Starting phenix.real_space_refine on Mon Dec 30 00:34:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvc_34123/12_2024/7yvc_34123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvc_34123/12_2024/7yvc_34123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvc_34123/12_2024/7yvc_34123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvc_34123/12_2024/7yvc_34123.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvc_34123/12_2024/7yvc_34123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvc_34123/12_2024/7yvc_34123.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 78 5.16 5 C 7380 2.51 5 N 1935 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11662 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3747 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 446} Chain breaks: 1 Chain: "B" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3747 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 446} Chain breaks: 1 Chain: "C" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3747 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 446} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.66, per 1000 atoms: 0.66 Number of scatterers: 11662 At special positions: 0 Unit cell: (110.2, 117.16, 136.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 78 16.00 O 2268 8.00 N 1935 7.00 C 7380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 233 " distance=2.04 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 217 " distance=2.04 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 431 " distance=2.04 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 411 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 233 " distance=2.04 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 217 " distance=2.04 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 431 " distance=2.04 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 363 " - pdb=" SG CYS B 411 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 233 " distance=2.04 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 217 " distance=2.04 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 431 " distance=2.04 Simple disulfide: pdb=" SG CYS C 354 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 363 " - pdb=" SG CYS C 411 " distance=2.03 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 381 " distance=2.03 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 Atom "HETATM11477 O5 NAG L 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM11603 O5 NAG A 702 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 701 " - " ASN A 401 " " NAG A 702 " - " ASN A 377 " " NAG B 701 " - " ASN B 377 " " NAG B 702 " - " ASN B 401 " " NAG C 701 " - " ASN C 377 " " NAG C 702 " - " ASN C 401 " " NAG D 1 " - " ASN A 393 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 169 " " NAG G 1 " - " ASN A 221 " " NAG H 1 " - " ASN B 393 " " NAG I 1 " - " ASN B 331 " " NAG J 1 " - " ASN B 169 " " NAG K 1 " - " ASN B 221 " " NAG L 1 " - " ASN C 393 " " NAG M 1 " - " ASN C 331 " " NAG N 1 " - " ASN C 169 " " NAG O 1 " - " ASN C 221 " Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.5 seconds 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2658 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 44.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 91 through 118 removed outlier: 3.584A pdb=" N TRP A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 102 " --> pdb=" O MET A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 161 through 174 removed outlier: 4.010A pdb=" N LYS A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.697A pdb=" N MET A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 removed outlier: 4.090A pdb=" N PHE A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 346 through 364 Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'A' and resid 406 through 422 removed outlier: 3.530A pdb=" N ALA A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 removed outlier: 4.033A pdb=" N CYS A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.952A pdb=" N MET A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 576 removed outlier: 3.945A pdb=" N GLY A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 118 removed outlier: 3.700A pdb=" N GLY B 102 " --> pdb=" O MET B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 161 through 174 removed outlier: 4.010A pdb=" N LYS B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.695A pdb=" N MET B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 4.090A pdb=" N PHE B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 346 through 364 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 406 through 422 removed outlier: 3.530A pdb=" N ALA B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 removed outlier: 4.032A pdb=" N CYS B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 475 through 487 Processing helix chain 'B' and resid 510 through 526 removed outlier: 3.952A pdb=" N MET B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 576 removed outlier: 3.945A pdb=" N GLY B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 118 removed outlier: 3.699A pdb=" N GLY C 102 " --> pdb=" O MET C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.011A pdb=" N LYS C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 174 " --> pdb=" O PHE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.696A pdb=" N MET C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 removed outlier: 4.090A pdb=" N PHE C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 346 through 364 Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'C' and resid 406 through 422 removed outlier: 3.530A pdb=" N ALA C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 removed outlier: 4.033A pdb=" N CYS C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 453 No H-bonds generated for 'chain 'C' and resid 451 through 453' Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 475 through 487 Processing helix chain 'C' and resid 510 through 526 removed outlier: 3.951A pdb=" N MET C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 576 removed outlier: 3.945A pdb=" N GLY C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU C 563 " --> pdb=" O GLY C 559 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL A 540 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA A 319 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR A 542 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 321 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN A 544 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 323 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR A 311 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER A 261 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU A 207 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL A 540 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA A 319 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR A 542 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 321 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN A 544 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 323 " --> pdb=" O GLN A 544 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 135 removed outlier: 4.408A pdb=" N VAL A 134 " --> pdb=" O MET A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 227 removed outlier: 6.307A pdb=" N ASN A 232 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN A 143 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL B 540 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 319 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TYR B 542 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 321 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN B 544 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR B 323 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR B 311 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER B 261 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU B 207 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL B 540 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 319 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TYR B 542 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 321 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN B 544 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR B 323 " --> pdb=" O GLN B 544 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 135 removed outlier: 4.406A pdb=" N VAL B 134 " --> pdb=" O MET B 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 222 through 227 removed outlier: 6.307A pdb=" N ASN B 232 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN B 143 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL C 540 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA C 319 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR C 542 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 321 " --> pdb=" O TYR C 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN C 544 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 323 " --> pdb=" O GLN C 544 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR C 311 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER C 261 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU C 207 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL C 540 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA C 319 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR C 542 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 321 " --> pdb=" O TYR C 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN C 544 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 323 " --> pdb=" O GLN C 544 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 134 through 135 removed outlier: 4.408A pdb=" N VAL C 134 " --> pdb=" O MET C 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 222 through 227 removed outlier: 6.307A pdb=" N ASN C 232 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN C 143 " --> pdb=" O ASN C 232 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1638 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: 3.65 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3708 1.34 - 1.46: 2811 1.46 - 1.58: 5271 1.58 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 11904 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 ... (remaining 11899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 15661 2.08 - 4.16: 371 4.16 - 6.24: 51 6.24 - 8.32: 12 8.32 - 10.40: 9 Bond angle restraints: 16104 Sorted by residual: angle pdb=" C TYR B 230 " pdb=" N PHE B 231 " pdb=" CA PHE B 231 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C TYR A 230 " pdb=" N PHE A 231 " pdb=" CA PHE A 231 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C TYR C 230 " pdb=" N PHE C 231 " pdb=" CA PHE C 231 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 angle pdb=" CB ARG C 391 " pdb=" CG ARG C 391 " pdb=" CD ARG C 391 " ideal model delta sigma weight residual 111.30 101.30 10.00 2.30e+00 1.89e-01 1.89e+01 angle pdb=" CB ARG B 391 " pdb=" CG ARG B 391 " pdb=" CD ARG B 391 " ideal model delta sigma weight residual 111.30 101.31 9.99 2.30e+00 1.89e-01 1.89e+01 ... (remaining 16099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6858 17.81 - 35.62: 604 35.62 - 53.43: 114 53.43 - 71.24: 26 71.24 - 89.06: 30 Dihedral angle restraints: 7632 sinusoidal: 3522 harmonic: 4110 Sorted by residual: dihedral pdb=" CB CYS B 210 " pdb=" SG CYS B 210 " pdb=" SG CYS B 217 " pdb=" CB CYS B 217 " ideal model delta sinusoidal sigma weight residual -86.00 -20.73 -65.27 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS A 210 " pdb=" SG CYS A 210 " pdb=" SG CYS A 217 " pdb=" CB CYS A 217 " ideal model delta sinusoidal sigma weight residual -86.00 -20.74 -65.26 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS C 210 " pdb=" SG CYS C 210 " pdb=" SG CYS C 217 " pdb=" CB CYS C 217 " ideal model delta sinusoidal sigma weight residual -86.00 -20.76 -65.24 1 1.00e+01 1.00e-02 5.58e+01 ... (remaining 7629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 1847 0.196 - 0.393: 7 0.393 - 0.589: 6 0.589 - 0.785: 1 0.785 - 0.982: 2 Chirality restraints: 1863 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 401 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 169 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.20 0.80 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 221 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.40e+01 ... (remaining 1860 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 221 " -0.003 2.00e-02 2.50e+03 1.36e-01 2.30e+02 pdb=" CG ASN C 221 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 221 " -0.123 2.00e-02 2.50e+03 pdb=" ND2 ASN C 221 " 0.231 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.115 2.00e-02 2.50e+03 1.20e-01 1.81e+02 pdb=" CG ASN C 331 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.174 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 221 " -0.025 2.00e-02 2.50e+03 1.12e-01 1.56e+02 pdb=" CG ASN A 221 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 221 " 0.093 2.00e-02 2.50e+03 pdb=" ND2 ASN A 221 " -0.184 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.137 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 105 2.59 - 3.17: 9651 3.17 - 3.75: 17018 3.75 - 4.32: 24321 4.32 - 4.90: 40463 Nonbonded interactions: 91558 Sorted by model distance: nonbonded pdb=" OD1 ASN C 169 " pdb=" C1 NAG N 1 " model vdw 2.017 2.776 nonbonded pdb=" OD1 ASN C 393 " pdb=" C1 NAG L 1 " model vdw 2.131 2.776 nonbonded pdb=" OD1 ASP A 166 " pdb=" NH1 ARG A 391 " model vdw 2.236 3.120 nonbonded pdb=" OD1 ASP B 166 " pdb=" NH1 ARG B 391 " model vdw 2.236 3.120 nonbonded pdb=" ND2 ASN A 221 " pdb=" N2 NAG G 1 " model vdw 2.236 2.560 ... (remaining 91553 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 91 through 577 or resid 701 through 702)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.760 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.780 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.007 0.080 11904 Z= 0.433 Angle : 0.821 10.396 16104 Z= 0.430 Chirality : 0.066 0.982 1863 Planarity : 0.004 0.046 2037 Dihedral : 14.939 89.055 4920 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.48 % Allowed : 0.71 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1389 helix: -0.16 (0.21), residues: 570 sheet: 0.74 (0.31), residues: 231 loop : -1.39 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 564 HIS 0.003 0.001 HIS A 209 PHE 0.015 0.002 PHE C 554 TYR 0.017 0.002 TYR C 448 ARG 0.019 0.001 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 561 LEU cc_start: 0.8126 (mt) cc_final: 0.7867 (mt) REVERT: B 247 MET cc_start: 0.9039 (mmm) cc_final: 0.8796 (tpt) REVERT: B 561 LEU cc_start: 0.8082 (mt) cc_final: 0.7394 (mp) REVERT: C 561 LEU cc_start: 0.8134 (mt) cc_final: 0.7767 (mt) outliers start: 6 outliers final: 0 residues processed: 92 average time/residue: 1.3969 time to fit residues: 139.7589 Evaluate side-chains 60 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 0.0270 chunk 125 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11904 Z= 0.176 Angle : 0.645 8.639 16104 Z= 0.326 Chirality : 0.047 0.451 1863 Planarity : 0.004 0.039 2037 Dihedral : 7.375 59.402 2154 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.95 % Allowed : 6.18 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1389 helix: 0.69 (0.22), residues: 552 sheet: 0.69 (0.31), residues: 243 loop : -1.17 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 564 HIS 0.002 0.001 HIS B 292 PHE 0.011 0.001 PHE B 222 TYR 0.008 0.001 TYR C 156 ARG 0.006 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7525 (tpp) cc_final: 0.6965 (tpp) REVERT: A 554 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7600 (t80) REVERT: A 561 LEU cc_start: 0.7929 (mt) cc_final: 0.7727 (mt) REVERT: B 475 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8457 (mtm) REVERT: B 554 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7430 (t80) REVERT: B 561 LEU cc_start: 0.7781 (mt) cc_final: 0.7423 (mt) REVERT: C 554 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.6337 (t80) REVERT: C 561 LEU cc_start: 0.8058 (mt) cc_final: 0.7820 (mt) outliers start: 12 outliers final: 1 residues processed: 77 average time/residue: 1.2488 time to fit residues: 106.1671 Evaluate side-chains 61 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11904 Z= 0.174 Angle : 0.593 8.041 16104 Z= 0.302 Chirality : 0.045 0.429 1863 Planarity : 0.003 0.037 2037 Dihedral : 6.832 59.995 2154 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.55 % Allowed : 8.79 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1389 helix: 0.89 (0.23), residues: 558 sheet: 0.83 (0.31), residues: 243 loop : -1.11 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 564 HIS 0.002 0.001 HIS A 292 PHE 0.009 0.001 PHE B 222 TYR 0.009 0.001 TYR C 448 ARG 0.003 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 1.464 Fit side-chains REVERT: A 98 MET cc_start: 0.7471 (tpp) cc_final: 0.7022 (tpp) REVERT: A 554 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7461 (t80) REVERT: B 475 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8186 (mtm) REVERT: B 554 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7149 (t80) REVERT: B 561 LEU cc_start: 0.7705 (mt) cc_final: 0.7217 (mt) REVERT: C 98 MET cc_start: 0.7323 (tpt) cc_final: 0.6907 (tpp) REVERT: C 333 THR cc_start: 0.9040 (p) cc_final: 0.8819 (t) REVERT: C 554 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6424 (t80) outliers start: 7 outliers final: 1 residues processed: 65 average time/residue: 1.2240 time to fit residues: 87.9859 Evaluate side-chains 62 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11904 Z= 0.300 Angle : 0.634 8.267 16104 Z= 0.319 Chirality : 0.047 0.473 1863 Planarity : 0.004 0.042 2037 Dihedral : 6.729 59.029 2154 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.71 % Allowed : 10.85 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1389 helix: 0.88 (0.22), residues: 558 sheet: 0.84 (0.32), residues: 243 loop : -1.07 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.004 0.001 HIS B 283 PHE 0.012 0.001 PHE C 226 TYR 0.016 0.001 TYR B 448 ARG 0.002 0.000 ARG B 423 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 104 THR cc_start: 0.8275 (p) cc_final: 0.8033 (t) REVERT: A 554 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7404 (t80) REVERT: B 104 THR cc_start: 0.8391 (p) cc_final: 0.8139 (t) REVERT: B 475 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8454 (mtm) REVERT: B 554 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7137 (t80) REVERT: B 561 LEU cc_start: 0.7799 (mt) cc_final: 0.7340 (mt) REVERT: C 98 MET cc_start: 0.7459 (tpt) cc_final: 0.6971 (tpp) REVERT: C 333 THR cc_start: 0.9081 (p) cc_final: 0.8880 (t) REVERT: C 554 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.6520 (t80) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 1.2067 time to fit residues: 89.6196 Evaluate side-chains 67 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 113 optimal weight: 0.0370 chunk 92 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11904 Z= 0.173 Angle : 0.562 7.944 16104 Z= 0.286 Chirality : 0.045 0.437 1863 Planarity : 0.003 0.039 2037 Dihedral : 6.328 56.944 2154 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.95 % Allowed : 11.56 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1389 helix: 1.19 (0.23), residues: 540 sheet: 0.89 (0.31), residues: 243 loop : -0.86 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 564 HIS 0.002 0.001 HIS B 292 PHE 0.009 0.001 PHE C 222 TYR 0.008 0.001 TYR B 448 ARG 0.002 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.438 Fit side-chains REVERT: A 98 MET cc_start: 0.7422 (tpp) cc_final: 0.7045 (tpp) REVERT: A 554 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7229 (t80) REVERT: B 104 THR cc_start: 0.8378 (p) cc_final: 0.8127 (t) REVERT: B 475 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8157 (mtm) REVERT: B 554 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7117 (t80) REVERT: C 98 MET cc_start: 0.7306 (tpt) cc_final: 0.6837 (tpp) REVERT: C 554 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.6477 (t80) outliers start: 12 outliers final: 2 residues processed: 71 average time/residue: 1.1341 time to fit residues: 89.6617 Evaluate side-chains 62 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN C 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11904 Z= 0.221 Angle : 0.582 7.882 16104 Z= 0.294 Chirality : 0.046 0.448 1863 Planarity : 0.003 0.041 2037 Dihedral : 6.248 57.298 2154 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.35 % Allowed : 12.91 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), residues: 1389 helix: 1.22 (0.23), residues: 543 sheet: 0.91 (0.31), residues: 243 loop : -0.78 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS B 283 PHE 0.009 0.001 PHE C 226 TYR 0.012 0.001 TYR B 448 ARG 0.002 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 1.515 Fit side-chains revert: symmetry clash REVERT: A 554 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: B 98 MET cc_start: 0.7231 (tpp) cc_final: 0.6949 (tpp) REVERT: B 104 THR cc_start: 0.8381 (p) cc_final: 0.8135 (t) REVERT: B 475 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8437 (mtm) REVERT: B 554 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: C 98 MET cc_start: 0.7594 (tpt) cc_final: 0.7115 (tpp) outliers start: 17 outliers final: 5 residues processed: 71 average time/residue: 1.2453 time to fit residues: 98.3682 Evaluate side-chains 64 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11904 Z= 0.215 Angle : 0.577 9.268 16104 Z= 0.292 Chirality : 0.046 0.447 1863 Planarity : 0.003 0.040 2037 Dihedral : 6.154 56.706 2154 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.74 % Allowed : 13.22 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1389 helix: 1.23 (0.23), residues: 543 sheet: 0.93 (0.32), residues: 243 loop : -0.75 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS B 283 PHE 0.009 0.001 PHE C 226 TYR 0.012 0.001 TYR B 448 ARG 0.002 0.000 ARG C 423 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7305 (tpp) cc_final: 0.6916 (tpp) REVERT: B 104 THR cc_start: 0.8379 (p) cc_final: 0.8135 (t) REVERT: B 475 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8312 (mtm) REVERT: C 98 MET cc_start: 0.7572 (tpt) cc_final: 0.7192 (tpp) outliers start: 22 outliers final: 9 residues processed: 79 average time/residue: 1.1901 time to fit residues: 103.7485 Evaluate side-chains 66 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11904 Z= 0.171 Angle : 0.561 8.078 16104 Z= 0.285 Chirality : 0.045 0.436 1863 Planarity : 0.003 0.039 2037 Dihedral : 6.010 55.988 2154 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.35 % Allowed : 14.33 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1389 helix: 1.29 (0.23), residues: 543 sheet: 0.95 (0.32), residues: 243 loop : -0.70 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS B 292 PHE 0.009 0.001 PHE C 226 TYR 0.010 0.001 TYR B 448 ARG 0.002 0.000 ARG C 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7170 (tpp) cc_final: 0.6856 (tpp) REVERT: B 98 MET cc_start: 0.7254 (tpp) cc_final: 0.7005 (tpp) REVERT: B 104 THR cc_start: 0.8378 (p) cc_final: 0.8132 (t) REVERT: B 475 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8285 (mtm) outliers start: 17 outliers final: 13 residues processed: 76 average time/residue: 1.1007 time to fit residues: 93.1769 Evaluate side-chains 72 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 74 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11904 Z= 0.160 Angle : 0.565 8.408 16104 Z= 0.286 Chirality : 0.045 0.429 1863 Planarity : 0.003 0.039 2037 Dihedral : 5.929 55.840 2154 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.19 % Allowed : 14.89 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1389 helix: 1.26 (0.23), residues: 543 sheet: 1.00 (0.32), residues: 243 loop : -0.69 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS B 292 PHE 0.034 0.001 PHE C 554 TYR 0.009 0.001 TYR B 448 ARG 0.002 0.000 ARG C 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7270 (tpp) cc_final: 0.6956 (tpp) REVERT: B 98 MET cc_start: 0.7296 (tpp) cc_final: 0.7050 (tpp) REVERT: B 104 THR cc_start: 0.8376 (p) cc_final: 0.8129 (t) REVERT: B 475 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8226 (mtm) outliers start: 15 outliers final: 13 residues processed: 75 average time/residue: 1.1927 time to fit residues: 100.3423 Evaluate side-chains 73 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11904 Z= 0.268 Angle : 0.612 12.818 16104 Z= 0.305 Chirality : 0.047 0.453 1863 Planarity : 0.003 0.041 2037 Dihedral : 6.028 56.806 2154 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.19 % Allowed : 15.12 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1389 helix: 1.20 (0.23), residues: 543 sheet: 0.99 (0.32), residues: 243 loop : -0.73 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 564 HIS 0.003 0.001 HIS C 283 PHE 0.026 0.001 PHE C 554 TYR 0.014 0.001 TYR B 448 ARG 0.002 0.000 ARG B 423 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7336 (tpp) cc_final: 0.7036 (tpp) REVERT: B 98 MET cc_start: 0.7324 (tpp) cc_final: 0.7062 (tpp) REVERT: B 104 THR cc_start: 0.8386 (p) cc_final: 0.8143 (t) REVERT: B 475 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8326 (mtm) outliers start: 15 outliers final: 10 residues processed: 73 average time/residue: 1.1043 time to fit residues: 89.8950 Evaluate side-chains 70 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 0.0030 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.114715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.075190 restraints weight = 17825.825| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.77 r_work: 0.2848 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11904 Z= 0.170 Angle : 0.582 15.819 16104 Z= 0.292 Chirality : 0.045 0.436 1863 Planarity : 0.003 0.040 2037 Dihedral : 5.932 56.011 2154 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.19 % Allowed : 15.20 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.23), residues: 1389 helix: 1.24 (0.23), residues: 543 sheet: 1.01 (0.32), residues: 243 loop : -0.70 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 564 HIS 0.003 0.001 HIS B 292 PHE 0.023 0.001 PHE C 554 TYR 0.010 0.001 TYR B 448 ARG 0.002 0.000 ARG C 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3067.64 seconds wall clock time: 56 minutes 49.38 seconds (3409.38 seconds total)