Starting phenix.real_space_refine on Sat Mar 7 09:15:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zbn_14587/03_2026/7zbn_14587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zbn_14587/03_2026/7zbn_14587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zbn_14587/03_2026/7zbn_14587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zbn_14587/03_2026/7zbn_14587.map" model { file = "/net/cci-nas-00/data/ceres_data/7zbn_14587/03_2026/7zbn_14587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zbn_14587/03_2026/7zbn_14587.cif" } resolution = 2.62 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 104 5.16 5 C 13520 2.51 5 N 3636 2.21 5 O 3860 1.98 5 H 20466 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 41588 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 9830 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 25, 'TRANS': 591} Chain breaks: 2 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: "B" Number of atoms: 9896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9896 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 26, 'TRANS': 594} Chain breaks: 2 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: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 534 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "F" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 534 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "C" Number of atoms: 9830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 9830 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 25, 'TRANS': 591} Chain breaks: 2 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: "D" Number of atoms: 9896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9896 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 26, 'TRANS': 594} Chain breaks: 2 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: "G" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 534 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "H" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 534 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Time building chain proxies: 7.29, per 1000 atoms: 0.18 Number of scatterers: 41588 At special positions: 0 Unit cell: (120.7, 108.63, 137.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 2 15.00 O 3860 8.00 N 3636 7.00 C 13520 6.00 H 20466 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4880 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 12 sheets defined 56.9% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 4.442A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 119 through 124 removed outlier: 5.026A pdb=" N TRP A 124 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 145 through 168 Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.714A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.516A pdb=" N ARG A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.656A pdb=" N ARG A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 294 through 312 Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 376 through 410 Processing helix chain 'A' and resid 415 through 420 removed outlier: 4.199A pdb=" N LEU A 420 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 559 through 577 Processing helix chain 'A' and resid 578 through 592 Processing helix chain 'A' and resid 593 through 596 Processing helix chain 'A' and resid 597 through 617 removed outlier: 5.237A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 59 removed outlier: 4.444A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 84 through 97 Processing helix chain 'B' and resid 119 through 124 removed outlier: 4.887A pdb=" N TRP B 124 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 145 through 168 Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.702A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLY B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 217 removed outlier: 3.740A pdb=" N ARG B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.725A pdb=" N ARG B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 376 through 410 Processing helix chain 'B' and resid 415 through 420 removed outlier: 4.224A pdb=" N LEU B 420 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 513 through 522 Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 544 through 548 Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 578 through 592 Processing helix chain 'B' and resid 593 through 596 Processing helix chain 'B' and resid 597 through 617 removed outlier: 5.238A pdb=" N ARG B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 320 through 331 removed outlier: 3.770A pdb=" N ILE E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 311 Processing helix chain 'F' and resid 320 through 330 removed outlier: 3.760A pdb=" N ILE F 324 " --> pdb=" O SER F 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.441A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 84 through 97 Processing helix chain 'C' and resid 119 through 124 removed outlier: 5.030A pdb=" N TRP C 124 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 145 through 168 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.712A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLY C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 removed outlier: 3.527A pdb=" N ARG C 211 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.657A pdb=" N ARG C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 259 through 270 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 376 through 410 Processing helix chain 'C' and resid 415 through 420 removed outlier: 4.189A pdb=" N LEU C 420 " --> pdb=" O MET C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 492 through 499 Processing helix chain 'C' and resid 513 through 522 Processing helix chain 'C' and resid 532 through 542 Processing helix chain 'C' and resid 544 through 548 Processing helix chain 'C' and resid 559 through 577 Processing helix chain 'C' and resid 578 through 592 Processing helix chain 'C' and resid 593 through 596 Processing helix chain 'C' and resid 597 through 617 removed outlier: 5.235A pdb=" N ARG C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 removed outlier: 4.446A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 84 through 97 Processing helix chain 'D' and resid 119 through 124 removed outlier: 4.885A pdb=" N TRP D 124 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 Processing helix chain 'D' and resid 145 through 168 Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.697A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 removed outlier: 3.733A pdb=" N ARG D 211 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 removed outlier: 3.701A pdb=" N ARG D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 259 through 270 Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 294 through 312 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 376 through 410 Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.225A pdb=" N LEU D 420 " --> pdb=" O MET D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 436 Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 492 through 499 Processing helix chain 'D' and resid 513 through 522 Processing helix chain 'D' and resid 532 through 542 Processing helix chain 'D' and resid 544 through 548 Processing helix chain 'D' and resid 559 through 577 Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 593 through 596 Processing helix chain 'D' and resid 597 through 617 removed outlier: 5.235A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 311 Processing helix chain 'G' and resid 320 through 331 removed outlier: 3.775A pdb=" N ILE G 324 " --> pdb=" O SER G 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 311 Processing helix chain 'H' and resid 320 through 330 removed outlier: 3.759A pdb=" N ILE H 324 " --> pdb=" O SER H 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 4.786A pdb=" N LYS A 100 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 62 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL A 115 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 64 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A 117 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY A 66 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 29 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 65 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 175 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE A 201 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA A 177 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR A 203 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE A 179 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL A 254 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR A 200 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR A 256 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE A 202 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 276 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 477 removed outlier: 9.032A pdb=" N LEU A 502 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR A 529 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER A 526 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU A 553 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER A 528 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 375 removed outlier: 6.325A pdb=" N ASN A 447 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 4.018A pdb=" N LEU B 113 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 29 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 65 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU B 31 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 175 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE B 201 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA B 177 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N THR B 203 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 179 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL B 254 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR B 200 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR B 256 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 202 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 276 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 477 removed outlier: 9.014A pdb=" N LEU B 502 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N THR B 529 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER B 526 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU B 553 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER B 528 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 372 through 375 removed outlier: 6.280A pdb=" N ASN B 447 " --> pdb=" O ASN B 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 79 removed outlier: 4.792A pdb=" N LYS C 100 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR C 62 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL C 115 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 64 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU C 117 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY C 66 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 29 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 65 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C 175 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE C 201 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA C 177 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR C 203 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE C 179 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL C 254 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR C 200 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR C 256 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE C 202 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 276 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 477 removed outlier: 9.034A pdb=" N LEU C 502 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR C 529 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER C 526 " --> pdb=" O TYR C 551 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU C 553 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER C 528 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 372 through 375 removed outlier: 6.317A pdb=" N ASN C 447 " --> pdb=" O ASN C 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 77 through 79 removed outlier: 4.019A pdb=" N LEU D 113 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU D 29 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL D 65 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU D 31 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 175 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE D 201 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA D 177 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N THR D 203 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE D 179 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL D 254 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR D 200 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR D 256 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE D 202 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 276 " --> pdb=" O PHE D 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 473 through 477 removed outlier: 9.011A pdb=" N LEU D 502 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N THR D 529 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER D 526 " --> pdb=" O TYR D 551 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU D 553 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER D 528 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 372 through 375 removed outlier: 6.286A pdb=" N ASN D 447 " --> pdb=" O ASN D 373 " (cutoff:3.500A) 1097 hydrogen bonds defined for protein. 3207 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: 11.35 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20414 1.03 - 1.23: 79 1.23 - 1.42: 9509 1.42 - 1.61: 11980 1.61 - 1.81: 156 Bond restraints: 42138 Sorted by residual: bond pdb=" CB THR B 589 " pdb=" CG2 THR B 589 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.90e+00 bond pdb=" CB THR D 589 " pdb=" CG2 THR D 589 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.86e+00 bond pdb=" CB THR A 589 " pdb=" CG2 THR A 589 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CB THR C 589 " pdb=" CG2 THR C 589 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" CG LEU B 188 " pdb=" CD1 LEU B 188 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.34e+00 ... (remaining 42133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 73556 1.36 - 2.73: 2012 2.73 - 4.09: 134 4.09 - 5.46: 18 5.46 - 6.82: 6 Bond angle restraints: 75726 Sorted by residual: angle pdb=" N GLU D 235 " pdb=" CA GLU D 235 " pdb=" CB GLU D 235 " ideal model delta sigma weight residual 110.32 114.99 -4.67 1.70e+00 3.46e-01 7.54e+00 angle pdb=" N GLU B 235 " pdb=" CA GLU B 235 " pdb=" CB GLU B 235 " ideal model delta sigma weight residual 110.32 114.92 -4.60 1.70e+00 3.46e-01 7.33e+00 angle pdb=" N ALA C 206 " pdb=" CA ALA C 206 " pdb=" C ALA C 206 " ideal model delta sigma weight residual 110.80 106.51 4.29 2.13e+00 2.20e-01 4.05e+00 angle pdb=" N ALA A 206 " pdb=" CA ALA A 206 " pdb=" C ALA A 206 " ideal model delta sigma weight residual 110.80 106.55 4.25 2.13e+00 2.20e-01 3.98e+00 angle pdb=" CA LEU C 282 " pdb=" CB LEU C 282 " pdb=" CG LEU C 282 " ideal model delta sigma weight residual 116.30 123.12 -6.82 3.50e+00 8.16e-02 3.80e+00 ... (remaining 75721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 17800 17.40 - 34.81: 1486 34.81 - 52.21: 437 52.21 - 69.61: 175 69.61 - 87.01: 36 Dihedral angle restraints: 19934 sinusoidal: 10518 harmonic: 9416 Sorted by residual: dihedral pdb=" CA ASP A 219 " pdb=" C ASP A 219 " pdb=" N PHE A 220 " pdb=" CA PHE A 220 " ideal model delta harmonic sigma weight residual -180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASP C 219 " pdb=" C ASP C 219 " pdb=" N PHE C 220 " pdb=" CA PHE C 220 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP B 561 " pdb=" CB ASP B 561 " pdb=" CG ASP B 561 " pdb=" OD1 ASP B 561 " ideal model delta sinusoidal sigma weight residual -30.00 -85.95 55.95 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 19931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2775 0.064 - 0.128: 320 0.128 - 0.192: 13 0.192 - 0.256: 0 0.256 - 0.320: 2 Chirality restraints: 3110 Sorted by residual: chirality pdb=" CB ILE C 524 " pdb=" CA ILE C 524 " pdb=" CG1 ILE C 524 " pdb=" CG2 ILE C 524 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE A 524 " pdb=" CA ILE A 524 " pdb=" CG1 ILE A 524 " pdb=" CG2 ILE A 524 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA HIS D 180 " pdb=" N HIS D 180 " pdb=" C HIS D 180 " pdb=" CB HIS D 180 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 3107 not shown) Planarity restraints: 6276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 585 " 0.008 2.00e-02 2.50e+03 1.46e-02 3.20e+00 pdb=" CD GLN D 585 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN D 585 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN D 585 " 0.006 2.00e-02 2.50e+03 pdb="HE21 GLN D 585 " 0.003 2.00e-02 2.50e+03 pdb="HE22 GLN D 585 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 585 " -0.008 2.00e-02 2.50e+03 1.28e-02 2.46e+00 pdb=" CD GLN B 585 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLN B 585 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN B 585 " -0.005 2.00e-02 2.50e+03 pdb="HE21 GLN B 585 " -0.003 2.00e-02 2.50e+03 pdb="HE22 GLN B 585 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 591 " 0.134 9.50e-02 1.11e+02 4.49e-02 2.29e+00 pdb=" NE ARG D 591 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG D 591 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 591 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 591 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG D 591 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG D 591 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 591 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 591 " -0.000 2.00e-02 2.50e+03 ... (remaining 6273 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 2728 2.18 - 2.79: 87903 2.79 - 3.39: 130191 3.39 - 4.00: 175777 4.00 - 4.60: 270414 Nonbonded interactions: 667013 Sorted by model distance: nonbonded pdb=" O PRO D 506 " pdb="HH11 ARG D 555 " model vdw 1.578 2.450 nonbonded pdb=" O PRO B 506 " pdb="HH11 ARG B 555 " model vdw 1.583 2.450 nonbonded pdb=" O PRO A 506 " pdb="HH11 ARG A 555 " model vdw 1.591 2.450 nonbonded pdb=" O PRO C 506 " pdb="HH11 ARG C 555 " model vdw 1.592 2.450 nonbonded pdb=" OD2 ASP D 145 " pdb=" HE2 HIS D 240 " model vdw 1.610 2.450 ... (remaining 667008 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 13 through 637 or (resid 638 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)))) selection = chain 'C' selection = (chain 'D' and (resid 13 through 637 or (resid 638 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.090 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: 0.180 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 40.280 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 0.065 21672 Z= 0.247 Angle : 0.551 6.825 29356 Z= 0.299 Chirality : 0.041 0.320 3110 Planarity : 0.004 0.060 3790 Dihedral : 15.388 87.014 7866 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.17), residues: 2572 helix: 0.71 (0.13), residues: 1352 sheet: -1.53 (0.25), residues: 376 loop : 0.56 (0.24), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 194 TYR 0.014 0.002 TYR D 332 PHE 0.019 0.002 PHE B 307 TRP 0.013 0.002 TRP B 129 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00550 (21672) covalent geometry : angle 0.55119 (29356) hydrogen bonds : bond 0.12444 ( 1097) hydrogen bonds : angle 6.59121 ( 3207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7825 (ttt) cc_final: 0.7526 (ttm) REVERT: B 88 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7794 (ttmm) REVERT: B 92 ASP cc_start: 0.7085 (m-30) cc_final: 0.6884 (m-30) REVERT: B 427 MET cc_start: 0.7814 (ttt) cc_final: 0.7534 (ttm) REVERT: C 427 MET cc_start: 0.7817 (ttt) cc_final: 0.7518 (ttm) REVERT: D 88 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7775 (ttmm) REVERT: D 92 ASP cc_start: 0.7031 (m-30) cc_final: 0.6825 (m-30) REVERT: D 246 ARG cc_start: 0.8286 (ttt180) cc_final: 0.8078 (ttt180) REVERT: D 427 MET cc_start: 0.7820 (ttt) cc_final: 0.7528 (ttm) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 1.4524 time to fit residues: 559.9744 Evaluate side-chains 295 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.174124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.145273 restraints weight = 54155.363| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.20 r_work: 0.3354 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21672 Z= 0.166 Angle : 0.510 5.159 29356 Z= 0.276 Chirality : 0.039 0.136 3110 Planarity : 0.004 0.034 3790 Dihedral : 4.994 74.244 2886 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.67 % Allowed : 7.47 % Favored : 91.86 % 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: 0.53 (0.17), residues: 2572 helix: 0.98 (0.13), residues: 1364 sheet: -2.07 (0.25), residues: 380 loop : 0.84 (0.24), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 272 TYR 0.011 0.001 TYR D 332 PHE 0.012 0.001 PHE D 307 TRP 0.012 0.001 TRP E 308 HIS 0.006 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00349 (21672) covalent geometry : angle 0.50984 (29356) hydrogen bonds : bond 0.04807 ( 1097) hydrogen bonds : angle 5.21873 ( 3207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 318 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.8268 (ttt) cc_final: 0.7992 (ttm) REVERT: B 88 LYS cc_start: 0.8001 (ttpp) cc_final: 0.7560 (ttmm) REVERT: B 92 ASP cc_start: 0.7481 (m-30) cc_final: 0.7167 (m-30) REVERT: B 181 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6412 (mp0) REVERT: B 245 GLU cc_start: 0.8246 (tt0) cc_final: 0.8022 (tt0) REVERT: B 427 MET cc_start: 0.8203 (ttt) cc_final: 0.7922 (ttm) REVERT: C 427 MET cc_start: 0.8238 (ttt) cc_final: 0.7952 (ttm) REVERT: D 88 LYS cc_start: 0.8021 (ttpp) cc_final: 0.7553 (ttmm) REVERT: D 92 ASP cc_start: 0.7444 (m-30) cc_final: 0.7116 (m-30) REVERT: D 147 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6463 (mm-30) REVERT: D 181 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: D 427 MET cc_start: 0.8185 (ttt) cc_final: 0.7906 (ttm) outliers start: 15 outliers final: 1 residues processed: 328 average time/residue: 1.4614 time to fit residues: 538.9613 Evaluate side-chains 298 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 294 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 436 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 185 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 436 GLN B 38 ASN B 436 GLN C 38 ASN C 436 GLN D 38 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.171844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142480 restraints weight = 53993.071| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.21 r_work: 0.3336 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21672 Z= 0.228 Angle : 0.536 5.024 29356 Z= 0.289 Chirality : 0.040 0.138 3110 Planarity : 0.004 0.045 3790 Dihedral : 5.071 71.402 2886 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.34 % Allowed : 8.68 % Favored : 89.98 % 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: 0.50 (0.17), residues: 2572 helix: 0.95 (0.13), residues: 1364 sheet: -2.13 (0.25), residues: 360 loop : 0.78 (0.24), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 74 TYR 0.010 0.002 TYR B 332 PHE 0.018 0.002 PHE D 307 TRP 0.013 0.002 TRP E 308 HIS 0.005 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00500 (21672) covalent geometry : angle 0.53622 (29356) hydrogen bonds : bond 0.04947 ( 1097) hydrogen bonds : angle 5.13698 ( 3207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 299 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LYS cc_start: 0.7489 (tttt) cc_final: 0.6914 (ttpp) REVERT: A 427 MET cc_start: 0.8296 (ttt) cc_final: 0.8026 (ttm) REVERT: A 443 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7719 (t) REVERT: B 88 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7601 (ttmm) REVERT: B 92 ASP cc_start: 0.7541 (m-30) cc_final: 0.7224 (m-30) REVERT: B 147 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7069 (mt-10) REVERT: B 181 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6498 (mp0) REVERT: B 422 LYS cc_start: 0.7456 (tttt) cc_final: 0.6979 (ttpp) REVERT: B 427 MET cc_start: 0.8202 (ttt) cc_final: 0.7930 (ttm) REVERT: B 443 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7653 (t) REVERT: C 422 LYS cc_start: 0.7476 (tttt) cc_final: 0.6924 (ttpp) REVERT: C 427 MET cc_start: 0.8259 (ttt) cc_final: 0.7978 (ttm) REVERT: C 443 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7681 (t) REVERT: D 88 LYS cc_start: 0.8022 (ttpp) cc_final: 0.7575 (ttmm) REVERT: D 92 ASP cc_start: 0.7499 (m-30) cc_final: 0.7177 (m-30) REVERT: D 147 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6481 (mm-30) REVERT: D 181 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: D 422 LYS cc_start: 0.7457 (tttt) cc_final: 0.6984 (ttpp) REVERT: D 427 MET cc_start: 0.8209 (ttt) cc_final: 0.7934 (ttm) REVERT: D 443 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7680 (t) REVERT: G 309 GLU cc_start: 0.5937 (mp0) cc_final: 0.5649 (mp0) outliers start: 30 outliers final: 5 residues processed: 315 average time/residue: 1.5281 time to fit residues: 537.4459 Evaluate side-chains 303 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 291 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 443 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 134 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 256 optimal weight: 20.0000 chunk 170 optimal weight: 4.9990 chunk 8 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN B 585 GLN C 38 ASN D 436 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.172126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.143523 restraints weight = 53818.487| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.18 r_work: 0.3339 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21672 Z= 0.217 Angle : 0.529 5.015 29356 Z= 0.283 Chirality : 0.040 0.135 3110 Planarity : 0.004 0.040 3790 Dihedral : 5.055 72.477 2886 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.52 % Allowed : 9.08 % Favored : 89.40 % 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: 0.49 (0.17), residues: 2572 helix: 0.97 (0.13), residues: 1364 sheet: -2.22 (0.26), residues: 360 loop : 0.79 (0.24), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 638 TYR 0.009 0.002 TYR C 325 PHE 0.017 0.002 PHE D 307 TRP 0.012 0.001 TRP G 308 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00475 (21672) covalent geometry : angle 0.52857 (29356) hydrogen bonds : bond 0.04796 ( 1097) hydrogen bonds : angle 5.03893 ( 3207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 315 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: A 296 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7960 (mp) REVERT: A 422 LYS cc_start: 0.7476 (tttt) cc_final: 0.6859 (tmmt) REVERT: A 427 MET cc_start: 0.8295 (ttt) cc_final: 0.8031 (ttm) REVERT: A 443 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7687 (t) REVERT: B 88 LYS cc_start: 0.8024 (ttpp) cc_final: 0.7593 (ttmm) REVERT: B 92 ASP cc_start: 0.7578 (m-30) cc_final: 0.7271 (m-30) REVERT: B 181 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6502 (mp0) REVERT: B 296 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7904 (mp) REVERT: B 422 LYS cc_start: 0.7450 (tttt) cc_final: 0.6908 (tmmt) REVERT: B 427 MET cc_start: 0.8243 (ttt) cc_final: 0.7978 (ttm) REVERT: B 443 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7635 (t) REVERT: E 309 GLU cc_start: 0.5851 (mm-30) cc_final: 0.5615 (mp0) REVERT: C 181 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: C 296 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7936 (mp) REVERT: C 422 LYS cc_start: 0.7493 (tttt) cc_final: 0.6839 (tmmt) REVERT: C 427 MET cc_start: 0.8260 (ttt) cc_final: 0.7993 (ttm) REVERT: C 443 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7639 (t) REVERT: D 88 LYS cc_start: 0.7985 (ttpp) cc_final: 0.7729 (mtpp) REVERT: D 92 ASP cc_start: 0.7563 (m-30) cc_final: 0.7270 (m-30) REVERT: D 147 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6517 (mm-30) REVERT: D 181 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: D 296 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7916 (mp) REVERT: D 422 LYS cc_start: 0.7450 (tttt) cc_final: 0.6979 (ttpp) REVERT: D 427 MET cc_start: 0.8226 (ttt) cc_final: 0.7957 (ttm) REVERT: D 443 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7658 (t) outliers start: 34 outliers final: 10 residues processed: 328 average time/residue: 1.5530 time to fit residues: 570.7093 Evaluate side-chains 310 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 287 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 562 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 200 optimal weight: 0.0060 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN C 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.172313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143714 restraints weight = 53863.172| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.18 r_work: 0.3330 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21672 Z= 0.205 Angle : 0.525 6.174 29356 Z= 0.280 Chirality : 0.039 0.137 3110 Planarity : 0.004 0.050 3790 Dihedral : 5.015 72.734 2886 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.70 % Allowed : 10.42 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2572 helix: 1.02 (0.13), residues: 1364 sheet: -2.28 (0.26), residues: 360 loop : 0.79 (0.25), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 74 TYR 0.009 0.002 TYR C 332 PHE 0.016 0.002 PHE C 307 TRP 0.011 0.001 TRP G 308 HIS 0.005 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00448 (21672) covalent geometry : angle 0.52548 (29356) hydrogen bonds : bond 0.04678 ( 1097) hydrogen bonds : angle 4.96900 ( 3207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 300 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: A 296 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7974 (mp) REVERT: A 419 MET cc_start: 0.8304 (mmt) cc_final: 0.7952 (mmt) REVERT: A 422 LYS cc_start: 0.7496 (tttt) cc_final: 0.6864 (tmmt) REVERT: A 427 MET cc_start: 0.8281 (ttt) cc_final: 0.8021 (ttm) REVERT: A 443 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7670 (t) REVERT: B 88 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7564 (ttmm) REVERT: B 92 ASP cc_start: 0.7690 (m-30) cc_final: 0.7378 (m-30) REVERT: B 296 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7939 (mp) REVERT: B 422 LYS cc_start: 0.7471 (tttt) cc_final: 0.6908 (tmmt) REVERT: B 427 MET cc_start: 0.8235 (ttt) cc_final: 0.7980 (ttm) REVERT: B 443 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7646 (t) REVERT: C 181 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: C 296 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7937 (mp) REVERT: C 422 LYS cc_start: 0.7503 (tttt) cc_final: 0.6889 (tmmt) REVERT: C 427 MET cc_start: 0.8254 (ttt) cc_final: 0.7994 (ttm) REVERT: C 443 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7643 (t) REVERT: D 88 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7753 (mtpp) REVERT: D 92 ASP cc_start: 0.7641 (m-30) cc_final: 0.7329 (m-30) REVERT: D 147 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6545 (mm-30) REVERT: D 181 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6536 (mp0) REVERT: D 296 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7956 (mp) REVERT: D 422 LYS cc_start: 0.7472 (tttt) cc_final: 0.6897 (tmmt) REVERT: D 427 MET cc_start: 0.8246 (ttt) cc_final: 0.7984 (ttm) REVERT: D 443 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7661 (t) outliers start: 38 outliers final: 14 residues processed: 317 average time/residue: 1.5682 time to fit residues: 555.1745 Evaluate side-chains 312 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 436 GLN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 436 GLN Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 562 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 31 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN C 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.172833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.144372 restraints weight = 53950.407| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.18 r_work: 0.3339 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21672 Z= 0.189 Angle : 0.517 5.090 29356 Z= 0.274 Chirality : 0.039 0.139 3110 Planarity : 0.004 0.033 3790 Dihedral : 4.958 73.147 2886 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.52 % Allowed : 11.09 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2572 helix: 1.10 (0.13), residues: 1364 sheet: -2.35 (0.25), residues: 370 loop : 0.83 (0.25), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 74 TYR 0.009 0.002 TYR D 332 PHE 0.015 0.002 PHE D 307 TRP 0.012 0.001 TRP G 308 HIS 0.005 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00412 (21672) covalent geometry : angle 0.51718 (29356) hydrogen bonds : bond 0.04554 ( 1097) hydrogen bonds : angle 4.90242 ( 3207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: A 296 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8044 (mp) REVERT: A 422 LYS cc_start: 0.7517 (tttt) cc_final: 0.6850 (tmmt) REVERT: A 427 MET cc_start: 0.8288 (ttt) cc_final: 0.8038 (ttm) REVERT: A 443 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7629 (t) REVERT: B 88 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7564 (ttmm) REVERT: B 92 ASP cc_start: 0.7703 (m-30) cc_final: 0.7390 (m-30) REVERT: B 296 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8036 (mp) REVERT: B 422 LYS cc_start: 0.7476 (tttt) cc_final: 0.6896 (tmmt) REVERT: B 427 MET cc_start: 0.8232 (ttt) cc_final: 0.7949 (ttm) REVERT: B 443 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7623 (t) REVERT: C 296 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8046 (mp) REVERT: C 422 LYS cc_start: 0.7488 (tttt) cc_final: 0.6869 (tmmt) REVERT: C 427 MET cc_start: 0.8271 (ttt) cc_final: 0.8015 (ttm) REVERT: C 443 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7605 (t) REVERT: D 88 LYS cc_start: 0.7984 (ttpp) cc_final: 0.7743 (mtpp) REVERT: D 92 ASP cc_start: 0.7651 (m-30) cc_final: 0.7339 (m-30) REVERT: D 147 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6527 (mm-30) REVERT: D 296 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8023 (mp) REVERT: D 422 LYS cc_start: 0.7488 (tttt) cc_final: 0.6913 (tmmt) REVERT: D 427 MET cc_start: 0.8257 (ttt) cc_final: 0.8004 (ttm) REVERT: D 443 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7663 (t) outliers start: 34 outliers final: 15 residues processed: 312 average time/residue: 1.5878 time to fit residues: 552.9997 Evaluate side-chains 304 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 279 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 436 GLN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 436 GLN Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 562 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN B 38 ASN C 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.173786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.144596 restraints weight = 53743.622| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.21 r_work: 0.3345 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21672 Z= 0.166 Angle : 0.505 5.461 29356 Z= 0.266 Chirality : 0.038 0.139 3110 Planarity : 0.004 0.034 3790 Dihedral : 4.878 73.715 2886 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.39 % Allowed : 11.90 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2572 helix: 1.20 (0.13), residues: 1364 sheet: -2.41 (0.25), residues: 380 loop : 0.88 (0.25), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 74 TYR 0.008 0.001 TYR A 508 PHE 0.013 0.001 PHE D 307 TRP 0.011 0.001 TRP G 308 HIS 0.004 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00363 (21672) covalent geometry : angle 0.50477 (29356) hydrogen bonds : bond 0.04372 ( 1097) hydrogen bonds : angle 4.81278 ( 3207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 294 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 422 LYS cc_start: 0.7515 (tttt) cc_final: 0.6849 (tmmt) REVERT: A 427 MET cc_start: 0.8284 (ttt) cc_final: 0.8030 (ttm) REVERT: A 443 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7565 (t) REVERT: B 88 LYS cc_start: 0.8005 (ttpp) cc_final: 0.7559 (ttmm) REVERT: B 92 ASP cc_start: 0.7682 (m-30) cc_final: 0.7366 (m-30) REVERT: B 147 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6493 (mm-30) REVERT: B 296 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8037 (mp) REVERT: B 422 LYS cc_start: 0.7481 (tttt) cc_final: 0.6896 (tmmt) REVERT: B 427 MET cc_start: 0.8258 (ttt) cc_final: 0.7984 (ttm) REVERT: B 443 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7573 (t) REVERT: C 181 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: C 296 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8097 (mp) REVERT: C 427 MET cc_start: 0.8288 (ttt) cc_final: 0.8041 (ttm) REVERT: C 443 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7552 (t) REVERT: D 147 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6514 (mm-30) REVERT: D 296 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8037 (mp) REVERT: D 422 LYS cc_start: 0.7476 (tttt) cc_final: 0.6902 (tmmt) REVERT: D 427 MET cc_start: 0.8250 (ttt) cc_final: 0.7990 (ttm) REVERT: D 443 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7630 (t) outliers start: 31 outliers final: 12 residues processed: 311 average time/residue: 1.6127 time to fit residues: 558.4728 Evaluate side-chains 300 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 277 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 436 GLN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 436 GLN Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 562 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 112 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 192 optimal weight: 0.0970 chunk 88 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN C 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.174343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.145307 restraints weight = 53955.343| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.21 r_work: 0.3357 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21672 Z= 0.159 Angle : 0.508 6.398 29356 Z= 0.266 Chirality : 0.038 0.140 3110 Planarity : 0.004 0.075 3790 Dihedral : 4.820 73.740 2886 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.65 % Allowed : 11.99 % Favored : 86.36 % 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: 0.70 (0.17), residues: 2572 helix: 1.26 (0.13), residues: 1364 sheet: -2.45 (0.25), residues: 380 loop : 0.90 (0.25), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 74 TYR 0.008 0.001 TYR A 600 PHE 0.013 0.001 PHE D 307 TRP 0.010 0.001 TRP G 308 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00349 (21672) covalent geometry : angle 0.50793 (29356) hydrogen bonds : bond 0.04269 ( 1097) hydrogen bonds : angle 4.75778 ( 3207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 293 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8108 (mp) REVERT: A 422 LYS cc_start: 0.7517 (tttt) cc_final: 0.6822 (tmmt) REVERT: A 427 MET cc_start: 0.8288 (ttt) cc_final: 0.8030 (ttm) REVERT: A 443 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7550 (t) REVERT: B 88 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7567 (ttmm) REVERT: B 92 ASP cc_start: 0.7707 (m-30) cc_final: 0.7396 (m-30) REVERT: B 147 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6422 (mm-30) REVERT: B 296 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 422 LYS cc_start: 0.7486 (tttt) cc_final: 0.6874 (tmmt) REVERT: B 427 MET cc_start: 0.8269 (ttt) cc_final: 0.8016 (ttm) REVERT: B 443 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7539 (t) REVERT: C 296 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8072 (mp) REVERT: C 422 LYS cc_start: 0.7483 (tttt) cc_final: 0.6851 (tmmt) REVERT: C 427 MET cc_start: 0.8282 (ttt) cc_final: 0.8026 (ttm) REVERT: C 443 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7526 (t) REVERT: D 92 ASP cc_start: 0.7600 (m-30) cc_final: 0.7313 (m-30) REVERT: D 147 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6584 (mm-30) REVERT: D 296 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8083 (mp) REVERT: D 422 LYS cc_start: 0.7472 (tttt) cc_final: 0.6865 (tmmt) REVERT: D 427 MET cc_start: 0.8241 (ttt) cc_final: 0.7988 (ttm) REVERT: D 443 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7595 (t) outliers start: 37 outliers final: 11 residues processed: 312 average time/residue: 1.6099 time to fit residues: 560.3359 Evaluate side-chains 301 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 280 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 436 GLN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 436 GLN Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 562 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 228 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 242 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN C 38 ASN D 336 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.174697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.145722 restraints weight = 53870.226| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.21 r_work: 0.3360 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21672 Z= 0.156 Angle : 0.511 6.690 29356 Z= 0.266 Chirality : 0.038 0.139 3110 Planarity : 0.004 0.080 3790 Dihedral : 4.802 73.618 2886 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.16 % Allowed : 12.88 % Favored : 85.96 % 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: 0.73 (0.17), residues: 2572 helix: 1.29 (0.13), residues: 1376 sheet: -2.40 (0.25), residues: 376 loop : 0.86 (0.25), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 74 TYR 0.007 0.001 TYR C 221 PHE 0.013 0.001 PHE D 307 TRP 0.010 0.001 TRP G 308 HIS 0.004 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00344 (21672) covalent geometry : angle 0.51102 (29356) hydrogen bonds : bond 0.04222 ( 1097) hydrogen bonds : angle 4.70940 ( 3207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8102 (mp) REVERT: A 422 LYS cc_start: 0.7524 (tttt) cc_final: 0.6852 (tmmt) REVERT: A 427 MET cc_start: 0.8274 (ttt) cc_final: 0.8018 (ttm) REVERT: A 443 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7530 (t) REVERT: B 88 LYS cc_start: 0.8018 (ttpp) cc_final: 0.7585 (ttmm) REVERT: B 92 ASP cc_start: 0.7695 (m-30) cc_final: 0.7376 (m-30) REVERT: B 147 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6406 (mm-30) REVERT: B 296 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8088 (mp) REVERT: B 422 LYS cc_start: 0.7485 (tttt) cc_final: 0.6856 (tmmt) REVERT: B 427 MET cc_start: 0.8278 (ttt) cc_final: 0.8027 (ttm) REVERT: B 443 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7501 (t) REVERT: C 181 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: C 296 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8080 (mp) REVERT: C 422 LYS cc_start: 0.7482 (tttt) cc_final: 0.6864 (tmmt) REVERT: C 427 MET cc_start: 0.8288 (ttt) cc_final: 0.8032 (ttm) REVERT: C 443 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7496 (t) REVERT: D 92 ASP cc_start: 0.7625 (m-30) cc_final: 0.7333 (m-30) REVERT: D 147 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6589 (mm-30) REVERT: D 296 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8085 (mp) REVERT: D 422 LYS cc_start: 0.7463 (tttt) cc_final: 0.6866 (tmmt) REVERT: D 427 MET cc_start: 0.8257 (ttt) cc_final: 0.8008 (ttm) REVERT: D 443 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7564 (t) outliers start: 26 outliers final: 10 residues processed: 300 average time/residue: 1.6574 time to fit residues: 552.4463 Evaluate side-chains 295 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 436 GLN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 436 GLN Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 98 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 214 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 417 ASN B 336 ASN C 38 ASN D 336 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.174017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.145587 restraints weight = 53844.072| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.18 r_work: 0.3357 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21672 Z= 0.176 Angle : 0.530 9.176 29356 Z= 0.276 Chirality : 0.039 0.142 3110 Planarity : 0.005 0.077 3790 Dihedral : 4.826 72.661 2886 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.25 % Allowed : 13.15 % Favored : 85.60 % 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: 0.69 (0.17), residues: 2572 helix: 1.26 (0.13), residues: 1364 sheet: -2.42 (0.25), residues: 380 loop : 0.88 (0.25), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 74 TYR 0.008 0.001 TYR B 600 PHE 0.015 0.002 PHE D 307 TRP 0.010 0.001 TRP G 308 HIS 0.005 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00388 (21672) covalent geometry : angle 0.53005 (29356) hydrogen bonds : bond 0.04350 ( 1097) hydrogen bonds : angle 4.75350 ( 3207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8109 (mp) REVERT: A 422 LYS cc_start: 0.7522 (tttt) cc_final: 0.6876 (tmmt) REVERT: A 427 MET cc_start: 0.8259 (ttt) cc_final: 0.8007 (ttm) REVERT: A 443 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7526 (t) REVERT: B 88 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7603 (ttmm) REVERT: B 92 ASP cc_start: 0.7676 (m-30) cc_final: 0.7371 (m-30) REVERT: B 146 ARG cc_start: 0.6979 (ttp-110) cc_final: 0.6741 (tmm160) REVERT: B 147 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6557 (mm-30) REVERT: B 296 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8096 (mp) REVERT: B 422 LYS cc_start: 0.7443 (tttt) cc_final: 0.6878 (tmmt) REVERT: B 427 MET cc_start: 0.8258 (ttt) cc_final: 0.8007 (ttm) REVERT: B 443 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7526 (t) REVERT: C 181 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: C 296 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8112 (mp) REVERT: C 422 LYS cc_start: 0.7474 (tttt) cc_final: 0.6844 (tmmt) REVERT: C 427 MET cc_start: 0.8256 (ttt) cc_final: 0.8004 (ttm) REVERT: C 443 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7496 (t) REVERT: D 92 ASP cc_start: 0.7594 (m-30) cc_final: 0.7292 (m-30) REVERT: D 146 ARG cc_start: 0.7040 (ttp-110) cc_final: 0.6750 (ttp-110) REVERT: D 147 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6596 (mm-30) REVERT: D 296 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8091 (mp) REVERT: D 422 LYS cc_start: 0.7443 (tttt) cc_final: 0.6877 (tmmt) REVERT: D 427 MET cc_start: 0.8208 (ttt) cc_final: 0.7956 (ttm) REVERT: D 443 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7587 (t) outliers start: 28 outliers final: 13 residues processed: 292 average time/residue: 1.6659 time to fit residues: 540.5846 Evaluate side-chains 298 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 436 GLN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 562 ASP Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 436 GLN Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 561 ASP Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 562 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 209 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.171182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141819 restraints weight = 54245.233| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.30 r_work: 0.3328 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21672 Z= 0.239 Angle : 0.576 8.600 29356 Z= 0.303 Chirality : 0.041 0.184 3110 Planarity : 0.005 0.078 3790 Dihedral : 5.000 71.043 2886 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.07 % Allowed : 13.77 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2572 helix: 1.05 (0.13), residues: 1364 sheet: -2.41 (0.25), residues: 380 loop : 0.82 (0.25), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 74 TYR 0.010 0.002 TYR D 325 PHE 0.019 0.002 PHE D 307 TRP 0.012 0.002 TRP G 308 HIS 0.006 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00530 (21672) covalent geometry : angle 0.57618 (29356) hydrogen bonds : bond 0.04838 ( 1097) hydrogen bonds : angle 4.93921 ( 3207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14064.42 seconds wall clock time: 238 minutes 41.69 seconds (14321.69 seconds total)