2710 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.45 % Allowed : 12.77 % Favored : 85.78 % 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 are not related in a simple way. whole: 1.54 (0.17), residues: 2326 helix: 2.24 (0.15), residues: 1148 sheet: 0.22 (0.33), residues: 250 loop : -0.27 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.011 0.001 TYR D 26 PHE 0.014 0.001 PHE E 168 TRP 0.012 0.001 TRP G 32 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00245 (18946) covalent geometry : angle 0.47732 (25604) hydrogen bonds : bond 0.03630 ( 953) hydrogen bonds : angle 4.20459 ( 2727) Misc. bond : bond 0.00060 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.93 seconds wall clock time: 82 minutes 50.96 seconds (4970.96 seconds total)