Starting phenix.real_space_refine on Wed Jul 30 05:34:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvb_34122/07_2025/7yvb_34122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvb_34122/07_2025/7yvb_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_34122/07_2025/7yvb_34122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvb_34122/07_2025/7yvb_34122.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvb_34122/07_2025/7yvb_34122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvb_34122/07_2025/7yvb_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.94, per 1000 atoms: 0.67 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: 3.51 Conformation dependent library (CDL) restraints added in 1.6 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: 1.56 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: 3.77 Time building geometry restraints manager: 4.04 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: 0.07 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: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.660 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.960 ------------------------------------------------------------------------------- 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 12183 Z= 0.376 Angle : 0.798 9.219 16533 Z= 0.444 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 18) link_NAG-ASN : angle 2.42651 ( 54) link_BETA1-4 : bond 0.00257 ( 12) link_BETA1-4 : angle 1.36385 ( 36) hydrogen bonds : bond 0.12707 ( 598) hydrogen bonds : angle 6.07902 ( 1758) SS BOND : bond 0.00552 ( 15) SS BOND : angle 1.54217 ( 30) covalent geometry : bond 0.00684 (12138) covalent geometry : angle 0.78370 (16413) *********************** 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 : 1.708 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: 1.4214 time to fit residues: 245.5166 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 : 1.335 ------------------------------------------------------------------------------- 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: 5.9990 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.094824 restraints weight = 15098.044| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.36 r_work: 0.2883 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12183 Z= 0.166 Angle : 0.656 9.241 16533 Z= 0.331 Chirality : 0.044 0.258 1890 Planarity : 0.004 0.059 2076 Dihedral : 8.239 57.364 2188 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.71 % Allowed : 9.19 % 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: -0.01 (0.22), residues: 1404 helix: 0.87 (0.22), residues: 600 sheet: -0.12 (0.31), residues: 228 loop : -0.81 (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 0.028 0.002 PHE B 462 TYR 0.016 0.001 TYR B 448 ARG 0.013 0.001 ARG C 484 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 18) link_NAG-ASN : angle 2.03063 ( 54) link_BETA1-4 : bond 0.00204 ( 12) link_BETA1-4 : angle 1.52708 ( 36) hydrogen bonds : bond 0.04019 ( 598) hydrogen bonds : angle 4.66688 ( 1758) SS BOND : bond 0.00479 ( 15) SS BOND : angle 1.32854 ( 30) covalent geometry : bond 0.00364 (12138) covalent geometry : angle 0.64112 (16413) *********************** 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 140 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.437 Fit side-chains REVERT: A 121 GLN cc_start: 0.8340 (mm110) cc_final: 0.8001 (mp10) REVERT: A 182 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8331 (mmm) REVERT: A 341 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: A 515 MET cc_start: 0.8747 (mtm) cc_final: 0.8536 (mtm) REVERT: B 337 LEU cc_start: 0.8875 (mt) cc_final: 0.8558 (mt) REVERT: B 477 ILE cc_start: 0.8538 (mt) cc_final: 0.8278 (mm) REVERT: B 515 MET cc_start: 0.8992 (mtm) cc_final: 0.8787 (mtm) REVERT: B 535 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8033 (mt-10) REVERT: C 98 MET cc_start: 0.5586 (ptt) cc_final: 0.5294 (ptm) REVERT: C 121 GLN cc_start: 0.8452 (mm110) cc_final: 0.8053 (mp10) REVERT: C 163 ASN cc_start: 0.8400 (m-40) cc_final: 0.8187 (t0) REVERT: C 182 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8389 (mtt) REVERT: C 227 ASP cc_start: 0.8548 (t0) cc_final: 0.8335 (t0) REVERT: C 321 LEU cc_start: 0.8820 (tp) cc_final: 0.8597 (tp) REVERT: R 3 ARG cc_start: 0.8703 (mtt-85) cc_final: 0.8407 (mtt90) outliers start: 22 outliers final: 2 residues processed: 124 average time/residue: 1.3552 time to fit residues: 182.4929 Evaluate side-chains 104 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain C residue 182 MET 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 102 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.093675 restraints weight = 15268.074| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.22 r_work: 0.2916 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12183 Z= 0.151 Angle : 0.615 9.370 16533 Z= 0.306 Chirality : 0.043 0.256 1890 Planarity : 0.004 0.053 2076 Dihedral : 7.548 57.575 2184 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.26 % Allowed : 10.98 % Favored : 86.76 % 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: -0.17 (0.31), residues: 228 loop : -0.75 (0.26), residues: 576 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 0.024 0.002 PHE B 462 TYR 0.015 0.001 TYR B 448 ARG 0.008 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 18) link_NAG-ASN : angle 1.86753 ( 54) link_BETA1-4 : bond 0.00398 ( 12) link_BETA1-4 : angle 1.44093 ( 36) hydrogen bonds : bond 0.03613 ( 598) hydrogen bonds : angle 4.46738 ( 1758) SS BOND : bond 0.00378 ( 15) SS BOND : angle 1.21970 ( 30) covalent geometry : bond 0.00335 (12138) covalent geometry : angle 0.60166 (16413) *********************** 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 147 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.225 Fit side-chains REVERT: A 121 GLN cc_start: 0.8325 (mm110) cc_final: 0.7841 (mm110) REVERT: A 163 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.7930 (t0) REVERT: A 341 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: A 515 MET cc_start: 0.8684 (mtm) cc_final: 0.8470 (mtm) REVERT: A 535 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7998 (mt-10) REVERT: B 121 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7725 (mm110) REVERT: B 337 LEU cc_start: 0.8875 (mt) cc_final: 0.8641 (mt) REVERT: B 515 MET cc_start: 0.8943 (mtm) cc_final: 0.8690 (mtm) REVERT: C 98 MET cc_start: 0.5644 (ptt) cc_final: 0.5349 (ptm) REVERT: C 121 GLN cc_start: 0.8443 (mm110) cc_final: 0.7867 (mm110) REVERT: C 163 ASN cc_start: 0.8413 (m-40) cc_final: 0.8179 (t0) REVERT: C 192 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8422 (pt) REVERT: C 227 ASP cc_start: 0.8508 (t0) cc_final: 0.8265 (t0) REVERT: C 543 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.8015 (mtp-110) REVERT: C 576 MET cc_start: 0.3692 (pmm) cc_final: 0.3329 (pmm) REVERT: R 3 ARG cc_start: 0.8597 (mtt-85) cc_final: 0.8372 (mtt-85) outliers start: 29 outliers final: 7 residues processed: 128 average time/residue: 1.2600 time to fit residues: 175.3878 Evaluate side-chains 111 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 25 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN B 119 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 = 0.3639 r_free = 0.3639 target = 0.134284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093275 restraints weight = 15199.448| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.22 r_work: 0.2907 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12183 Z= 0.161 Angle : 0.605 9.317 16533 Z= 0.300 Chirality : 0.043 0.252 1890 Planarity : 0.004 0.051 2076 Dihedral : 7.427 57.571 2184 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.02 % Allowed : 12.77 % Favored : 85.20 % 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: 0.28 (0.22), residues: 1404 helix: 1.14 (0.22), residues: 600 sheet: -0.09 (0.31), residues: 228 loop : -0.64 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 564 HIS 0.004 0.001 HIS B 283 PHE 0.016 0.001 PHE B 462 TYR 0.015 0.001 TYR B 448 ARG 0.009 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 18) link_NAG-ASN : angle 1.88038 ( 54) link_BETA1-4 : bond 0.00374 ( 12) link_BETA1-4 : angle 1.44447 ( 36) hydrogen bonds : bond 0.03523 ( 598) hydrogen bonds : angle 4.36480 ( 1758) SS BOND : bond 0.00334 ( 15) SS BOND : angle 1.17159 ( 30) covalent geometry : bond 0.00359 (12138) covalent geometry : angle 0.59170 (16413) *********************** 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 144 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.372 Fit side-chains REVERT: A 121 GLN cc_start: 0.8328 (mm110) cc_final: 0.7907 (mm110) REVERT: A 132 MET cc_start: 0.8633 (ptm) cc_final: 0.8396 (ptp) REVERT: A 346 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8695 (p) REVERT: A 535 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8010 (mt-10) REVERT: B 121 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: B 307 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8629 (pt) REVERT: B 337 LEU cc_start: 0.8893 (mt) cc_final: 0.8642 (mt) REVERT: B 515 MET cc_start: 0.8928 (mtm) cc_final: 0.8651 (mtm) REVERT: C 98 MET cc_start: 0.5782 (ptt) cc_final: 0.5432 (ptm) REVERT: C 121 GLN cc_start: 0.8489 (mm110) cc_final: 0.7922 (mm110) REVERT: C 163 ASN cc_start: 0.8443 (m-40) cc_final: 0.8191 (t0) REVERT: C 192 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8383 (pt) REVERT: C 543 ARG cc_start: 0.8319 (ttp-110) cc_final: 0.8020 (ttp-110) REVERT: R 3 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.8353 (mtt-85) outliers start: 26 outliers final: 8 residues processed: 130 average time/residue: 1.1655 time to fit residues: 166.1435 Evaluate side-chains 122 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 297 MET 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 43 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN B 183 ASN C 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.091139 restraints weight = 15292.393| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.20 r_work: 0.2876 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12183 Z= 0.219 Angle : 0.636 9.165 16533 Z= 0.317 Chirality : 0.044 0.245 1890 Planarity : 0.004 0.050 2076 Dihedral : 7.310 58.010 2184 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.73 % Allowed : 13.79 % Favored : 83.49 % 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: 1.10 (0.22), residues: 600 sheet: -0.09 (0.31), residues: 228 loop : -0.60 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 564 HIS 0.005 0.001 HIS A 283 PHE 0.014 0.002 PHE B 554 TYR 0.019 0.002 TYR B 448 ARG 0.011 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 18) link_NAG-ASN : angle 1.97861 ( 54) link_BETA1-4 : bond 0.00311 ( 12) link_BETA1-4 : angle 1.49707 ( 36) hydrogen bonds : bond 0.03690 ( 598) hydrogen bonds : angle 4.40645 ( 1758) SS BOND : bond 0.00348 ( 15) SS BOND : angle 1.24803 ( 30) covalent geometry : bond 0.00497 (12138) covalent geometry : angle 0.62233 (16413) *********************** 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 153 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 2.112 Fit side-chains REVERT: A 121 GLN cc_start: 0.8339 (mm110) cc_final: 0.7930 (mm110) REVERT: A 132 MET cc_start: 0.8612 (ptm) cc_final: 0.8392 (ptp) REVERT: A 160 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: A 182 MET cc_start: 0.9007 (mmm) cc_final: 0.8738 (mmt) REVERT: A 535 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7969 (mt-10) REVERT: B 121 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: B 307 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8838 (mt) REVERT: B 320 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8187 (mt) REVERT: B 337 LEU cc_start: 0.8916 (mt) cc_final: 0.8624 (mt) REVERT: B 515 MET cc_start: 0.8948 (mtm) cc_final: 0.8669 (mtm) REVERT: C 121 GLN cc_start: 0.8418 (mm110) cc_final: 0.7918 (mm110) REVERT: C 192 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8402 (pt) REVERT: C 518 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7790 (tt0) REVERT: C 543 ARG cc_start: 0.8250 (ttp-110) cc_final: 0.7857 (ttp-110) REVERT: R 3 ARG cc_start: 0.8617 (mtt-85) cc_final: 0.8359 (mtt-85) outliers start: 35 outliers final: 16 residues processed: 138 average time/residue: 1.6234 time to fit residues: 245.4033 Evaluate side-chains 126 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 313 SER 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 199 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 550 LEU 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 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 77 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 124 optimal weight: 0.3980 chunk 88 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 140 optimal weight: 0.0050 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099078 restraints weight = 15182.796| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.35 r_work: 0.2903 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12183 Z= 0.122 Angle : 0.590 9.343 16533 Z= 0.291 Chirality : 0.042 0.255 1890 Planarity : 0.004 0.048 2076 Dihedral : 6.982 56.941 2184 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.10 % Allowed : 14.80 % Favored : 83.10 % 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: 0.40 (0.23), residues: 1404 helix: 1.20 (0.22), residues: 597 sheet: -0.11 (0.32), residues: 228 loop : -0.48 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 564 HIS 0.002 0.001 HIS B 283 PHE 0.011 0.001 PHE B 170 TYR 0.014 0.001 TYR A 448 ARG 0.011 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 18) link_NAG-ASN : angle 1.72717 ( 54) link_BETA1-4 : bond 0.00392 ( 12) link_BETA1-4 : angle 1.38467 ( 36) hydrogen bonds : bond 0.03323 ( 598) hydrogen bonds : angle 4.29644 ( 1758) SS BOND : bond 0.00261 ( 15) SS BOND : angle 1.07098 ( 30) covalent geometry : bond 0.00270 (12138) covalent geometry : angle 0.57807 (16413) *********************** 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 149 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.150 Fit side-chains REVERT: A 121 GLN cc_start: 0.8335 (mm110) cc_final: 0.7973 (mm110) REVERT: A 132 MET cc_start: 0.8535 (ptm) cc_final: 0.8285 (ptp) REVERT: A 163 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.7989 (t0) REVERT: A 182 MET cc_start: 0.9111 (mmm) cc_final: 0.8850 (mmt) REVERT: A 227 ASP cc_start: 0.8387 (t0) cc_final: 0.8181 (t0) REVERT: A 265 ASP cc_start: 0.8546 (t0) cc_final: 0.8075 (t0) REVERT: A 346 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8769 (p) REVERT: A 535 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7959 (mt-10) REVERT: B 121 GLN cc_start: 0.8117 (mp10) cc_final: 0.7839 (mp10) REVERT: B 192 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8462 (pt) REVERT: B 307 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8617 (pt) REVERT: B 337 LEU cc_start: 0.8907 (mt) cc_final: 0.8684 (mt) REVERT: B 515 MET cc_start: 0.8938 (mtm) cc_final: 0.8666 (mtm) REVERT: B 543 ARG cc_start: 0.8318 (ttp-110) cc_final: 0.8060 (ttp-110) REVERT: C 98 MET cc_start: 0.5723 (ptt) cc_final: 0.5333 (ptm) REVERT: C 121 GLN cc_start: 0.8407 (mm110) cc_final: 0.7925 (mm110) REVERT: C 163 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8321 (t0) REVERT: C 265 ASP cc_start: 0.8483 (t70) cc_final: 0.8181 (t70) REVERT: C 518 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7816 (tt0) REVERT: C 543 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.7850 (ttp-110) REVERT: R 3 ARG cc_start: 0.8591 (mtt-85) cc_final: 0.8060 (mtt-85) outliers start: 27 outliers final: 9 residues processed: 139 average time/residue: 1.4989 time to fit residues: 229.6702 Evaluate side-chains 124 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 163 ASN 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 550 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 14 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 136 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093966 restraints weight = 15423.029| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.23 r_work: 0.2919 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12183 Z= 0.143 Angle : 0.614 9.279 16533 Z= 0.303 Chirality : 0.043 0.251 1890 Planarity : 0.004 0.050 2076 Dihedral : 6.932 57.616 2184 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.71 % Allowed : 15.42 % Favored : 82.87 % 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: 0.35 (0.23), residues: 1404 helix: 1.20 (0.22), residues: 597 sheet: -0.28 (0.31), residues: 237 loop : -0.48 (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 0.015 0.001 PHE B 554 TYR 0.014 0.001 TYR B 448 ARG 0.012 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 18) link_NAG-ASN : angle 1.75458 ( 54) link_BETA1-4 : bond 0.00383 ( 12) link_BETA1-4 : angle 1.38946 ( 36) hydrogen bonds : bond 0.03374 ( 598) hydrogen bonds : angle 4.29031 ( 1758) SS BOND : bond 0.00303 ( 15) SS BOND : angle 1.96624 ( 30) covalent geometry : bond 0.00319 (12138) covalent geometry : angle 0.59870 (16413) *********************** 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 137 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.548 Fit side-chains REVERT: A 121 GLN cc_start: 0.8300 (mm110) cc_final: 0.7922 (mm110) REVERT: A 132 MET cc_start: 0.8520 (ptm) cc_final: 0.8261 (ptp) REVERT: A 163 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.7937 (t0) REVERT: A 265 ASP cc_start: 0.8570 (t0) cc_final: 0.8103 (t0) REVERT: A 346 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8668 (p) REVERT: A 535 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7930 (mt-10) REVERT: B 121 GLN cc_start: 0.8063 (mp10) cc_final: 0.7806 (mp10) REVERT: B 307 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8586 (pt) REVERT: B 337 LEU cc_start: 0.8850 (mt) cc_final: 0.8623 (mt) REVERT: B 515 MET cc_start: 0.8865 (mtm) cc_final: 0.8587 (mtm) REVERT: B 543 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7942 (ttp80) REVERT: C 98 MET cc_start: 0.5841 (ptt) cc_final: 0.5475 (ptm) REVERT: C 121 GLN cc_start: 0.8366 (mm110) cc_final: 0.7868 (mm110) REVERT: C 192 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8387 (pt) REVERT: C 265 ASP cc_start: 0.8450 (t70) cc_final: 0.8180 (t70) REVERT: C 518 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7722 (tt0) REVERT: C 543 ARG cc_start: 0.8221 (ttp-110) cc_final: 0.7746 (ttp-110) REVERT: R 2 MET cc_start: 0.9329 (ptt) cc_final: 0.9093 (ptm) REVERT: R 3 ARG cc_start: 0.8567 (mtt-85) cc_final: 0.8259 (mtt-85) outliers start: 22 outliers final: 11 residues processed: 129 average time/residue: 1.1533 time to fit residues: 163.6854 Evaluate side-chains 122 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN 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 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 340 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 47 optimal weight: 20.0000 chunk 61 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.0670 chunk 127 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.093283 restraints weight = 15289.298| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.23 r_work: 0.2922 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12183 Z= 0.147 Angle : 0.615 9.266 16533 Z= 0.303 Chirality : 0.043 0.251 1890 Planarity : 0.004 0.052 2076 Dihedral : 6.818 57.481 2184 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.92 % Favored : 96.01 % Rotamer: Outliers : 1.79 % Allowed : 15.97 % Favored : 82.24 % 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: 0.36 (0.23), residues: 1404 helix: 1.21 (0.22), residues: 597 sheet: -0.27 (0.31), residues: 237 loop : -0.48 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 564 HIS 0.004 0.001 HIS B 283 PHE 0.015 0.001 PHE A 554 TYR 0.014 0.001 TYR B 448 ARG 0.013 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 18) link_NAG-ASN : angle 1.76184 ( 54) link_BETA1-4 : bond 0.00345 ( 12) link_BETA1-4 : angle 1.38124 ( 36) hydrogen bonds : bond 0.03372 ( 598) hydrogen bonds : angle 4.28586 ( 1758) SS BOND : bond 0.00290 ( 15) SS BOND : angle 1.79867 ( 30) covalent geometry : bond 0.00329 (12138) covalent geometry : angle 0.60062 (16413) *********************** 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 139 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.301 Fit side-chains REVERT: A 121 GLN cc_start: 0.8309 (mm110) cc_final: 0.7937 (mm110) REVERT: A 132 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8305 (ptp) REVERT: A 163 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.7935 (t0) REVERT: A 265 ASP cc_start: 0.8523 (t0) cc_final: 0.8024 (t0) REVERT: A 346 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8686 (p) REVERT: A 535 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7989 (mt-10) REVERT: B 121 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: B 307 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8606 (pt) REVERT: B 337 LEU cc_start: 0.8839 (mt) cc_final: 0.8617 (mt) REVERT: B 515 MET cc_start: 0.8859 (mtm) cc_final: 0.8576 (mtm) REVERT: B 543 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.7972 (ttp80) REVERT: C 98 MET cc_start: 0.5832 (ptt) cc_final: 0.5468 (ptm) REVERT: C 121 GLN cc_start: 0.8338 (mm110) cc_final: 0.7858 (mm110) REVERT: C 163 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8281 (t0) REVERT: C 192 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8377 (pt) REVERT: C 265 ASP cc_start: 0.8438 (t70) cc_final: 0.8183 (t70) REVERT: C 543 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7983 (mtp-110) REVERT: R 2 MET cc_start: 0.9317 (ptt) cc_final: 0.9109 (ptm) REVERT: R 3 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.8268 (mtt-85) outliers start: 23 outliers final: 12 residues processed: 130 average time/residue: 1.2004 time to fit residues: 171.4778 Evaluate side-chains 124 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 340 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 550 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 0.0020 chunk 108 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.135667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099756 restraints weight = 15193.870| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.38 r_work: 0.2906 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12183 Z= 0.121 Angle : 0.609 9.306 16533 Z= 0.299 Chirality : 0.042 0.252 1890 Planarity : 0.004 0.061 2076 Dihedral : 6.686 57.222 2184 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.71 % Allowed : 16.59 % 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: 0.36 (0.23), residues: 1404 helix: 1.23 (0.22), residues: 597 sheet: -0.30 (0.31), residues: 237 loop : -0.50 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 564 HIS 0.003 0.000 HIS B 283 PHE 0.016 0.001 PHE B 554 TYR 0.013 0.001 TYR A 448 ARG 0.015 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 18) link_NAG-ASN : angle 1.65561 ( 54) link_BETA1-4 : bond 0.00395 ( 12) link_BETA1-4 : angle 1.34068 ( 36) hydrogen bonds : bond 0.03277 ( 598) hydrogen bonds : angle 4.26088 ( 1758) SS BOND : bond 0.00293 ( 15) SS BOND : angle 1.79454 ( 30) covalent geometry : bond 0.00267 (12138) covalent geometry : angle 0.59530 (16413) *********************** 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 135 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.352 Fit side-chains REVERT: A 121 GLN cc_start: 0.8336 (mm110) cc_final: 0.7969 (mm110) REVERT: A 132 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8261 (ptp) REVERT: A 265 ASP cc_start: 0.8543 (t0) cc_final: 0.8065 (t0) REVERT: A 346 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8748 (p) REVERT: A 432 TYR cc_start: 0.8364 (m-80) cc_final: 0.8071 (m-80) REVERT: A 535 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8082 (mt-10) REVERT: B 121 GLN cc_start: 0.8135 (mp10) cc_final: 0.7861 (mp10) REVERT: B 307 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8638 (pt) REVERT: B 515 MET cc_start: 0.8883 (mtm) cc_final: 0.8652 (mtm) REVERT: B 543 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.7952 (ttp80) REVERT: C 98 MET cc_start: 0.5833 (ptt) cc_final: 0.5495 (ptm) REVERT: C 121 GLN cc_start: 0.8361 (mm110) cc_final: 0.7881 (mm110) REVERT: C 163 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8334 (t0) REVERT: C 192 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8409 (pt) REVERT: C 265 ASP cc_start: 0.8415 (t70) cc_final: 0.8137 (t70) REVERT: C 543 ARG cc_start: 0.8262 (ttp-110) cc_final: 0.8019 (mtp-110) REVERT: R 3 ARG cc_start: 0.8592 (mtt-85) cc_final: 0.8044 (mtt-85) outliers start: 22 outliers final: 10 residues processed: 128 average time/residue: 1.4592 time to fit residues: 203.6483 Evaluate side-chains 120 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 340 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 58 optimal weight: 0.0270 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 120 optimal weight: 0.2980 overall best weight: 0.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN C 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.094840 restraints weight = 15153.955| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.21 r_work: 0.2942 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12183 Z= 0.129 Angle : 0.624 9.900 16533 Z= 0.305 Chirality : 0.043 0.251 1890 Planarity : 0.004 0.062 2076 Dihedral : 6.637 57.487 2184 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.32 % Allowed : 17.21 % Favored : 81.46 % 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: 0.57 (0.23), residues: 1404 helix: 1.43 (0.22), residues: 579 sheet: -0.29 (0.31), residues: 237 loop : -0.30 (0.27), residues: 588 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 0.021 0.001 PHE A 554 TYR 0.015 0.001 TYR B 117 ARG 0.015 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 18) link_NAG-ASN : angle 1.65452 ( 54) link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 1.32878 ( 36) hydrogen bonds : bond 0.03302 ( 598) hydrogen bonds : angle 4.25724 ( 1758) SS BOND : bond 0.00335 ( 15) SS BOND : angle 1.71104 ( 30) covalent geometry : bond 0.00287 (12138) covalent geometry : angle 0.61141 (16413) ********************** 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 126 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.384 Fit side-chains REVERT: A 121 GLN cc_start: 0.8308 (mm110) cc_final: 0.7928 (mm110) REVERT: A 265 ASP cc_start: 0.8500 (t0) cc_final: 0.8008 (t0) REVERT: A 346 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8663 (p) REVERT: A 432 TYR cc_start: 0.8324 (m-80) cc_final: 0.8025 (m-80) REVERT: A 535 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 121 GLN cc_start: 0.8092 (mp10) cc_final: 0.7780 (mp10) REVERT: B 307 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8610 (pt) REVERT: B 515 MET cc_start: 0.8803 (mtm) cc_final: 0.8554 (mtm) REVERT: B 543 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7873 (ttp80) REVERT: C 98 MET cc_start: 0.5819 (ptt) cc_final: 0.5461 (ptm) REVERT: C 121 GLN cc_start: 0.8312 (mm110) cc_final: 0.7875 (mm110) REVERT: C 163 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8301 (t0) REVERT: C 192 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8370 (pt) REVERT: C 265 ASP cc_start: 0.8371 (t70) cc_final: 0.8085 (t70) REVERT: C 543 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7938 (mtp-110) REVERT: R 2 MET cc_start: 0.9320 (ptt) cc_final: 0.9119 (ptm) REVERT: R 3 ARG cc_start: 0.8554 (mtt-85) cc_final: 0.7997 (mtt-85) outliers start: 17 outliers final: 13 residues processed: 122 average time/residue: 1.2504 time to fit residues: 166.5392 Evaluate side-chains 118 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 313 SER 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 192 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 340 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 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 80 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 chunk 138 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN C 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100187 restraints weight = 15163.684| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.31 r_work: 0.2916 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12183 Z= 0.129 Angle : 0.623 10.804 16533 Z= 0.304 Chirality : 0.042 0.252 1890 Planarity : 0.004 0.059 2076 Dihedral : 6.575 57.360 2184 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.48 % Allowed : 17.76 % Favored : 80.76 % 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: 0.58 (0.23), residues: 1404 helix: 1.43 (0.22), residues: 579 sheet: -0.27 (0.31), residues: 237 loop : -0.30 (0.27), residues: 588 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 0.024 0.001 PHE B 554 TYR 0.012 0.001 TYR A 448 ARG 0.014 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 18) link_NAG-ASN : angle 1.63723 ( 54) link_BETA1-4 : bond 0.00375 ( 12) link_BETA1-4 : angle 1.31576 ( 36) hydrogen bonds : bond 0.03281 ( 598) hydrogen bonds : angle 4.26645 ( 1758) SS BOND : bond 0.00305 ( 15) SS BOND : angle 1.65718 ( 30) covalent geometry : bond 0.00287 (12138) covalent geometry : angle 0.61081 (16413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9766.84 seconds wall clock time: 173 minutes 22.23 seconds (10402.23 seconds total)