Starting phenix.real_space_refine on Mon Dec 30 03:03:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvb_34122/12_2024/7yvb_34122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvb_34122/12_2024/7yvb_34122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvb_34122/12_2024/7yvb_34122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvb_34122/12_2024/7yvb_34122.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvb_34122/12_2024/7yvb_34122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvb_34122/12_2024/7yvb_34122.cif" } resolution = 2.9 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= 0.004 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: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 7530 2.51 5 N 1974 2.21 5 O 2304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 11889 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3781 Classifications: {'peptide': 471} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 449} Chain breaks: 1 Chain: "B" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3781 Classifications: {'peptide': 471} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 449} Chain breaks: 1 Chain: "C" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3781 Classifications: {'peptide': 471} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 449} Chain breaks: 1 Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} 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: 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: "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: 7.61, per 1000 atoms: 0.64 Number of scatterers: 11889 At special positions: 0 Unit cell: (104.86, 113.42, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2304 8.00 N 1974 7.00 C 7530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 233 " distance=2.03 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 435 " distance=2.04 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 429 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 435 " distance=2.04 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 429 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 435 " distance=2.04 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 431 " distance=2.03 Simple disulfide: pdb=" SG CYS C 354 " - pdb=" SG CYS C 429 " distance=2.04 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 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: 3.74 Conformation dependent library (CDL) restraints added in 1.7 seconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 24 sheets defined 43.6% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 91 through 119 removed outlier: 3.570A pdb=" N TRP A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.592A pdb=" N MET A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 removed outlier: 3.837A pdb=" N PHE A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 removed outlier: 3.504A pdb=" N ALA A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) 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 346 through 363 Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'A' and resid 406 through 421 Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 454 through 467 removed outlier: 3.565A pdb=" N ARG A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 Processing helix chain 'A' and resid 509 through 526 Processing helix chain 'A' and resid 549 through 577 removed outlier: 5.204A pdb=" N GLY A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A 566 " --> pdb=" O GLY A 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 119 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 161 through 174 removed outlier: 3.518A pdb=" N THR B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.591A pdb=" N MET B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.838A pdb=" N PHE B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 200 removed outlier: 3.504A pdb=" N ALA B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) 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 346 through 363 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 406 through 421 Processing helix chain 'B' and resid 423 through 428 Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.565A pdb=" N ARG B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 487 Processing helix chain 'B' and resid 509 through 526 Processing helix chain 'B' and resid 549 through 577 removed outlier: 5.204A pdb=" N GLY B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B 566 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 119 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.591A pdb=" N MET C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 removed outlier: 3.837A pdb=" N PHE C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.504A pdb=" N ALA C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) 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 346 through 363 Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'C' and resid 406 through 421 Processing helix chain 'C' and resid 423 through 428 Processing helix chain 'C' and resid 454 through 467 removed outlier: 3.565A pdb=" N ARG C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 487 Processing helix chain 'C' and resid 509 through 526 Processing helix chain 'C' and resid 549 through 577 removed outlier: 5.204A pdb=" N GLY C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU C 563 " --> pdb=" O GLY C 559 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY C 566 " --> pdb=" O GLY C 562 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL A 540 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 319 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR A 542 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 321 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN A 544 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR A 323 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 311 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER A 261 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU A 207 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS A 210 " --> pdb=" O CYS A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL A 540 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 319 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR A 542 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 321 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN A 544 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 7.346A 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: 3.968A 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 226 removed outlier: 6.197A pdb=" N ASN A 232 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 143 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.037A pdb=" N HIS A 175 " --> pdb=" O ILE A 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA7, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA8, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA9, first strand: chain 'B' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL B 540 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 319 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR B 542 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU B 321 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN B 544 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR B 323 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR B 311 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER B 261 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B 207 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS B 210 " --> pdb=" O CYS B 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL B 540 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 319 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR B 542 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU B 321 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN B 544 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR B 323 " --> pdb=" O GLN B 544 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.968A pdb=" N VAL B 134 " --> pdb=" O MET B 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 222 through 226 removed outlier: 6.197A pdb=" N ASN B 232 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 143 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 175 through 176 removed outlier: 7.037A pdb=" N HIS B 175 " --> pdb=" O ILE B 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 272 through 273 Processing sheet with id=AB6, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AB7, first strand: chain 'B' and resid 365 through 366 Processing sheet with id=AB8, first strand: chain 'C' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL C 540 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA C 319 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR C 542 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 321 " --> pdb=" O TYR C 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN C 544 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR C 323 " --> pdb=" O GLN C 544 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR C 311 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER C 261 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU C 207 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS C 210 " --> pdb=" O CYS C 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL C 540 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA C 319 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR C 542 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 321 " --> pdb=" O TYR C 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN C 544 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR C 323 " --> pdb=" O GLN C 544 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.968A pdb=" N VAL C 134 " --> pdb=" O MET C 247 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 222 through 226 removed outlier: 6.197A pdb=" N ASN C 232 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN C 143 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 175 through 176 removed outlier: 7.037A pdb=" N HIS C 175 " --> pdb=" O ILE C 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 272 through 273 Processing sheet with id=AC5, first strand: chain 'C' and resid 336 through 337 Processing sheet with id=AC6, first strand: chain 'C' and resid 365 through 366 622 hydrogen bonds defined for protein. 1758 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: 4.30 Time building geometry restraints manager: 4.17 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: 3780 1.34 - 1.46: 2845 1.46 - 1.58: 5393 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 12138 Sorted by residual: bond pdb=" C PRO A 434 " pdb=" N CYS A 435 " ideal model delta sigma weight residual 1.335 1.482 -0.147 1.30e-02 5.92e+03 1.27e+02 bond pdb=" C PRO C 434 " pdb=" N CYS C 435 " ideal model delta sigma weight residual 1.335 1.482 -0.147 1.30e-02 5.92e+03 1.27e+02 bond pdb=" C PRO B 434 " pdb=" N CYS B 435 " ideal model delta sigma weight residual 1.335 1.482 -0.147 1.30e-02 5.92e+03 1.27e+02 bond pdb=" C GLN B 472 " pdb=" N HIS B 473 " ideal model delta sigma weight residual 1.331 1.477 -0.146 1.51e-02 4.39e+03 9.37e+01 bond pdb=" C GLN A 472 " pdb=" N HIS A 473 " ideal model delta sigma weight residual 1.331 1.477 -0.146 1.51e-02 4.39e+03 9.34e+01 ... (remaining 12133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 15779 1.84 - 3.69: 553 3.69 - 5.53: 60 5.53 - 7.38: 9 7.38 - 9.22: 12 Bond angle restraints: 16413 Sorted by residual: angle pdb=" C MET C 475 " pdb=" N LYS C 476 " pdb=" CA LYS C 476 " ideal model delta sigma weight residual 120.29 111.96 8.33 1.42e+00 4.96e-01 3.44e+01 angle pdb=" C MET B 475 " pdb=" N LYS B 476 " pdb=" CA LYS B 476 " ideal model delta sigma weight residual 120.29 111.96 8.33 1.42e+00 4.96e-01 3.44e+01 angle pdb=" C MET A 475 " pdb=" N LYS A 476 " pdb=" CA LYS A 476 " ideal model delta sigma weight residual 120.29 112.00 8.29 1.42e+00 4.96e-01 3.41e+01 angle pdb=" C GLY C 228 " pdb=" N ASN C 229 " pdb=" CA ASN C 229 " ideal model delta sigma weight residual 121.54 129.97 -8.43 1.91e+00 2.74e-01 1.95e+01 angle pdb=" C GLY B 228 " pdb=" N ASN B 229 " pdb=" CA ASN B 229 " ideal model delta sigma weight residual 121.54 129.96 -8.42 1.91e+00 2.74e-01 1.94e+01 ... (remaining 16408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6859 17.69 - 35.39: 676 35.39 - 53.08: 166 53.08 - 70.77: 36 70.77 - 88.46: 12 Dihedral angle restraints: 7749 sinusoidal: 3567 harmonic: 4182 Sorted by residual: dihedral pdb=" CB CYS A 354 " pdb=" SG CYS A 354 " pdb=" SG CYS A 429 " pdb=" CB CYS A 429 " ideal model delta sinusoidal sigma weight residual -86.00 -22.44 -63.56 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS B 354 " pdb=" SG CYS B 354 " pdb=" SG CYS B 429 " pdb=" CB CYS B 429 " ideal model delta sinusoidal sigma weight residual -86.00 -22.70 -63.30 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CB CYS C 354 " pdb=" SG CYS C 354 " pdb=" SG CYS C 429 " pdb=" CB CYS C 429 " ideal model delta sinusoidal sigma weight residual -86.00 -22.74 -63.26 1 1.00e+01 1.00e-02 5.28e+01 ... (remaining 7746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1318 0.044 - 0.088: 401 0.088 - 0.132: 144 0.132 - 0.176: 24 0.176 - 0.220: 3 Chirality restraints: 1890 Sorted by residual: chirality pdb=" CB ILE A 208 " pdb=" CA ILE A 208 " pdb=" CG1 ILE A 208 " pdb=" CG2 ILE A 208 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE C 208 " pdb=" CA ILE C 208 " pdb=" CG1 ILE C 208 " pdb=" CG2 ILE C 208 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE B 208 " pdb=" CA ILE B 208 " pdb=" CG1 ILE B 208 " pdb=" CG2 ILE B 208 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1887 not shown) Planarity restraints: 2094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 462 " 0.016 2.00e-02 2.50e+03 1.96e-02 6.76e+00 pdb=" CG PHE C 462 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 462 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 462 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE C 462 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 462 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 462 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 462 " 0.016 2.00e-02 2.50e+03 1.95e-02 6.69e+00 pdb=" CG PHE A 462 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 462 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 462 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 462 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 462 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 462 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 462 " -0.016 2.00e-02 2.50e+03 1.95e-02 6.67e+00 pdb=" CG PHE B 462 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 462 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 462 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE B 462 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 462 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 462 " -0.001 2.00e-02 2.50e+03 ... (remaining 2091 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1802 2.75 - 3.29: 11735 3.29 - 3.83: 20550 3.83 - 4.36: 24642 4.36 - 4.90: 41705 Nonbonded interactions: 100434 Sorted by model distance: nonbonded pdb=" OG SER A 284 " pdb=" OG SER B 447 " model vdw 2.215 3.040 nonbonded pdb=" OG SER A 447 " pdb=" OG SER C 284 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 284 " pdb=" OG SER C 447 " model vdw 2.215 3.040 nonbonded pdb=" O GLY C 295 " pdb=" N ARG C 344 " model vdw 2.225 3.120 nonbonded pdb=" O GLY A 295 " pdb=" N ARG A 344 " model vdw 2.225 3.120 ... (remaining 100429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 0.970 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: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.140 Process input model: 31.340 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:14.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 0.147 12138 Z= 0.439 Angle : 0.784 9.219 16413 Z= 0.441 Chirality : 0.048 0.220 1890 Planarity : 0.005 0.063 2076 Dihedral : 14.818 88.463 4998 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.17 % Allowed : 1.40 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -0.41 (0.22), residues: 1404 helix: 0.35 (0.21), residues: 591 sheet: 0.08 (0.33), residues: 213 loop : -0.95 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 564 HIS 0.003 0.001 HIS B 283 PHE 0.045 0.002 PHE C 462 TYR 0.018 0.002 TYR A 448 ARG 0.008 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.451 Fit side-chains REVERT: A 121 GLN cc_start: 0.7953 (mm110) cc_final: 0.7741 (mm110) REVERT: B 576 MET cc_start: 0.3038 (pmm) cc_final: 0.2711 (pmm) REVERT: C 121 GLN cc_start: 0.8025 (mm110) cc_final: 0.7765 (mm110) REVERT: C 576 MET cc_start: 0.3654 (pmm) cc_final: 0.3242 (pmm) REVERT: P 2 MET cc_start: 0.9176 (ptt) cc_final: 0.8943 (ptt) REVERT: Q 3 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7809 (mtt90) outliers start: 15 outliers final: 0 residues processed: 160 average time/residue: 1.4311 time to fit residues: 246.8881 Evaluate side-chains 100 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 3 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 128 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 191 ASN A 322 HIS B 191 ASN C 172 GLN C 191 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12138 Z= 0.222 Angle : 0.638 9.377 16413 Z= 0.326 Chirality : 0.044 0.252 1890 Planarity : 0.004 0.060 2076 Dihedral : 8.211 57.134 2188 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.56 % Allowed : 9.35 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.03 (0.22), residues: 1404 helix: 0.91 (0.22), residues: 600 sheet: -0.13 (0.32), residues: 228 loop : -0.80 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 564 HIS 0.003 0.001 HIS B 283 PHE 0.030 0.002 PHE B 462 TYR 0.016 0.001 TYR C 432 ARG 0.006 0.001 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.325 Fit side-chains REVERT: A 341 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7740 (pt0) REVERT: A 515 MET cc_start: 0.8517 (mtm) cc_final: 0.8307 (mtm) REVERT: A 548 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.8166 (t80) REVERT: B 337 LEU cc_start: 0.8824 (mt) cc_final: 0.8602 (mt) REVERT: B 515 MET cc_start: 0.8736 (mtm) cc_final: 0.8466 (mtm) REVERT: C 98 MET cc_start: 0.5665 (ptt) cc_final: 0.5327 (ptm) REVERT: C 576 MET cc_start: 0.4069 (pmm) cc_final: 0.3712 (pmm) outliers start: 20 outliers final: 2 residues processed: 125 average time/residue: 1.3663 time to fit residues: 185.3897 Evaluate side-chains 103 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 0.0470 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 191 ASN B 119 GLN C 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12138 Z= 0.227 Angle : 0.602 9.330 16413 Z= 0.303 Chirality : 0.043 0.257 1890 Planarity : 0.004 0.053 2076 Dihedral : 7.559 57.701 2184 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.34 % Allowed : 11.21 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.12 (0.22), residues: 1404 helix: 1.03 (0.22), residues: 600 sheet: -0.19 (0.31), residues: 228 loop : -0.75 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 564 HIS 0.003 0.001 HIS C 283 PHE 0.024 0.002 PHE B 462 TYR 0.015 0.001 TYR B 448 ARG 0.008 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.450 Fit side-chains REVERT: A 163 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.7928 (t0) REVERT: A 182 MET cc_start: 0.8451 (mmm) cc_final: 0.8234 (mmm) REVERT: A 341 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: A 515 MET cc_start: 0.8510 (mtm) cc_final: 0.8291 (mtm) REVERT: B 121 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7621 (mm110) REVERT: B 337 LEU cc_start: 0.8858 (mt) cc_final: 0.8646 (mt) REVERT: B 477 ILE cc_start: 0.8681 (mp) cc_final: 0.8459 (mm) REVERT: B 515 MET cc_start: 0.8718 (mtm) cc_final: 0.8406 (mtm) REVERT: C 98 MET cc_start: 0.5784 (ptt) cc_final: 0.5407 (ptm) REVERT: R 3 ARG cc_start: 0.8422 (mtt90) cc_final: 0.8124 (mtt-85) outliers start: 30 outliers final: 8 residues processed: 132 average time/residue: 1.3025 time to fit residues: 187.1422 Evaluate side-chains 112 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 86 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 122 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN B 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12138 Z= 0.172 Angle : 0.569 9.373 16413 Z= 0.285 Chirality : 0.042 0.256 1890 Planarity : 0.004 0.051 2076 Dihedral : 7.193 57.187 2184 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.87 % Allowed : 13.63 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.29 (0.22), residues: 1404 helix: 1.17 (0.22), residues: 600 sheet: -0.18 (0.31), residues: 228 loop : -0.61 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 564 HIS 0.002 0.001 HIS B 283 PHE 0.016 0.002 PHE B 462 TYR 0.012 0.001 TYR A 448 ARG 0.012 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.409 Fit side-chains REVERT: A 265 ASP cc_start: 0.7525 (t0) cc_final: 0.7255 (t0) REVERT: A 346 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8924 (p) REVERT: B 477 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8488 (mm) REVERT: B 515 MET cc_start: 0.8637 (mtm) cc_final: 0.8397 (mtm) REVERT: C 98 MET cc_start: 0.5767 (ptt) cc_final: 0.5373 (ptm) REVERT: R 3 ARG cc_start: 0.8327 (mtt90) cc_final: 0.8021 (mtt-85) outliers start: 24 outliers final: 7 residues processed: 129 average time/residue: 1.1636 time to fit residues: 165.2408 Evaluate side-chains 114 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 12138 Z= 0.586 Angle : 0.732 9.115 16413 Z= 0.371 Chirality : 0.049 0.233 1890 Planarity : 0.005 0.050 2076 Dihedral : 7.573 58.892 2184 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.04 % Allowed : 14.17 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.04 (0.22), residues: 1404 helix: 0.85 (0.21), residues: 603 sheet: -0.20 (0.30), residues: 237 loop : -0.66 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 564 HIS 0.008 0.002 HIS B 283 PHE 0.017 0.002 PHE B 463 TYR 0.030 0.002 TYR B 448 ARG 0.010 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 1.471 Fit side-chains REVERT: A 341 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7761 (pt0) REVERT: A 346 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8876 (p) REVERT: B 320 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7990 (mt) REVERT: B 477 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8497 (mm) REVERT: B 515 MET cc_start: 0.8722 (mtm) cc_final: 0.8479 (mtm) REVERT: C 98 MET cc_start: 0.5979 (ptt) cc_final: 0.5559 (ptm) REVERT: C 163 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.7947 (t0) REVERT: R 3 ARG cc_start: 0.8424 (mtt90) cc_final: 0.7946 (mtt-85) outliers start: 39 outliers final: 16 residues processed: 133 average time/residue: 1.1400 time to fit residues: 166.6821 Evaluate side-chains 123 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 136 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 172 GLN B 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12138 Z= 0.199 Angle : 0.603 9.287 16413 Z= 0.303 Chirality : 0.042 0.248 1890 Planarity : 0.004 0.051 2076 Dihedral : 7.197 56.895 2184 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.57 % Allowed : 14.64 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.27 (0.22), residues: 1404 helix: 1.08 (0.22), residues: 600 sheet: -0.19 (0.31), residues: 228 loop : -0.54 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 564 HIS 0.003 0.001 HIS B 283 PHE 0.014 0.002 PHE B 554 TYR 0.015 0.001 TYR A 448 ARG 0.013 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.490 Fit side-chains REVERT: A 182 MET cc_start: 0.8969 (mmt) cc_final: 0.8694 (mmt) REVERT: A 307 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8565 (pt) REVERT: A 346 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8848 (p) REVERT: B 477 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8478 (mm) REVERT: B 515 MET cc_start: 0.8701 (mtm) cc_final: 0.8438 (mtm) REVERT: C 98 MET cc_start: 0.5951 (ptt) cc_final: 0.5546 (ptm) REVERT: C 192 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8346 (pt) outliers start: 33 outliers final: 10 residues processed: 133 average time/residue: 1.1195 time to fit residues: 164.5213 Evaluate side-chains 117 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 82 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12138 Z= 0.201 Angle : 0.605 9.749 16413 Z= 0.301 Chirality : 0.042 0.251 1890 Planarity : 0.004 0.048 2076 Dihedral : 6.988 57.507 2184 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.64 % Allowed : 15.81 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.34 (0.23), residues: 1404 helix: 1.15 (0.22), residues: 597 sheet: -0.20 (0.32), residues: 228 loop : -0.48 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 564 HIS 0.003 0.001 HIS B 283 PHE 0.011 0.001 PHE C 277 TYR 0.014 0.001 TYR A 448 ARG 0.012 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.434 Fit side-chains REVERT: A 182 MET cc_start: 0.8970 (mmt) cc_final: 0.8723 (mmp) REVERT: A 265 ASP cc_start: 0.7572 (t0) cc_final: 0.7297 (t0) REVERT: A 307 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8627 (pt) REVERT: A 346 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8926 (p) REVERT: B 477 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8508 (mm) REVERT: B 515 MET cc_start: 0.8693 (mtm) cc_final: 0.8454 (mtm) outliers start: 21 outliers final: 12 residues processed: 128 average time/residue: 1.1040 time to fit residues: 155.9301 Evaluate side-chains 123 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12138 Z= 0.274 Angle : 0.636 9.217 16413 Z= 0.316 Chirality : 0.043 0.247 1890 Planarity : 0.004 0.053 2076 Dihedral : 6.968 57.843 2184 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.94 % Rotamer: Outliers : 1.71 % Allowed : 16.28 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.32 (0.22), residues: 1404 helix: 1.14 (0.22), residues: 597 sheet: -0.19 (0.31), residues: 228 loop : -0.50 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 564 HIS 0.005 0.001 HIS B 283 PHE 0.017 0.002 PHE B 554 TYR 0.016 0.001 TYR B 448 ARG 0.014 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.417 Fit side-chains REVERT: A 182 MET cc_start: 0.9002 (mmt) cc_final: 0.8737 (mmp) REVERT: A 204 ARG cc_start: 0.7697 (ttp-110) cc_final: 0.7481 (mtm110) REVERT: A 307 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8586 (pt) REVERT: A 346 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8862 (p) REVERT: B 477 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8493 (mm) REVERT: B 515 MET cc_start: 0.8696 (mtm) cc_final: 0.8459 (mtm) REVERT: C 98 MET cc_start: 0.5702 (ptt) cc_final: 0.5314 (ptm) REVERT: C 163 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7939 (t0) outliers start: 22 outliers final: 17 residues processed: 121 average time/residue: 1.1595 time to fit residues: 154.3237 Evaluate side-chains 125 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 133 optimal weight: 0.0970 chunk 81 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12138 Z= 0.197 Angle : 0.614 9.267 16413 Z= 0.304 Chirality : 0.042 0.251 1890 Planarity : 0.004 0.057 2076 Dihedral : 6.798 57.266 2184 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.95 % Allowed : 15.81 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.34 (0.23), residues: 1404 helix: 1.20 (0.22), residues: 597 sheet: -0.31 (0.31), residues: 237 loop : -0.48 (0.26), residues: 570 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 0.013 0.001 PHE A 554 TYR 0.025 0.001 TYR B 117 ARG 0.016 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.396 Fit side-chains REVERT: A 307 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8626 (pt) REVERT: A 346 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8925 (p) REVERT: B 477 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8517 (mm) REVERT: B 515 MET cc_start: 0.8661 (mtm) cc_final: 0.8421 (mtm) REVERT: C 98 MET cc_start: 0.5790 (ptt) cc_final: 0.5404 (ptm) outliers start: 25 outliers final: 13 residues processed: 131 average time/residue: 1.2357 time to fit residues: 178.1704 Evaluate side-chains 123 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 354 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 140 optimal weight: 0.0370 chunk 129 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12138 Z= 0.223 Angle : 0.641 10.474 16413 Z= 0.317 Chirality : 0.043 0.249 1890 Planarity : 0.004 0.061 2076 Dihedral : 6.823 57.588 2184 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.40 % Allowed : 16.59 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.34 (0.23), residues: 1404 helix: 1.18 (0.22), residues: 597 sheet: -0.31 (0.31), residues: 237 loop : -0.47 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 564 HIS 0.003 0.001 HIS B 283 PHE 0.025 0.002 PHE B 554 TYR 0.023 0.001 TYR B 117 ARG 0.015 0.001 ARG A 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.443 Fit side-chains REVERT: A 307 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8612 (pt) REVERT: A 346 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8941 (p) REVERT: B 515 MET cc_start: 0.8660 (mtm) cc_final: 0.8417 (mtm) REVERT: C 98 MET cc_start: 0.5708 (ptt) cc_final: 0.5293 (ptm) outliers start: 18 outliers final: 14 residues processed: 119 average time/residue: 1.1502 time to fit residues: 150.7817 Evaluate side-chains 117 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 115 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 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 119 GLN A 172 GLN C 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093628 restraints weight = 15246.734| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.21 r_work: 0.2935 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12138 Z= 0.209 Angle : 0.635 11.131 16413 Z= 0.313 Chirality : 0.043 0.250 1890 Planarity : 0.004 0.061 2076 Dihedral : 6.759 57.425 2184 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.32 % Allowed : 16.98 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.33 (0.23), residues: 1404 helix: 1.18 (0.22), residues: 597 sheet: -0.32 (0.31), residues: 237 loop : -0.46 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 564 HIS 0.003 0.001 HIS B 283 PHE 0.021 0.001 PHE A 554 TYR 0.022 0.001 TYR B 117 ARG 0.016 0.001 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3844.01 seconds wall clock time: 69 minutes 58.86 seconds (4198.86 seconds total)