Starting phenix.real_space_refine on Fri Jul 3 04:16:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yvb_34122/07_2026/7yvb_34122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvb_34122/07_2026/7yvb_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yvb_34122/07_2026/7yvb_34122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvb_34122/07_2026/7yvb_34122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvb_34122/07_2026/7yvb_34122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvb_34122/07_2026/7yvb_34122.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yvb_34122/07_2026/7yvb_34122.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yvb_34122/07_2026/7yvb_34122.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 2.66, per 1000 atoms: 0.22 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: 1.02 Conformation dependent library (CDL) restraints added in 518.4 milliseconds 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: 0.38 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: 1.87 Time building geometry restraints manager: 1.35 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: 6331 17.69 - 35.39: 617 35.39 - 53.08: 138 53.08 - 70.77: 21 70.77 - 88.46: 12 Dihedral angle restraints: 7119 sinusoidal: 2937 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 7116 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: 0.03 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.700 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 : 14.783 88.463 4368 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (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 ARG 0.008 0.000 ARG B 204 TYR 0.018 0.002 TYR A 448 PHE 0.045 0.002 PHE C 462 TRP 0.009 0.002 TRP A 564 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.38 (12138) covalent geometry : angle 0.78370 / 0.44 (16413) SS BOND : bond 0.00552 / 0.36 ( 15) SS BOND : angle 1.54217 / 0.98 ( 30) hydrogen bonds : bond 0.12707 / 8.46 ( 598) hydrogen bonds : angle 6.07902 / 4.26 ( 1758) link_BETA1-4 : bond 0.00257 / 0.15 ( 12) link_BETA1-4 : angle 1.36385 / 0.97 ( 36) link_NAG-ASN : bond 0.00475 / 0.29 ( 18) link_NAG-ASN : angle 2.42651 / 1.63 ( 54) *********************** 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 : 0.354 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: 0.6256 time to fit residues: 107.6697 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 : 0.367 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 ASN A 322 HIS B 191 ASN B 322 HIS C 172 GLN C 191 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093895 restraints weight = 15099.364| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.22 r_work: 0.2922 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12183 Z= 0.141 Angle : 0.643 9.116 16533 Z= 0.324 Chirality : 0.044 0.267 1890 Planarity : 0.004 0.059 2076 Dihedral : 5.179 38.726 1558 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.56 % Allowed : 9.35 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.22), residues: 1404 helix: 0.90 (0.22), residues: 600 sheet: -0.14 (0.32), residues: 228 loop : -0.78 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 484 TYR 0.015 0.001 TYR C 432 PHE 0.029 0.002 PHE B 462 TRP 0.013 0.002 TRP C 564 HIS 0.002 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (12138) covalent geometry : angle 0.62890 / 0.32 (16413) SS BOND : bond 0.00375 / 0.22 ( 15) SS BOND : angle 1.40852 / 0.94 ( 30) hydrogen bonds : bond 0.03939 / 2.63 ( 598) hydrogen bonds : angle 4.64868 / 3.28 ( 1758) link_BETA1-4 : bond 0.00309 / 0.21 ( 12) link_BETA1-4 : angle 1.36399 / 0.94 ( 36) link_NAG-ASN : bond 0.00248 / 0.15 ( 18) link_NAG-ASN : angle 1.96076 / 1.33 ( 54) *********************** 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 141 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.452 Fit side-chains REVERT: A 121 GLN cc_start: 0.8311 (mm110) cc_final: 0.7969 (mp10) REVERT: A 182 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8208 (mmm) REVERT: A 341 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7777 (pt0) REVERT: A 515 MET cc_start: 0.8697 (mtm) cc_final: 0.8485 (mtm) REVERT: B 337 LEU cc_start: 0.8860 (mt) cc_final: 0.8566 (mt) REVERT: B 477 ILE cc_start: 0.8502 (mt) cc_final: 0.8257 (mm) REVERT: B 515 MET cc_start: 0.8952 (mtm) cc_final: 0.8732 (mtm) REVERT: B 535 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8007 (mt-10) REVERT: C 98 MET cc_start: 0.5601 (ptt) cc_final: 0.5292 (ptm) REVERT: C 121 GLN cc_start: 0.8428 (mm110) cc_final: 0.8012 (mp10) REVERT: C 163 ASN cc_start: 0.8368 (m-40) cc_final: 0.8164 (t0) REVERT: C 182 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8290 (mtt) REVERT: C 227 ASP cc_start: 0.8492 (t0) cc_final: 0.8274 (t0) REVERT: C 321 LEU cc_start: 0.8793 (tp) cc_final: 0.8553 (tp) REVERT: C 543 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7958 (mtp-110) REVERT: R 3 ARG cc_start: 0.8670 (mtt-85) cc_final: 0.8370 (mtt90) outliers start: 20 outliers final: 2 residues processed: 127 average time/residue: 0.4956 time to fit residues: 68.2907 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 : 0.446 ------------------------------------------------------------------------------- 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 0 optimal weight: 30.0000 chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 GLN A 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.091431 restraints weight = 15347.207| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.17 r_work: 0.2878 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12183 Z= 0.226 Angle : 0.660 9.207 16533 Z= 0.330 Chirality : 0.045 0.245 1890 Planarity : 0.004 0.053 2076 Dihedral : 5.041 27.769 1554 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.34 % Allowed : 11.06 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1404 helix: 0.96 (0.22), residues: 600 sheet: -0.12 (0.31), residues: 228 loop : -0.79 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 3 TYR 0.020 0.002 TYR B 448 PHE 0.021 0.002 PHE B 462 TRP 0.011 0.002 TRP C 564 HIS 0.006 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (12138) covalent geometry : angle 0.64601 / 0.33 (16413) SS BOND : bond 0.00402 / 0.24 ( 15) SS BOND : angle 1.45825 / 0.95 ( 30) hydrogen bonds : bond 0.03901 / 2.60 ( 598) hydrogen bonds : angle 4.55513 / 3.21 ( 1758) link_BETA1-4 : bond 0.00281 / 0.15 ( 12) link_BETA1-4 : angle 1.35663 / 0.96 ( 36) link_NAG-ASN : bond 0.00446 / 0.28 ( 18) link_NAG-ASN : angle 1.98689 / 1.34 ( 54) *********************** 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 149 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.316 Fit side-chains REVERT: A 121 GLN cc_start: 0.8330 (mm110) cc_final: 0.7867 (mm110) REVERT: A 163 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.7991 (t0) REVERT: A 341 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: A 515 MET cc_start: 0.8745 (mtm) cc_final: 0.8531 (mtm) REVERT: A 535 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 121 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7759 (mm110) REVERT: B 307 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8884 (mt) REVERT: B 337 LEU cc_start: 0.8954 (mt) cc_final: 0.8667 (mt) REVERT: B 477 ILE cc_start: 0.8648 (mt) cc_final: 0.8433 (mm) REVERT: B 515 MET cc_start: 0.8997 (mtm) cc_final: 0.8693 (mtm) REVERT: C 98 MET cc_start: 0.5731 (ptt) cc_final: 0.5389 (ptm) REVERT: C 121 GLN cc_start: 0.8505 (mm110) cc_final: 0.7953 (mm110) REVERT: C 192 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8423 (pt) REVERT: C 227 ASP cc_start: 0.8591 (t0) cc_final: 0.8346 (t0) REVERT: C 543 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7988 (ttp80) REVERT: C 576 MET cc_start: 0.3624 (pmm) cc_final: 0.3292 (pmm) REVERT: R 3 ARG cc_start: 0.8647 (mtt-85) cc_final: 0.8434 (mtt-85) outliers start: 30 outliers final: 9 residues processed: 132 average time/residue: 0.4727 time to fit residues: 68.2607 Evaluate side-chains 117 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 A residue 359 LEU Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 132 MET 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 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 59 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 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 = 0.3633 r_free = 0.3633 target = 0.133856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092841 restraints weight = 15302.278| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.22 r_work: 0.2902 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1655 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= 0.157 Angle : 0.604 9.299 16533 Z= 0.301 Chirality : 0.043 0.265 1890 Planarity : 0.004 0.052 2076 Dihedral : 4.865 26.590 1554 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.79 % Allowed : 13.63 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.22), residues: 1404 helix: 1.08 (0.22), residues: 600 sheet: -0.13 (0.32), residues: 228 loop : -0.64 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 242 TYR 0.015 0.001 TYR B 448 PHE 0.014 0.002 PHE B 462 TRP 0.012 0.001 TRP A 564 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (12138) covalent geometry : angle 0.59181 / 0.30 (16413) SS BOND : bond 0.00319 / 0.19 ( 15) SS BOND : angle 1.14536 / 0.74 ( 30) hydrogen bonds : bond 0.03524 / 2.36 ( 598) hydrogen bonds : angle 4.38232 / 3.09 ( 1758) link_BETA1-4 : bond 0.00311 / 0.19 ( 12) link_BETA1-4 : angle 1.32259 / 0.92 ( 36) link_NAG-ASN : bond 0.00278 / 0.18 ( 18) link_NAG-ASN : angle 1.82824 / 1.24 ( 54) *********************** 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 138 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.356 Fit side-chains REVERT: A 121 GLN cc_start: 0.8327 (mm110) cc_final: 0.7904 (mm110) REVERT: A 346 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8613 (p) REVERT: A 535 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8026 (mt-10) REVERT: B 121 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7768 (mp10) REVERT: B 337 LEU cc_start: 0.8894 (mt) cc_final: 0.8643 (mt) REVERT: B 515 MET cc_start: 0.8953 (mtm) cc_final: 0.8685 (mtm) REVERT: C 98 MET cc_start: 0.5820 (ptt) cc_final: 0.5439 (ptm) REVERT: C 121 GLN cc_start: 0.8500 (mm110) cc_final: 0.7923 (mm110) REVERT: C 163 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8321 (t0) REVERT: C 192 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8364 (pt) REVERT: C 227 ASP cc_start: 0.8540 (t0) cc_final: 0.8274 (t0) REVERT: C 518 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7713 (tt0) REVERT: C 543 ARG cc_start: 0.8212 (ttp-110) cc_final: 0.7910 (ttp80) REVERT: R 3 ARG cc_start: 0.8595 (mtt-85) cc_final: 0.8371 (mtt-85) outliers start: 23 outliers final: 5 residues processed: 127 average time/residue: 0.4760 time to fit residues: 66.2571 Evaluate side-chains 112 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 67 optimal weight: 0.0030 chunk 94 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.135258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099381 restraints weight = 15352.850| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.40 r_work: 0.2879 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1862 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= 0.125 Angle : 0.584 9.357 16533 Z= 0.288 Chirality : 0.042 0.262 1890 Planarity : 0.004 0.049 2076 Dihedral : 4.676 25.436 1554 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.10 % Allowed : 14.02 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1404 helix: 1.20 (0.22), residues: 600 sheet: -0.15 (0.31), residues: 228 loop : -0.50 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 242 TYR 0.013 0.001 TYR A 448 PHE 0.011 0.001 PHE C 277 TRP 0.011 0.001 TRP B 564 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (12138) covalent geometry : angle 0.57334 / 0.29 (16413) SS BOND : bond 0.00287 / 0.17 ( 15) SS BOND : angle 1.07339 / 0.70 ( 30) hydrogen bonds : bond 0.03335 / 2.22 ( 598) hydrogen bonds : angle 4.31668 / 3.06 ( 1758) link_BETA1-4 : bond 0.00358 / 0.22 ( 12) link_BETA1-4 : angle 1.25334 / 0.88 ( 36) link_NAG-ASN : bond 0.00198 / 0.14 ( 18) link_NAG-ASN : angle 1.70312 / 1.17 ( 54) *********************** 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 151 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.342 Fit side-chains REVERT: A 121 GLN cc_start: 0.8393 (mm110) cc_final: 0.7971 (mm110) REVERT: A 160 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: A 163 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.7990 (t0) REVERT: A 227 ASP cc_start: 0.8344 (t0) cc_final: 0.8110 (t0) REVERT: A 265 ASP cc_start: 0.8601 (t0) cc_final: 0.8105 (t0) REVERT: A 535 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8026 (mt-10) REVERT: B 121 GLN cc_start: 0.8099 (mp10) cc_final: 0.7857 (mp10) REVERT: B 337 LEU cc_start: 0.8908 (mt) cc_final: 0.8689 (mt) REVERT: B 515 MET cc_start: 0.8949 (mtm) cc_final: 0.8672 (mtm) REVERT: B 543 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.7938 (ttp80) REVERT: C 98 MET cc_start: 0.5713 (ptt) cc_final: 0.5381 (ptm) REVERT: C 121 GLN cc_start: 0.8435 (mm110) cc_final: 0.7914 (mm110) REVERT: C 163 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8345 (t0) REVERT: C 192 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8430 (pt) REVERT: C 265 ASP cc_start: 0.8503 (t0) cc_final: 0.8214 (t70) REVERT: C 518 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7819 (tt0) REVERT: C 543 ARG cc_start: 0.8250 (ttp-110) cc_final: 0.7916 (ttp80) REVERT: R 3 ARG cc_start: 0.8603 (mtt-85) cc_final: 0.8364 (mtt-85) outliers start: 27 outliers final: 9 residues processed: 141 average time/residue: 0.4336 time to fit residues: 67.1712 Evaluate side-chains 119 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 320 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 97 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 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 = 0.3610 r_free = 0.3610 target = 0.131951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091130 restraints weight = 15413.259| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.17 r_work: 0.2873 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12183 Z= 0.240 Angle : 0.655 9.216 16533 Z= 0.327 Chirality : 0.045 0.257 1890 Planarity : 0.004 0.048 2076 Dihedral : 5.000 36.636 1554 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.96 % Allowed : 14.56 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1404 helix: 1.10 (0.22), residues: 600 sheet: -0.12 (0.31), residues: 228 loop : -0.53 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 242 TYR 0.021 0.002 TYR B 448 PHE 0.014 0.002 PHE A 463 TRP 0.010 0.001 TRP C 564 HIS 0.005 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (12138) covalent geometry : angle 0.63994 / 0.32 (16413) SS BOND : bond 0.00436 / 0.28 ( 15) SS BOND : angle 1.99796 / 1.01 ( 30) hydrogen bonds : bond 0.03734 / 2.49 ( 598) hydrogen bonds : angle 4.39545 / 3.11 ( 1758) link_BETA1-4 : bond 0.00255 / 0.13 ( 12) link_BETA1-4 : angle 1.37861 / 0.98 ( 36) link_NAG-ASN : bond 0.00419 / 0.26 ( 18) link_NAG-ASN : angle 1.89134 / 1.28 ( 54) *********************** 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: 38 poor density : 111 time to evaluate : 0.469 Fit side-chains REVERT: A 121 GLN cc_start: 0.8315 (mm110) cc_final: 0.7946 (mm110) REVERT: A 163 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.7977 (t0) REVERT: A 182 MET cc_start: 0.9209 (mmt) cc_final: 0.8818 (mmt) REVERT: A 341 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: A 346 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8609 (p) REVERT: A 535 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7943 (mt-10) REVERT: B 121 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7734 (mp10) REVERT: B 307 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8856 (mt) REVERT: B 320 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8199 (mt) REVERT: B 337 LEU cc_start: 0.8946 (mt) cc_final: 0.8662 (mt) REVERT: B 515 MET cc_start: 0.8965 (mtm) cc_final: 0.8693 (mtm) REVERT: C 121 GLN cc_start: 0.8450 (mm110) cc_final: 0.7973 (mm110) REVERT: C 163 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8081 (t0) REVERT: C 192 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8436 (pt) REVERT: C 518 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7765 (tt0) REVERT: C 543 ARG cc_start: 0.8219 (ttp-110) cc_final: 0.7912 (ttp80) REVERT: R 3 ARG cc_start: 0.8629 (mtt-85) cc_final: 0.8338 (mtt-85) outliers start: 38 outliers final: 18 residues processed: 133 average time/residue: 0.5226 time to fit residues: 75.9700 Evaluate side-chains 131 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 359 LEU 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 550 LEU 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 320 LEU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 53 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 133 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 GLN A 172 GLN C 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.134166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093323 restraints weight = 15311.912| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.22 r_work: 0.2900 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1949 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= 0.145 Angle : 0.617 9.275 16533 Z= 0.305 Chirality : 0.043 0.260 1890 Planarity : 0.004 0.048 2076 Dihedral : 4.848 35.376 1554 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.41 % Allowed : 15.26 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1404 helix: 1.16 (0.22), residues: 597 sheet: -0.28 (0.31), residues: 237 loop : -0.49 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 242 TYR 0.015 0.001 TYR A 448 PHE 0.014 0.001 PHE A 554 TRP 0.011 0.001 TRP C 564 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12138) covalent geometry : angle 0.60317 / 0.30 (16413) SS BOND : bond 0.00292 / 0.18 ( 15) SS BOND : angle 1.79907 / 0.91 ( 30) hydrogen bonds : bond 0.03429 / 2.29 ( 598) hydrogen bonds : angle 4.32992 / 3.06 ( 1758) link_BETA1-4 : bond 0.00316 / 0.19 ( 12) link_BETA1-4 : angle 1.27682 / 0.90 ( 36) link_NAG-ASN : bond 0.00251 / 0.16 ( 18) link_NAG-ASN : angle 1.74553 / 1.19 ( 54) *********************** 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 150 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.417 Fit side-chains REVERT: A 121 GLN cc_start: 0.8302 (mm110) cc_final: 0.7929 (mm110) REVERT: A 163 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.7948 (t0) REVERT: A 182 MET cc_start: 0.9153 (mmt) cc_final: 0.8915 (mmt) REVERT: A 204 ARG cc_start: 0.8712 (mtm110) cc_final: 0.8488 (ttp-110) REVERT: A 227 ASP cc_start: 0.8368 (t0) cc_final: 0.8095 (t0) REVERT: A 265 ASP cc_start: 0.8576 (t0) cc_final: 0.8343 (t70) REVERT: A 346 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8611 (p) REVERT: A 535 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 121 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: B 307 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8583 (pt) REVERT: B 320 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8150 (mt) REVERT: B 337 LEU cc_start: 0.8882 (mt) cc_final: 0.8642 (mt) REVERT: B 515 MET cc_start: 0.8924 (mtm) cc_final: 0.8648 (mtm) REVERT: B 543 ARG cc_start: 0.8247 (ttp-110) cc_final: 0.7837 (ttp80) REVERT: C 98 MET cc_start: 0.5699 (ptt) cc_final: 0.5294 (ptm) REVERT: C 121 GLN cc_start: 0.8414 (mm110) cc_final: 0.7916 (mm110) REVERT: C 163 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8267 (t0) REVERT: C 192 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8390 (pt) REVERT: C 265 ASP cc_start: 0.8433 (t70) cc_final: 0.8140 (t70) REVERT: C 341 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7549 (pt0) REVERT: C 518 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7712 (tt0) REVERT: C 543 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7899 (ttp80) REVERT: R 3 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.8259 (mtt-85) outliers start: 31 outliers final: 13 residues processed: 137 average time/residue: 0.5212 time to fit residues: 77.6407 Evaluate side-chains 129 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 354 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 131 SER 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 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 320 LEU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 341 GLN 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 29 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.133870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092646 restraints weight = 15127.190| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.21 r_work: 0.2910 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2032 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= 0.151 Angle : 0.622 9.692 16533 Z= 0.306 Chirality : 0.043 0.257 1890 Planarity : 0.004 0.055 2076 Dihedral : 4.803 31.995 1554 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.02 % Allowed : 16.04 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1404 helix: 1.19 (0.22), residues: 597 sheet: -0.30 (0.31), residues: 237 loop : -0.53 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 242 TYR 0.014 0.001 TYR B 448 PHE 0.017 0.001 PHE B 554 TRP 0.011 0.001 TRP C 564 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (12138) covalent geometry : angle 0.60879 / 0.30 (16413) SS BOND : bond 0.00301 / 0.18 ( 15) SS BOND : angle 1.79458 / 0.92 ( 30) hydrogen bonds : bond 0.03414 / 2.28 ( 598) hydrogen bonds : angle 4.31340 / 3.06 ( 1758) link_BETA1-4 : bond 0.00333 / 0.19 ( 12) link_BETA1-4 : angle 1.25745 / 0.89 ( 36) link_NAG-ASN : bond 0.00250 / 0.16 ( 18) link_NAG-ASN : angle 1.70881 / 1.16 ( 54) *********************** 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 144 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.455 Fit side-chains REVERT: A 121 GLN cc_start: 0.8307 (mm110) cc_final: 0.7942 (mm110) REVERT: A 163 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.7972 (t0) REVERT: A 182 MET cc_start: 0.9155 (mmt) cc_final: 0.8843 (mmt) REVERT: A 265 ASP cc_start: 0.8564 (t0) cc_final: 0.8269 (t70) REVERT: A 346 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8631 (p) REVERT: A 535 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 121 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: B 307 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8584 (pt) REVERT: B 320 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8159 (mt) REVERT: B 337 LEU cc_start: 0.8861 (mt) cc_final: 0.8616 (mt) REVERT: B 515 MET cc_start: 0.8867 (mtm) cc_final: 0.8592 (mtm) REVERT: B 543 ARG cc_start: 0.8262 (ttp-110) cc_final: 0.7857 (ttp80) REVERT: C 98 MET cc_start: 0.5725 (ptt) cc_final: 0.5347 (ptm) REVERT: C 121 GLN cc_start: 0.8448 (mm110) cc_final: 0.7948 (mm110) REVERT: C 163 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8283 (t0) REVERT: C 192 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8411 (pt) REVERT: C 265 ASP cc_start: 0.8452 (t70) cc_final: 0.8146 (t70) REVERT: C 341 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: C 543 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7891 (ttp80) REVERT: R 3 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8304 (mtt-85) outliers start: 26 outliers final: 13 residues processed: 134 average time/residue: 0.5319 time to fit residues: 77.9277 Evaluate side-chains 127 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 354 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 131 SER 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 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 341 GLN 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 94 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.091845 restraints weight = 15065.819| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.20 r_work: 0.2897 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12183 Z= 0.179 Angle : 0.640 9.231 16533 Z= 0.316 Chirality : 0.044 0.256 1890 Planarity : 0.004 0.057 2076 Dihedral : 4.848 32.701 1554 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 2.10 % Allowed : 16.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.23), residues: 1404 helix: 1.16 (0.22), residues: 597 sheet: -0.30 (0.31), residues: 237 loop : -0.55 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 204 TYR 0.016 0.001 TYR B 448 PHE 0.016 0.002 PHE A 554 TRP 0.010 0.001 TRP C 564 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (12138) covalent geometry : angle 0.62762 / 0.31 (16413) SS BOND : bond 0.00303 / 0.19 ( 15) SS BOND : angle 1.74409 / 0.92 ( 30) hydrogen bonds : bond 0.03502 / 2.33 ( 598) hydrogen bonds : angle 4.34165 / 3.08 ( 1758) link_BETA1-4 : bond 0.00310 / 0.18 ( 12) link_BETA1-4 : angle 1.27540 / 0.91 ( 36) link_NAG-ASN : bond 0.00303 / 0.20 ( 18) link_NAG-ASN : angle 1.76017 / 1.19 ( 54) *********************** 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 138 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.510 Fit side-chains REVERT: A 121 GLN cc_start: 0.8337 (mm110) cc_final: 0.7970 (mm110) REVERT: A 163 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.7954 (t0) REVERT: A 182 MET cc_start: 0.9164 (mmt) cc_final: 0.8857 (mmt) REVERT: A 204 ARG cc_start: 0.8713 (ttp-110) cc_final: 0.8380 (mtm110) REVERT: A 265 ASP cc_start: 0.8565 (t0) cc_final: 0.8325 (t70) REVERT: A 346 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 121 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: B 307 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8595 (pt) REVERT: B 320 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8130 (mt) REVERT: B 337 LEU cc_start: 0.8868 (mt) cc_final: 0.8613 (mt) REVERT: B 515 MET cc_start: 0.8912 (mtm) cc_final: 0.8638 (mtm) REVERT: C 98 MET cc_start: 0.5715 (ptt) cc_final: 0.5336 (ptm) REVERT: C 121 GLN cc_start: 0.8394 (mm110) cc_final: 0.7888 (mm110) REVERT: C 163 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8318 (t0) REVERT: C 192 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8403 (pt) REVERT: C 265 ASP cc_start: 0.8456 (t70) cc_final: 0.8172 (t70) REVERT: C 341 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7556 (pt0) REVERT: C 543 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7836 (ttp80) outliers start: 27 outliers final: 17 residues processed: 127 average time/residue: 0.4906 time to fit residues: 68.2462 Evaluate side-chains 128 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER 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 354 CYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 131 SER 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 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 341 GLN Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 19 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 115 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099523 restraints weight = 15309.821| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.38 r_work: 0.2895 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2178 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= 0.130 Angle : 0.625 10.204 16533 Z= 0.306 Chirality : 0.042 0.259 1890 Planarity : 0.004 0.061 2076 Dihedral : 4.715 32.467 1554 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.56 % Allowed : 17.13 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1404 helix: 1.19 (0.22), residues: 597 sheet: -0.31 (0.31), residues: 237 loop : -0.52 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 242 TYR 0.015 0.001 TYR A 448 PHE 0.016 0.001 PHE B 554 TRP 0.013 0.002 TRP C 564 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (12138) covalent geometry : angle 0.61381 / 0.30 (16413) SS BOND : bond 0.00280 / 0.17 ( 15) SS BOND : angle 1.60886 / 0.85 ( 30) hydrogen bonds : bond 0.03334 / 2.21 ( 598) hydrogen bonds : angle 4.31196 / 3.06 ( 1758) link_BETA1-4 : bond 0.00374 / 0.23 ( 12) link_BETA1-4 : angle 1.22005 / 0.86 ( 36) link_NAG-ASN : bond 0.00204 / 0.14 ( 18) link_NAG-ASN : angle 1.62088 / 1.11 ( 54) ********************** 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 132 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.464 Fit side-chains REVERT: A 121 GLN cc_start: 0.8348 (mm110) cc_final: 0.7988 (mm110) REVERT: A 163 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8031 (t0) REVERT: A 204 ARG cc_start: 0.8711 (ttp-110) cc_final: 0.8380 (mtm110) REVERT: A 265 ASP cc_start: 0.8541 (t0) cc_final: 0.8061 (t0) REVERT: A 346 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8709 (p) REVERT: B 121 GLN cc_start: 0.8132 (mp10) cc_final: 0.7856 (mp10) REVERT: B 307 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8627 (pt) REVERT: B 320 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8264 (mt) REVERT: B 337 LEU cc_start: 0.8873 (mt) cc_final: 0.8671 (mt) REVERT: B 515 MET cc_start: 0.8939 (mtm) cc_final: 0.8664 (mtm) REVERT: C 98 MET cc_start: 0.5889 (ptt) cc_final: 0.5474 (ptm) REVERT: C 121 GLN cc_start: 0.8376 (mm110) cc_final: 0.7948 (mm110) REVERT: C 163 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8349 (t0) REVERT: C 265 ASP cc_start: 0.8430 (t70) cc_final: 0.8159 (t70) REVERT: C 543 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7909 (mtp-110) outliers start: 20 outliers final: 12 residues processed: 126 average time/residue: 0.5466 time to fit residues: 75.0705 Evaluate side-chains 120 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 340 ILE 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 163 ASN 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 89 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 56 optimal weight: 0.0030 chunk 94 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.135085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099233 restraints weight = 15220.325| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.38 r_work: 0.2894 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2245 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 : 0.629 10.413 16533 Z= 0.307 Chirality : 0.042 0.260 1890 Planarity : 0.004 0.063 2076 Dihedral : 4.672 32.364 1554 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.56 % Allowed : 17.21 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.23), residues: 1404 helix: 1.19 (0.22), residues: 597 sheet: -0.30 (0.31), residues: 237 loop : -0.51 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 242 TYR 0.015 0.001 TYR B 117 PHE 0.018 0.001 PHE A 554 TRP 0.012 0.002 TRP C 564 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (12138) covalent geometry : angle 0.61791 / 0.30 (16413) SS BOND : bond 0.00310 / 0.18 ( 15) SS BOND : angle 1.66972 / 0.92 ( 30) hydrogen bonds : bond 0.03319 / 2.19 ( 598) hydrogen bonds : angle 4.30337 / 3.06 ( 1758) link_BETA1-4 : bond 0.00344 / 0.21 ( 12) link_BETA1-4 : angle 1.20494 / 0.85 ( 36) link_NAG-ASN : bond 0.00197 / 0.14 ( 18) link_NAG-ASN : angle 1.60125 / 1.10 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3974.50 seconds wall clock time: 68 minutes 29.54 seconds (4109.54 seconds total)