Starting phenix.real_space_refine on Sat Jul 4 13:06:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b0s_11970/07_2026/7b0s_11970.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b0s_11970/07_2026/7b0s_11970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7b0s_11970/07_2026/7b0s_11970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b0s_11970/07_2026/7b0s_11970.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7b0s_11970/07_2026/7b0s_11970.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b0s_11970/07_2026/7b0s_11970.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b0s_11970/07_2026/7b0s_11970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b0s_11970/07_2026/7b0s_11970.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 Cl 4 4.86 5 C 13766 2.51 5 N 3452 2.21 5 O 3726 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21076 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5219 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 5219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5219 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 5215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5215 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 5219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5219 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' CA': 1, '44E': 1, 'S9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' CA': 1, '44E': 1, 'S9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' CA': 1, '44E': 1, 'S9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' CA': 1, '44E': 1, 'S9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.71, per 1000 atoms: 0.22 Number of scatterers: 21076 At special positions: 0 Unit cell: (139.23, 139.23, 137.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 4 19.99 Cl 4 17.00 S 108 16.00 P 4 15.00 F 12 9.00 O 3726 8.00 N 3452 7.00 C 13766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 782.3 milliseconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 0 sheets defined 73.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 45 through 59 removed outlier: 3.919A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 109 through 117 Processing helix chain 'A' and resid 144 through 152 removed outlier: 3.708A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 165 removed outlier: 3.624A pdb=" N GLN A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 215 through 234 removed outlier: 4.075A pdb=" N LYS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 258 removed outlier: 3.919A pdb=" N HIS A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 305 through 316 removed outlier: 3.703A pdb=" N ASP A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.690A pdb=" N VAL A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 350 removed outlier: 4.257A pdb=" N LEU A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 361 through 383 removed outlier: 3.730A pdb=" N ILE A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 Proline residue: A 408 - end of helix removed outlier: 4.663A pdb=" N ASP A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 457 removed outlier: 3.950A pdb=" N LEU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 472 through 492 removed outlier: 3.551A pdb=" N VAL A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 499 removed outlier: 4.122A pdb=" N THR A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 513 through 518 removed outlier: 4.404A pdb=" N LYS A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 539 removed outlier: 4.477A pdb=" N CYS A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 526 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 Processing helix chain 'A' and resid 590 through 612 Processing helix chain 'A' and resid 613 through 626 removed outlier: 3.889A pdb=" N ILE A 617 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A 619 " --> pdb=" O MET A 615 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 645 removed outlier: 3.829A pdb=" N SER A 645 " --> pdb=" O LYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 721 removed outlier: 3.598A pdb=" N TYR A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 721 " --> pdb=" O VAL A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 753 removed outlier: 3.500A pdb=" N PHE A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 45 through 59 removed outlier: 3.918A pdb=" N GLU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 144 through 152 removed outlier: 3.708A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 165 removed outlier: 3.624A pdb=" N GLN B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 215 through 234 removed outlier: 4.075A pdb=" N LYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 258 removed outlier: 3.919A pdb=" N HIS B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 305 through 316 removed outlier: 3.703A pdb=" N ASP B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.690A pdb=" N VAL B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 350 removed outlier: 4.258A pdb=" N LEU B 343 " --> pdb=" O MET B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 361 through 383 removed outlier: 3.731A pdb=" N ILE B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 Proline residue: B 408 - end of helix removed outlier: 4.663A pdb=" N ASP B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 457 removed outlier: 3.950A pdb=" N LEU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 468 Processing helix chain 'B' and resid 472 through 492 removed outlier: 3.551A pdb=" N VAL B 480 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 4.121A pdb=" N THR B 497 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 512 Processing helix chain 'B' and resid 513 through 518 removed outlier: 4.404A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 539 removed outlier: 4.476A pdb=" N CYS B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 Processing helix chain 'B' and resid 590 through 612 Processing helix chain 'B' and resid 613 through 626 removed outlier: 3.888A pdb=" N ILE B 617 " --> pdb=" O LEU B 613 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 619 " --> pdb=" O MET B 615 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 645 removed outlier: 3.829A pdb=" N SER B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 721 removed outlier: 3.598A pdb=" N TYR B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 721 " --> pdb=" O VAL B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 753 removed outlier: 3.500A pdb=" N PHE B 735 " --> pdb=" O THR B 731 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU B 737 " --> pdb=" O GLU B 733 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 45 through 59 removed outlier: 3.919A pdb=" N GLU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.708A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 165 removed outlier: 3.624A pdb=" N GLN C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS C 164 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 215 through 234 removed outlier: 4.075A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 258 removed outlier: 3.919A pdb=" N HIS C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 305 through 316 removed outlier: 3.704A pdb=" N ASP C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 339 removed outlier: 3.690A pdb=" N VAL C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 350 removed outlier: 4.257A pdb=" N LEU C 343 " --> pdb=" O MET C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 361 through 383 removed outlier: 3.730A pdb=" N ILE C 367 " --> pdb=" O PHE C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 Proline residue: C 408 - end of helix removed outlier: 4.663A pdb=" N ASP C 423 " --> pdb=" O LYS C 419 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY C 424 " --> pdb=" O GLN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 457 removed outlier: 3.950A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET C 437 " --> pdb=" O TRP C 433 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP C 438 " --> pdb=" O TRP C 434 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 Processing helix chain 'C' and resid 472 through 492 removed outlier: 3.551A pdb=" N VAL C 480 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 499 removed outlier: 4.122A pdb=" N THR C 497 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 512 Processing helix chain 'C' and resid 513 through 518 removed outlier: 4.404A pdb=" N LYS C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 539 removed outlier: 4.476A pdb=" N CYS C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU C 525 " --> pdb=" O PHE C 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 526 " --> pdb=" O ILE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 574 Processing helix chain 'C' and resid 590 through 612 Processing helix chain 'C' and resid 613 through 626 removed outlier: 3.889A pdb=" N ILE C 617 " --> pdb=" O LEU C 613 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET C 619 " --> pdb=" O MET C 615 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS C 626 " --> pdb=" O ASN C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 645 removed outlier: 3.829A pdb=" N SER C 645 " --> pdb=" O LYS C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 721 removed outlier: 3.598A pdb=" N TYR C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE C 721 " --> pdb=" O VAL C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 753 removed outlier: 3.500A pdb=" N PHE C 735 " --> pdb=" O THR C 731 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU C 737 " --> pdb=" O GLU C 733 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 742 " --> pdb=" O LEU C 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 59 removed outlier: 3.918A pdb=" N GLU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 109 through 117 Processing helix chain 'D' and resid 144 through 152 removed outlier: 3.708A pdb=" N THR D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 165 removed outlier: 3.624A pdb=" N GLN D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 215 through 234 removed outlier: 4.075A pdb=" N LYS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 258 removed outlier: 3.919A pdb=" N HIS D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 256 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.704A pdb=" N ASP D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 339 removed outlier: 3.690A pdb=" N VAL D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 350 removed outlier: 4.257A pdb=" N LEU D 343 " --> pdb=" O MET D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 359 Processing helix chain 'D' and resid 361 through 383 removed outlier: 3.730A pdb=" N ILE D 367 " --> pdb=" O PHE D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 Proline residue: D 408 - end of helix removed outlier: 4.663A pdb=" N ASP D 423 " --> pdb=" O LYS D 419 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY D 424 " --> pdb=" O GLN D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 457 removed outlier: 3.950A pdb=" N LEU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET D 437 " --> pdb=" O TRP D 433 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 438 " --> pdb=" O TRP D 434 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 457 " --> pdb=" O ILE D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 472 through 492 removed outlier: 3.551A pdb=" N VAL D 480 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE D 481 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 499 removed outlier: 4.122A pdb=" N THR D 497 " --> pdb=" O SER D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 512 Processing helix chain 'D' and resid 513 through 518 removed outlier: 4.404A pdb=" N LYS D 518 " --> pdb=" O LEU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 539 removed outlier: 4.476A pdb=" N CYS D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU D 525 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 526 " --> pdb=" O ILE D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 Processing helix chain 'D' and resid 590 through 612 Processing helix chain 'D' and resid 613 through 626 removed outlier: 3.889A pdb=" N ILE D 617 " --> pdb=" O LEU D 613 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET D 619 " --> pdb=" O MET D 615 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS D 626 " --> pdb=" O ASN D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 645 removed outlier: 3.829A pdb=" N SER D 645 " --> pdb=" O LYS D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 721 removed outlier: 3.598A pdb=" N TYR D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE D 721 " --> pdb=" O VAL D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 753 removed outlier: 3.500A pdb=" N PHE D 735 " --> pdb=" O THR D 731 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU D 737 " --> pdb=" O GLU D 733 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 742 " --> pdb=" O LEU D 738 " (cutoff:3.500A) 1200 hydrogen bonds defined for protein. 3516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3314 1.30 - 1.43: 5916 1.43 - 1.55: 12162 1.55 - 1.68: 4 1.68 - 1.80: 180 Bond restraints: 21576 Sorted by residual: bond pdb=" C6 S9Q B1001 " pdb=" N3 S9Q B1001 " ideal model delta sigma weight residual 1.287 1.478 -0.191 2.00e-02 2.50e+03 9.15e+01 bond pdb=" C6 S9Q C1001 " pdb=" N3 S9Q C1001 " ideal model delta sigma weight residual 1.287 1.478 -0.191 2.00e-02 2.50e+03 9.15e+01 bond pdb=" C6 S9Q A1001 " pdb=" N3 S9Q A1001 " ideal model delta sigma weight residual 1.287 1.478 -0.191 2.00e-02 2.50e+03 9.15e+01 bond pdb=" C6 S9Q D1001 " pdb=" N3 S9Q D1001 " ideal model delta sigma weight residual 1.287 1.478 -0.191 2.00e-02 2.50e+03 9.15e+01 bond pdb=" O13 44E B1003 " pdb=" P 44E B1003 " ideal model delta sigma weight residual 1.684 1.507 0.177 2.00e-02 2.50e+03 7.84e+01 ... (remaining 21571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.10: 29203 11.10 - 22.20: 28 22.20 - 33.31: 0 33.31 - 44.41: 0 44.41 - 55.51: 4 Bond angle restraints: 29235 Sorted by residual: angle pdb=" O13 44E A1003 " pdb=" P 44E A1003 " pdb=" O14 44E A1003 " ideal model delta sigma weight residual 54.79 110.30 -55.51 3.00e+00 1.11e-01 3.42e+02 angle pdb=" O13 44E C1003 " pdb=" P 44E C1003 " pdb=" O14 44E C1003 " ideal model delta sigma weight residual 54.79 110.30 -55.51 3.00e+00 1.11e-01 3.42e+02 angle pdb=" O13 44E B1003 " pdb=" P 44E B1003 " pdb=" O14 44E B1003 " ideal model delta sigma weight residual 54.79 110.27 -55.48 3.00e+00 1.11e-01 3.42e+02 angle pdb=" O13 44E D1003 " pdb=" P 44E D1003 " pdb=" O14 44E D1003 " ideal model delta sigma weight residual 54.79 110.27 -55.48 3.00e+00 1.11e-01 3.42e+02 angle pdb=" O12 44E C1003 " pdb=" P 44E C1003 " pdb=" O14 44E C1003 " ideal model delta sigma weight residual 127.76 110.12 17.64 3.00e+00 1.11e-01 3.46e+01 ... (remaining 29230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.75: 11846 24.75 - 49.51: 815 49.51 - 74.26: 96 74.26 - 99.01: 20 99.01 - 123.77: 8 Dihedral angle restraints: 12785 sinusoidal: 5189 harmonic: 7596 Sorted by residual: dihedral pdb=" C10 S9Q A1001 " pdb=" C9 S9Q A1001 " pdb=" N4 S9Q A1001 " pdb=" C8 S9Q A1001 " ideal model delta sinusoidal sigma weight residual -92.34 31.43 -123.77 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C10 S9Q B1001 " pdb=" C9 S9Q B1001 " pdb=" N4 S9Q B1001 " pdb=" C8 S9Q B1001 " ideal model delta sinusoidal sigma weight residual -92.34 31.43 -123.77 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C10 S9Q D1001 " pdb=" C9 S9Q D1001 " pdb=" N4 S9Q D1001 " pdb=" C8 S9Q D1001 " ideal model delta sinusoidal sigma weight residual -92.34 31.43 -123.77 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 12782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1746 0.033 - 0.065: 1070 0.065 - 0.097: 363 0.097 - 0.130: 85 0.130 - 0.162: 12 Chirality restraints: 3276 Sorted by residual: chirality pdb=" CA PRO B 304 " pdb=" N PRO B 304 " pdb=" C PRO B 304 " pdb=" CB PRO B 304 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PRO C 304 " pdb=" N PRO C 304 " pdb=" C PRO C 304 " pdb=" CB PRO C 304 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" C PRO A 304 " pdb=" CB PRO A 304 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 3273 not shown) Planarity restraints: 3619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 67 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 68 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 67 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO D 68 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 68 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 68 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 67 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO C 68 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 68 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 68 " 0.025 5.00e-02 4.00e+02 ... (remaining 3616 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4031 2.75 - 3.29: 20937 3.29 - 3.83: 33098 3.83 - 4.36: 36940 4.36 - 4.90: 64128 Nonbonded interactions: 159134 Sorted by model distance: nonbonded pdb=" OE2 GLU D 417 " pdb=" OH TYR D 429 " model vdw 2.214 3.040 nonbonded pdb=" OE2 GLU A 417 " pdb=" OH TYR A 429 " model vdw 2.214 3.040 nonbonded pdb=" OE2 GLU C 417 " pdb=" OH TYR C 429 " model vdw 2.214 3.040 nonbonded pdb=" OE2 GLU B 417 " pdb=" OH TYR B 429 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 523 " pdb=" OH TYR A 604 " model vdw 2.265 3.040 ... (remaining 159129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 1003)) selection = (chain 'B' and (resid 29 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 1003)) selection = chain 'C' selection = (chain 'D' and (resid 29 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 1003)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.130 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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 : 0.010 0.191 21576 Z= 0.470 Angle : 1.087 55.510 29235 Z= 0.475 Chirality : 0.045 0.162 3276 Planarity : 0.004 0.045 3619 Dihedral : 16.319 123.766 7841 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.35 % Allowed : 0.18 % Favored : 99.47 % 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: 2516 helix: 0.24 (0.13), residues: 1800 sheet: None (None), residues: 0 loop : -1.72 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 715 TYR 0.018 0.002 TYR B 624 PHE 0.017 0.002 PHE B 300 TRP 0.011 0.002 TRP B 409 HIS 0.002 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.01019 / 0.47 (21576) covalent geometry : angle 1.08667 / 0.48 (29235) hydrogen bonds : bond 0.14885 / 9.82 ( 1200) hydrogen bonds : angle 5.43898 / 3.83 ( 3516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 222 time to evaluate : 0.837 Fit side-chains REVERT: A 335 PHE cc_start: 0.8202 (t80) cc_final: 0.7891 (t80) REVERT: A 421 MET cc_start: 0.8136 (tmm) cc_final: 0.7681 (tmm) REVERT: A 437 MET cc_start: 0.7770 (mtp) cc_final: 0.7508 (mtm) REVERT: A 441 MET cc_start: 0.8380 (mtm) cc_final: 0.7810 (mtp) REVERT: B 335 PHE cc_start: 0.8202 (t80) cc_final: 0.7892 (t80) REVERT: B 421 MET cc_start: 0.8127 (tmm) cc_final: 0.7670 (tmm) REVERT: B 437 MET cc_start: 0.7760 (mtp) cc_final: 0.7500 (mtm) REVERT: B 441 MET cc_start: 0.8388 (mtm) cc_final: 0.7808 (mtp) REVERT: C 335 PHE cc_start: 0.8200 (t80) cc_final: 0.7892 (t80) REVERT: C 421 MET cc_start: 0.8135 (tmm) cc_final: 0.7684 (tmm) REVERT: C 437 MET cc_start: 0.7752 (mtp) cc_final: 0.7498 (mtm) REVERT: C 441 MET cc_start: 0.8388 (mtm) cc_final: 0.7812 (mtp) REVERT: D 335 PHE cc_start: 0.8208 (t80) cc_final: 0.7898 (t80) REVERT: D 421 MET cc_start: 0.8135 (tmm) cc_final: 0.7673 (tmm) REVERT: D 437 MET cc_start: 0.7761 (mtp) cc_final: 0.7504 (mtm) REVERT: D 441 MET cc_start: 0.8372 (mtm) cc_final: 0.7809 (mtp) outliers start: 8 outliers final: 4 residues processed: 226 average time/residue: 0.1326 time to fit residues: 48.5932 Evaluate side-chains 185 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain D residue 420 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 395 GLN A 420 GLN B 80 ASN B 395 GLN C 80 ASN C 395 GLN C 420 GLN D 80 ASN D 395 GLN D 420 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.102024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.078580 restraints weight = 46840.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.078548 restraints weight = 28721.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.079169 restraints weight = 25589.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.080121 restraints weight = 19814.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.080166 restraints weight = 17204.737| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21576 Z= 0.130 Angle : 0.526 7.284 29235 Z= 0.272 Chirality : 0.037 0.142 3276 Planarity : 0.004 0.053 3619 Dihedral : 9.936 129.096 2900 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.22 % Allowed : 8.53 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2516 helix: 0.78 (0.13), residues: 1808 sheet: None (None), residues: 0 loop : -1.64 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 465 TYR 0.009 0.001 TYR C 582 PHE 0.013 0.001 PHE A 572 TRP 0.013 0.001 TRP D 314 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (21576) covalent geometry : angle 0.52619 / 0.27 (29235) hydrogen bonds : bond 0.04707 / 3.17 ( 1200) hydrogen bonds : angle 4.01063 / 2.82 ( 3516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 224 time to evaluate : 0.825 Fit side-chains REVERT: A 335 PHE cc_start: 0.8129 (t80) cc_final: 0.7926 (t80) REVERT: A 421 MET cc_start: 0.7943 (tmm) cc_final: 0.7405 (tmm) REVERT: A 437 MET cc_start: 0.7904 (mtp) cc_final: 0.7530 (mtm) REVERT: A 441 MET cc_start: 0.8397 (mtm) cc_final: 0.7645 (mtp) REVERT: B 335 PHE cc_start: 0.8128 (t80) cc_final: 0.7925 (t80) REVERT: B 421 MET cc_start: 0.7942 (tmm) cc_final: 0.7419 (tmm) REVERT: B 437 MET cc_start: 0.7904 (mtp) cc_final: 0.7526 (mtm) REVERT: B 441 MET cc_start: 0.8404 (mtm) cc_final: 0.7651 (mtp) REVERT: C 335 PHE cc_start: 0.8141 (t80) cc_final: 0.7938 (t80) REVERT: C 421 MET cc_start: 0.7942 (tmm) cc_final: 0.7411 (tmm) REVERT: C 437 MET cc_start: 0.7907 (mtp) cc_final: 0.7529 (mtm) REVERT: C 441 MET cc_start: 0.8407 (mtm) cc_final: 0.7657 (mtp) REVERT: D 335 PHE cc_start: 0.8129 (t80) cc_final: 0.7928 (t80) REVERT: D 421 MET cc_start: 0.7946 (tmm) cc_final: 0.7407 (tmm) REVERT: D 437 MET cc_start: 0.7903 (mtp) cc_final: 0.7529 (mtm) REVERT: D 441 MET cc_start: 0.8390 (mtm) cc_final: 0.7663 (mtp) outliers start: 5 outliers final: 5 residues processed: 229 average time/residue: 0.1431 time to fit residues: 51.4359 Evaluate side-chains 197 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 192 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain D residue 368 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 115 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 241 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 50 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN B 64 ASN B 420 GLN C 64 ASN D 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.101912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.078494 restraints weight = 47133.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.077874 restraints weight = 28607.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.078568 restraints weight = 27575.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.079200 restraints weight = 20980.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.079364 restraints weight = 18736.764| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21576 Z= 0.134 Angle : 0.501 6.355 29235 Z= 0.258 Chirality : 0.036 0.136 3276 Planarity : 0.004 0.054 3619 Dihedral : 9.591 128.889 2891 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.93 % Allowed : 13.17 % Favored : 85.90 % 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: 0.44 (0.18), residues: 2516 helix: 1.10 (0.13), residues: 1788 sheet: None (None), residues: 0 loop : -1.73 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 491 TYR 0.009 0.001 TYR C 538 PHE 0.010 0.001 PHE C 300 TRP 0.015 0.001 TRP A 314 HIS 0.002 0.000 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (21576) covalent geometry : angle 0.50122 / 0.26 (29235) hydrogen bonds : bond 0.04504 / 3.02 ( 1200) hydrogen bonds : angle 3.82671 / 2.70 ( 3516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 0.835 Fit side-chains REVERT: A 230 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8632 (tt) REVERT: A 409 TRP cc_start: 0.9063 (OUTLIER) cc_final: 0.8274 (m-90) REVERT: A 421 MET cc_start: 0.7929 (tmm) cc_final: 0.7370 (tmm) REVERT: A 437 MET cc_start: 0.7986 (mtp) cc_final: 0.7513 (mtm) REVERT: A 441 MET cc_start: 0.8413 (mtm) cc_final: 0.7667 (mtp) REVERT: A 622 ASN cc_start: 0.7882 (m110) cc_final: 0.7658 (m-40) REVERT: A 753 MET cc_start: 0.8006 (ttm) cc_final: 0.7474 (ttm) REVERT: B 230 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 409 TRP cc_start: 0.9052 (OUTLIER) cc_final: 0.8270 (m-90) REVERT: B 421 MET cc_start: 0.7929 (tmm) cc_final: 0.7369 (tmm) REVERT: B 437 MET cc_start: 0.7988 (mtp) cc_final: 0.7513 (mtm) REVERT: B 441 MET cc_start: 0.8430 (mtm) cc_final: 0.7677 (mtp) REVERT: B 622 ASN cc_start: 0.7887 (m110) cc_final: 0.7657 (m-40) REVERT: B 753 MET cc_start: 0.7926 (ttm) cc_final: 0.7375 (ttm) REVERT: C 230 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8630 (tt) REVERT: C 409 TRP cc_start: 0.9062 (OUTLIER) cc_final: 0.8273 (m-90) REVERT: C 421 MET cc_start: 0.7930 (tmm) cc_final: 0.7375 (tmm) REVERT: C 437 MET cc_start: 0.7987 (mtp) cc_final: 0.7514 (mtm) REVERT: C 441 MET cc_start: 0.8430 (mtm) cc_final: 0.7689 (mtp) REVERT: C 622 ASN cc_start: 0.7891 (m110) cc_final: 0.7661 (m-40) REVERT: C 753 MET cc_start: 0.7923 (ttm) cc_final: 0.7468 (ttm) REVERT: D 230 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8650 (tt) REVERT: D 409 TRP cc_start: 0.9066 (OUTLIER) cc_final: 0.8276 (m-90) REVERT: D 421 MET cc_start: 0.7935 (tmm) cc_final: 0.7378 (tmm) REVERT: D 437 MET cc_start: 0.7987 (mtp) cc_final: 0.7515 (mtm) REVERT: D 441 MET cc_start: 0.8417 (mtm) cc_final: 0.7688 (mtp) REVERT: D 622 ASN cc_start: 0.7892 (m110) cc_final: 0.7663 (m-40) outliers start: 21 outliers final: 9 residues processed: 239 average time/residue: 0.1306 time to fit residues: 50.6388 Evaluate side-chains 209 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 516 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 144 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 254 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 ASN B 442 ASN C 442 ASN D 442 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.102268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.078812 restraints weight = 46891.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.078316 restraints weight = 28663.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.078852 restraints weight = 26558.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.079771 restraints weight = 21069.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.079866 restraints weight = 18201.606| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21576 Z= 0.126 Angle : 0.505 6.830 29235 Z= 0.255 Chirality : 0.037 0.130 3276 Planarity : 0.004 0.055 3619 Dihedral : 9.466 129.375 2891 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.28 % Allowed : 15.20 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2516 helix: 1.24 (0.13), residues: 1800 sheet: None (None), residues: 0 loop : -1.65 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 491 TYR 0.009 0.001 TYR C 58 PHE 0.010 0.001 PHE D 300 TRP 0.013 0.001 TRP C 314 HIS 0.002 0.000 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (21576) covalent geometry : angle 0.50452 / 0.26 (29235) hydrogen bonds : bond 0.04233 / 2.84 ( 1200) hydrogen bonds : angle 3.73609 / 2.64 ( 3516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.755 Fit side-chains REVERT: A 230 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8656 (tt) REVERT: A 409 TRP cc_start: 0.9049 (OUTLIER) cc_final: 0.8355 (m-90) REVERT: A 421 MET cc_start: 0.7970 (tmm) cc_final: 0.7484 (tmm) REVERT: A 441 MET cc_start: 0.8305 (mtm) cc_final: 0.7336 (mtp) REVERT: A 622 ASN cc_start: 0.7859 (m110) cc_final: 0.7643 (m-40) REVERT: B 230 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8681 (tt) REVERT: B 409 TRP cc_start: 0.9041 (OUTLIER) cc_final: 0.8347 (m-90) REVERT: B 421 MET cc_start: 0.7923 (tmm) cc_final: 0.7427 (tmm) REVERT: B 441 MET cc_start: 0.8314 (mtm) cc_final: 0.7342 (mtp) REVERT: B 622 ASN cc_start: 0.7869 (m110) cc_final: 0.7648 (m-40) REVERT: B 753 MET cc_start: 0.7960 (ttm) cc_final: 0.7748 (ttm) REVERT: C 230 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8654 (tt) REVERT: C 409 TRP cc_start: 0.9053 (OUTLIER) cc_final: 0.8355 (m-90) REVERT: C 421 MET cc_start: 0.7970 (tmm) cc_final: 0.7488 (tmm) REVERT: C 441 MET cc_start: 0.8318 (mtm) cc_final: 0.7347 (mtp) REVERT: C 622 ASN cc_start: 0.7866 (m110) cc_final: 0.7643 (m-40) REVERT: D 230 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8691 (tt) REVERT: D 409 TRP cc_start: 0.9054 (OUTLIER) cc_final: 0.8356 (m-90) REVERT: D 421 MET cc_start: 0.7971 (tmm) cc_final: 0.7487 (tmm) REVERT: D 441 MET cc_start: 0.8310 (mtm) cc_final: 0.7346 (mtp) REVERT: D 622 ASN cc_start: 0.7868 (m110) cc_final: 0.7648 (m-40) outliers start: 29 outliers final: 12 residues processed: 238 average time/residue: 0.1199 time to fit residues: 46.7269 Evaluate side-chains 214 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 516 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 54 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.102804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.079290 restraints weight = 46795.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.079416 restraints weight = 28683.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.079970 restraints weight = 26040.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.080898 restraints weight = 20003.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.080936 restraints weight = 17462.580| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21576 Z= 0.121 Angle : 0.509 10.878 29235 Z= 0.255 Chirality : 0.036 0.165 3276 Planarity : 0.004 0.054 3619 Dihedral : 9.289 129.437 2888 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.68 % Allowed : 16.26 % Favored : 82.06 % 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: 0.78 (0.18), residues: 2516 helix: 1.35 (0.13), residues: 1808 sheet: None (None), residues: 0 loop : -1.67 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 196 TYR 0.015 0.001 TYR A 36 PHE 0.018 0.001 PHE D 335 TRP 0.012 0.001 TRP A 314 HIS 0.002 0.000 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (21576) covalent geometry : angle 0.50865 / 0.25 (29235) hydrogen bonds : bond 0.04052 / 2.72 ( 1200) hydrogen bonds : angle 3.67035 / 2.60 ( 3516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.847 Fit side-chains REVERT: A 230 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8695 (tt) REVERT: A 409 TRP cc_start: 0.9043 (OUTLIER) cc_final: 0.8430 (m-90) REVERT: A 421 MET cc_start: 0.8064 (tmm) cc_final: 0.7580 (tmm) REVERT: A 441 MET cc_start: 0.8307 (mtm) cc_final: 0.7730 (mtp) REVERT: A 622 ASN cc_start: 0.7867 (m110) cc_final: 0.7652 (m-40) REVERT: B 230 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8701 (tt) REVERT: B 409 TRP cc_start: 0.9032 (OUTLIER) cc_final: 0.8423 (m-90) REVERT: B 421 MET cc_start: 0.8069 (tmm) cc_final: 0.7584 (tmm) REVERT: B 441 MET cc_start: 0.8318 (mtm) cc_final: 0.7760 (mtp) REVERT: B 622 ASN cc_start: 0.7855 (m110) cc_final: 0.7604 (m-40) REVERT: B 752 MET cc_start: 0.7641 (ttt) cc_final: 0.7347 (ttp) REVERT: B 753 MET cc_start: 0.7855 (ttm) cc_final: 0.7612 (ttm) REVERT: C 230 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8696 (tt) REVERT: C 409 TRP cc_start: 0.9042 (OUTLIER) cc_final: 0.8429 (m-90) REVERT: C 421 MET cc_start: 0.8068 (tmm) cc_final: 0.7586 (tmm) REVERT: C 441 MET cc_start: 0.8323 (mtm) cc_final: 0.7743 (mtp) REVERT: C 622 ASN cc_start: 0.7869 (m110) cc_final: 0.7645 (m-40) REVERT: D 230 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8705 (tt) REVERT: D 409 TRP cc_start: 0.9044 (OUTLIER) cc_final: 0.8431 (m-90) REVERT: D 421 MET cc_start: 0.8065 (tmm) cc_final: 0.7582 (tmm) REVERT: D 441 MET cc_start: 0.8307 (mtm) cc_final: 0.7766 (mtp) REVERT: D 622 ASN cc_start: 0.7858 (m110) cc_final: 0.7605 (m-40) REVERT: D 752 MET cc_start: 0.7845 (ttt) cc_final: 0.7615 (ttp) outliers start: 38 outliers final: 14 residues processed: 233 average time/residue: 0.1252 time to fit residues: 48.8213 Evaluate side-chains 217 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 753 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 516 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 234 optimal weight: 0.0970 chunk 196 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 420 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.103742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.080442 restraints weight = 46759.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.080309 restraints weight = 28783.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.080918 restraints weight = 25632.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082227 restraints weight = 19840.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082230 restraints weight = 16334.936| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21576 Z= 0.105 Angle : 0.485 9.196 29235 Z= 0.243 Chirality : 0.036 0.157 3276 Planarity : 0.004 0.053 3619 Dihedral : 9.083 127.991 2888 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.37 % Allowed : 17.76 % Favored : 80.87 % 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: 0.91 (0.18), residues: 2516 helix: 1.47 (0.13), residues: 1820 sheet: None (None), residues: 0 loop : -1.74 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 196 TYR 0.012 0.001 TYR C 36 PHE 0.008 0.001 PHE C 300 TRP 0.011 0.001 TRP C 314 HIS 0.002 0.000 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (21576) covalent geometry : angle 0.48452 / 0.24 (29235) hydrogen bonds : bond 0.03644 / 2.44 ( 1200) hydrogen bonds : angle 3.58076 / 2.54 ( 3516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.814 Fit side-chains REVERT: A 230 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8706 (tt) REVERT: A 409 TRP cc_start: 0.9016 (OUTLIER) cc_final: 0.8487 (m-90) REVERT: A 421 MET cc_start: 0.8073 (tmm) cc_final: 0.7598 (tmm) REVERT: A 441 MET cc_start: 0.8296 (mtm) cc_final: 0.7772 (mtp) REVERT: A 442 ASN cc_start: 0.8803 (m110) cc_final: 0.8593 (m-40) REVERT: B 230 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8713 (tt) REVERT: B 409 TRP cc_start: 0.9003 (OUTLIER) cc_final: 0.8476 (m-90) REVERT: B 421 MET cc_start: 0.8045 (tmm) cc_final: 0.7571 (tmm) REVERT: B 430 ILE cc_start: 0.8917 (mm) cc_final: 0.8657 (mm) REVERT: B 441 MET cc_start: 0.8309 (mtm) cc_final: 0.7776 (mtp) REVERT: B 442 ASN cc_start: 0.8806 (m110) cc_final: 0.8596 (m-40) REVERT: B 752 MET cc_start: 0.7513 (ttt) cc_final: 0.7004 (ttm) REVERT: C 230 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8707 (tt) REVERT: C 409 TRP cc_start: 0.9017 (OUTLIER) cc_final: 0.8485 (m-90) REVERT: C 421 MET cc_start: 0.8074 (tmm) cc_final: 0.7604 (tmm) REVERT: C 441 MET cc_start: 0.8305 (mtm) cc_final: 0.7777 (mtp) REVERT: C 442 ASN cc_start: 0.8809 (m110) cc_final: 0.8598 (m-40) REVERT: D 230 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8719 (tt) REVERT: D 409 TRP cc_start: 0.9017 (OUTLIER) cc_final: 0.8486 (m-90) REVERT: D 421 MET cc_start: 0.8073 (tmm) cc_final: 0.7599 (tmm) REVERT: D 441 MET cc_start: 0.8307 (mtm) cc_final: 0.7778 (mtp) REVERT: D 442 ASN cc_start: 0.8807 (m110) cc_final: 0.8595 (m-40) outliers start: 31 outliers final: 13 residues processed: 247 average time/residue: 0.1310 time to fit residues: 52.3653 Evaluate side-chains 221 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 753 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 516 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 212 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.101057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.077995 restraints weight = 47007.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.077603 restraints weight = 28838.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.078192 restraints weight = 26254.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.079042 restraints weight = 20871.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.079109 restraints weight = 18341.484| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 21576 Z= 0.198 Angle : 0.553 7.478 29235 Z= 0.278 Chirality : 0.038 0.154 3276 Planarity : 0.004 0.053 3619 Dihedral : 9.145 131.817 2888 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.46 % Allowed : 18.74 % Favored : 79.81 % 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: 0.80 (0.17), residues: 2516 helix: 1.36 (0.13), residues: 1820 sheet: None (None), residues: 0 loop : -1.69 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 715 TYR 0.013 0.001 TYR A 624 PHE 0.013 0.001 PHE A 335 TRP 0.015 0.001 TRP C 314 HIS 0.002 0.000 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (21576) covalent geometry : angle 0.55333 / 0.28 (29235) hydrogen bonds : bond 0.04947 / 3.32 ( 1200) hydrogen bonds : angle 3.86332 / 2.74 ( 3516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.830 Fit side-chains REVERT: A 409 TRP cc_start: 0.9127 (OUTLIER) cc_final: 0.8523 (m-90) REVERT: A 421 MET cc_start: 0.8094 (tmm) cc_final: 0.7605 (tmm) REVERT: A 430 ILE cc_start: 0.8914 (mm) cc_final: 0.8661 (mm) REVERT: A 441 MET cc_start: 0.8319 (mtm) cc_final: 0.7435 (mtp) REVERT: B 409 TRP cc_start: 0.9111 (OUTLIER) cc_final: 0.8510 (m-90) REVERT: B 421 MET cc_start: 0.8056 (tmm) cc_final: 0.7579 (tmm) REVERT: B 430 ILE cc_start: 0.8872 (mm) cc_final: 0.8644 (mm) REVERT: B 441 MET cc_start: 0.8328 (mtm) cc_final: 0.7404 (mtp) REVERT: B 752 MET cc_start: 0.7663 (ttt) cc_final: 0.7378 (ttp) REVERT: C 409 TRP cc_start: 0.9123 (OUTLIER) cc_final: 0.8521 (m-90) REVERT: C 421 MET cc_start: 0.8094 (tmm) cc_final: 0.7607 (tmm) REVERT: C 430 ILE cc_start: 0.8879 (mm) cc_final: 0.8635 (mm) REVERT: C 441 MET cc_start: 0.8327 (mtm) cc_final: 0.7440 (mtp) REVERT: D 409 TRP cc_start: 0.9125 (OUTLIER) cc_final: 0.8523 (m-90) REVERT: D 421 MET cc_start: 0.8093 (tmm) cc_final: 0.7610 (tmm) REVERT: D 430 ILE cc_start: 0.8872 (mm) cc_final: 0.8625 (mm) REVERT: D 441 MET cc_start: 0.8322 (mtm) cc_final: 0.7403 (mtp) outliers start: 33 outliers final: 20 residues processed: 218 average time/residue: 0.1259 time to fit residues: 44.3761 Evaluate side-chains 211 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 516 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 141 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 106 optimal weight: 0.0870 chunk 178 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 230 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081798 restraints weight = 46418.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.081175 restraints weight = 27497.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081957 restraints weight = 25403.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082975 restraints weight = 19485.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083011 restraints weight = 16931.602| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21576 Z= 0.098 Angle : 0.502 11.470 29235 Z= 0.247 Chirality : 0.035 0.151 3276 Planarity : 0.004 0.053 3619 Dihedral : 8.803 127.485 2888 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.06 % Allowed : 19.71 % Favored : 79.23 % 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: 0.96 (0.18), residues: 2516 helix: 1.51 (0.13), residues: 1832 sheet: None (None), residues: 0 loop : -1.81 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 71 TYR 0.013 0.001 TYR B 36 PHE 0.010 0.001 PHE B 657 TRP 0.009 0.001 TRP C 314 HIS 0.002 0.000 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (21576) covalent geometry : angle 0.50155 / 0.25 (29235) hydrogen bonds : bond 0.03523 / 2.36 ( 1200) hydrogen bonds : angle 3.59048 / 2.55 ( 3516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.768 Fit side-chains REVERT: A 230 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8714 (tt) REVERT: A 409 TRP cc_start: 0.9021 (OUTLIER) cc_final: 0.8400 (m-90) REVERT: A 421 MET cc_start: 0.8040 (tmm) cc_final: 0.7570 (tmm) REVERT: A 430 ILE cc_start: 0.8848 (mm) cc_final: 0.8607 (mm) REVERT: A 441 MET cc_start: 0.8267 (mtm) cc_final: 0.7687 (mtp) REVERT: A 442 ASN cc_start: 0.8791 (m110) cc_final: 0.8585 (m-40) REVERT: B 230 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8713 (tt) REVERT: B 409 TRP cc_start: 0.9012 (OUTLIER) cc_final: 0.8392 (m-90) REVERT: B 421 MET cc_start: 0.7990 (tmm) cc_final: 0.7535 (tmm) REVERT: B 430 ILE cc_start: 0.8853 (mm) cc_final: 0.8619 (mm) REVERT: B 441 MET cc_start: 0.8275 (mtm) cc_final: 0.7692 (mtp) REVERT: B 442 ASN cc_start: 0.8790 (m110) cc_final: 0.8582 (m-40) REVERT: C 230 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8714 (tt) REVERT: C 409 TRP cc_start: 0.9020 (OUTLIER) cc_final: 0.8399 (m-90) REVERT: C 421 MET cc_start: 0.8037 (tmm) cc_final: 0.7582 (tmm) REVERT: C 430 ILE cc_start: 0.8847 (mm) cc_final: 0.8601 (mm) REVERT: C 441 MET cc_start: 0.8274 (mtm) cc_final: 0.7691 (mtp) REVERT: C 442 ASN cc_start: 0.8795 (m110) cc_final: 0.8591 (m-40) REVERT: D 230 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8721 (tt) REVERT: D 409 TRP cc_start: 0.9021 (OUTLIER) cc_final: 0.8400 (m-90) REVERT: D 421 MET cc_start: 0.8034 (tmm) cc_final: 0.7564 (tmm) REVERT: D 430 ILE cc_start: 0.8844 (mm) cc_final: 0.8598 (mm) REVERT: D 441 MET cc_start: 0.8264 (mtm) cc_final: 0.7691 (mtp) REVERT: D 753 MET cc_start: 0.8034 (ttm) cc_final: 0.7622 (tmm) outliers start: 24 outliers final: 12 residues processed: 230 average time/residue: 0.1293 time to fit residues: 48.3461 Evaluate side-chains 223 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 516 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 254 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 442 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.081557 restraints weight = 46502.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.080637 restraints weight = 27875.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.081350 restraints weight = 25819.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.082435 restraints weight = 20292.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.082502 restraints weight = 17309.298| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21576 Z= 0.105 Angle : 0.502 10.520 29235 Z= 0.247 Chirality : 0.036 0.149 3276 Planarity : 0.004 0.052 3619 Dihedral : 8.474 127.492 2888 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.88 % Allowed : 19.80 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2516 helix: 1.62 (0.13), residues: 1828 sheet: None (None), residues: 0 loop : -1.75 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.012 0.001 TYR A 36 PHE 0.017 0.001 PHE A 335 TRP 0.011 0.001 TRP B 314 HIS 0.002 0.000 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (21576) covalent geometry : angle 0.50248 / 0.25 (29235) hydrogen bonds : bond 0.03637 / 2.44 ( 1200) hydrogen bonds : angle 3.56851 / 2.53 ( 3516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.833 Fit side-chains REVERT: A 230 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8742 (tt) REVERT: A 409 TRP cc_start: 0.9031 (OUTLIER) cc_final: 0.8378 (m-90) REVERT: A 421 MET cc_start: 0.8008 (tmm) cc_final: 0.7553 (tmm) REVERT: A 430 ILE cc_start: 0.8898 (mm) cc_final: 0.8646 (mm) REVERT: A 441 MET cc_start: 0.8281 (mtm) cc_final: 0.7741 (mtp) REVERT: B 230 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8745 (tt) REVERT: B 409 TRP cc_start: 0.9021 (OUTLIER) cc_final: 0.8372 (m-90) REVERT: B 421 MET cc_start: 0.8001 (tmm) cc_final: 0.7545 (tmm) REVERT: B 430 ILE cc_start: 0.8900 (mm) cc_final: 0.8653 (mm) REVERT: B 441 MET cc_start: 0.8291 (mtm) cc_final: 0.7749 (mtp) REVERT: C 230 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8745 (tt) REVERT: C 409 TRP cc_start: 0.9029 (OUTLIER) cc_final: 0.8377 (m-90) REVERT: C 421 MET cc_start: 0.8004 (tmm) cc_final: 0.7551 (tmm) REVERT: C 430 ILE cc_start: 0.8898 (mm) cc_final: 0.8641 (mm) REVERT: C 441 MET cc_start: 0.8282 (mtm) cc_final: 0.7751 (mtp) REVERT: D 230 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8754 (tt) REVERT: D 409 TRP cc_start: 0.9028 (OUTLIER) cc_final: 0.8376 (m-90) REVERT: D 421 MET cc_start: 0.8002 (tmm) cc_final: 0.7553 (tmm) REVERT: D 430 ILE cc_start: 0.8896 (mm) cc_final: 0.8634 (mm) REVERT: D 441 MET cc_start: 0.8226 (mtm) cc_final: 0.7322 (mtp) REVERT: D 753 MET cc_start: 0.8017 (ttm) cc_final: 0.7798 (ppp) outliers start: 20 outliers final: 12 residues processed: 226 average time/residue: 0.1341 time to fit residues: 49.1814 Evaluate side-chains 218 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 516 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 245 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 203 optimal weight: 0.5980 chunk 108 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 ASN B 442 ASN C 442 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.104279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081873 restraints weight = 46529.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.080954 restraints weight = 27776.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.081694 restraints weight = 25755.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.082710 restraints weight = 20197.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.082775 restraints weight = 17449.304| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21576 Z= 0.106 Angle : 0.507 10.815 29235 Z= 0.251 Chirality : 0.036 0.147 3276 Planarity : 0.004 0.053 3619 Dihedral : 8.189 126.936 2888 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.88 % Allowed : 20.06 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2516 helix: 1.62 (0.13), residues: 1832 sheet: None (None), residues: 0 loop : -1.67 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 71 TYR 0.013 0.001 TYR B 58 PHE 0.010 0.001 PHE C 657 TRP 0.011 0.001 TRP B 314 HIS 0.003 0.000 HIS C 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (21576) covalent geometry : angle 0.50666 / 0.25 (29235) hydrogen bonds : bond 0.03551 / 2.38 ( 1200) hydrogen bonds : angle 3.57142 / 2.53 ( 3516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.626 Fit side-chains REVERT: A 230 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8731 (tt) REVERT: A 409 TRP cc_start: 0.9019 (OUTLIER) cc_final: 0.8453 (m-90) REVERT: A 421 MET cc_start: 0.7996 (tmm) cc_final: 0.7549 (tmm) REVERT: A 430 ILE cc_start: 0.8902 (mm) cc_final: 0.8637 (mm) REVERT: A 441 MET cc_start: 0.8257 (mtm) cc_final: 0.7747 (mtp) REVERT: B 230 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8745 (tt) REVERT: B 409 TRP cc_start: 0.9011 (OUTLIER) cc_final: 0.8352 (m-90) REVERT: B 421 MET cc_start: 0.8005 (tmm) cc_final: 0.7556 (tmm) REVERT: B 430 ILE cc_start: 0.8901 (mm) cc_final: 0.8653 (mm) REVERT: B 441 MET cc_start: 0.8259 (mtm) cc_final: 0.7754 (mtp) REVERT: B 753 MET cc_start: 0.7933 (ttp) cc_final: 0.7522 (ttp) REVERT: C 230 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8736 (tt) REVERT: C 409 TRP cc_start: 0.9018 (OUTLIER) cc_final: 0.8452 (m-90) REVERT: C 421 MET cc_start: 0.7985 (tmm) cc_final: 0.7541 (tmm) REVERT: C 430 ILE cc_start: 0.8903 (mm) cc_final: 0.8634 (mm) REVERT: C 441 MET cc_start: 0.8262 (mtm) cc_final: 0.7749 (mtp) REVERT: D 230 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8753 (tt) REVERT: D 409 TRP cc_start: 0.9017 (OUTLIER) cc_final: 0.8452 (m-90) REVERT: D 421 MET cc_start: 0.7995 (tmm) cc_final: 0.7550 (tmm) REVERT: D 430 ILE cc_start: 0.8898 (mm) cc_final: 0.8628 (mm) REVERT: D 441 MET cc_start: 0.8242 (mtm) cc_final: 0.7773 (mtp) outliers start: 20 outliers final: 12 residues processed: 225 average time/residue: 0.1293 time to fit residues: 47.0575 Evaluate side-chains 222 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 516 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 227 optimal weight: 1.9990 chunk 217 optimal weight: 0.1980 chunk 68 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 212 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.105337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.082232 restraints weight = 46392.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.082473 restraints weight = 26860.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.083100 restraints weight = 25692.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.083827 restraints weight = 19720.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.083963 restraints weight = 17820.344| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21576 Z= 0.095 Angle : 0.500 10.873 29235 Z= 0.245 Chirality : 0.035 0.146 3276 Planarity : 0.004 0.053 3619 Dihedral : 7.870 124.348 2888 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.88 % Allowed : 20.11 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 2516 helix: 1.72 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.67 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 71 TYR 0.012 0.001 TYR C 36 PHE 0.022 0.001 PHE C 657 TRP 0.010 0.001 TRP B 314 HIS 0.002 0.000 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (21576) covalent geometry : angle 0.49999 / 0.25 (29235) hydrogen bonds : bond 0.03219 / 2.16 ( 1200) hydrogen bonds : angle 3.50619 / 2.49 ( 3516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2785.08 seconds wall clock time: 49 minutes 11.61 seconds (2951.61 seconds total)