Starting phenix.real_space_refine on Sat Aug 23 12:25:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvb_34122/08_2025/7yvb_34122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvb_34122/08_2025/7yvb_34122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvb_34122/08_2025/7yvb_34122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvb_34122/08_2025/7yvb_34122.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvb_34122/08_2025/7yvb_34122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvb_34122/08_2025/7yvb_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-2.0-5787/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.52, per 1000 atoms: 0.30 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: 1.18 Conformation dependent library (CDL) restraints added in 609.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.49 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: 2.07 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3780 1.34 - 1.46: 2845 1.46 - 1.58: 5393 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 12138 Sorted by residual: bond pdb=" C PRO A 434 " pdb=" N CYS A 435 " ideal model delta sigma weight residual 1.335 1.482 -0.147 1.30e-02 5.92e+03 1.27e+02 bond pdb=" C PRO C 434 " pdb=" N CYS C 435 " ideal model delta sigma weight residual 1.335 1.482 -0.147 1.30e-02 5.92e+03 1.27e+02 bond pdb=" C PRO B 434 " pdb=" N CYS B 435 " ideal model delta sigma weight residual 1.335 1.482 -0.147 1.30e-02 5.92e+03 1.27e+02 bond pdb=" C GLN B 472 " pdb=" N HIS B 473 " ideal model delta sigma weight residual 1.331 1.477 -0.146 1.51e-02 4.39e+03 9.37e+01 bond pdb=" C GLN A 472 " pdb=" N HIS A 473 " ideal model delta sigma weight residual 1.331 1.477 -0.146 1.51e-02 4.39e+03 9.34e+01 ... (remaining 12133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 15779 1.84 - 3.69: 553 3.69 - 5.53: 60 5.53 - 7.38: 9 7.38 - 9.22: 12 Bond angle restraints: 16413 Sorted by residual: angle pdb=" C MET C 475 " pdb=" N LYS C 476 " pdb=" CA LYS C 476 " ideal model delta sigma weight residual 120.29 111.96 8.33 1.42e+00 4.96e-01 3.44e+01 angle pdb=" C MET B 475 " pdb=" N LYS B 476 " pdb=" CA LYS B 476 " ideal model delta sigma weight residual 120.29 111.96 8.33 1.42e+00 4.96e-01 3.44e+01 angle pdb=" C MET A 475 " pdb=" N LYS A 476 " pdb=" CA LYS A 476 " ideal model delta sigma weight residual 120.29 112.00 8.29 1.42e+00 4.96e-01 3.41e+01 angle pdb=" C GLY C 228 " pdb=" N ASN C 229 " pdb=" CA ASN C 229 " ideal model delta sigma weight residual 121.54 129.97 -8.43 1.91e+00 2.74e-01 1.95e+01 angle pdb=" C GLY B 228 " pdb=" N ASN B 229 " pdb=" CA ASN B 229 " ideal model delta sigma weight residual 121.54 129.96 -8.42 1.91e+00 2.74e-01 1.94e+01 ... (remaining 16408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6859 17.69 - 35.39: 676 35.39 - 53.08: 166 53.08 - 70.77: 36 70.77 - 88.46: 12 Dihedral angle restraints: 7749 sinusoidal: 3567 harmonic: 4182 Sorted by residual: dihedral pdb=" CB CYS A 354 " pdb=" SG CYS A 354 " pdb=" SG CYS A 429 " pdb=" CB CYS A 429 " ideal model delta sinusoidal sigma weight residual -86.00 -22.44 -63.56 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS B 354 " pdb=" SG CYS B 354 " pdb=" SG CYS B 429 " pdb=" CB CYS B 429 " ideal model delta sinusoidal sigma weight residual -86.00 -22.70 -63.30 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CB CYS C 354 " pdb=" SG CYS C 354 " pdb=" SG CYS C 429 " pdb=" CB CYS C 429 " ideal model delta sinusoidal sigma weight residual -86.00 -22.74 -63.26 1 1.00e+01 1.00e-02 5.28e+01 ... (remaining 7746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1318 0.044 - 0.088: 401 0.088 - 0.132: 144 0.132 - 0.176: 24 0.176 - 0.220: 3 Chirality restraints: 1890 Sorted by residual: chirality pdb=" CB ILE A 208 " pdb=" CA ILE A 208 " pdb=" CG1 ILE A 208 " pdb=" CG2 ILE A 208 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE C 208 " pdb=" CA ILE C 208 " pdb=" CG1 ILE C 208 " pdb=" CG2 ILE C 208 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE B 208 " pdb=" CA ILE B 208 " pdb=" CG1 ILE B 208 " pdb=" CG2 ILE B 208 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1887 not shown) Planarity restraints: 2094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 462 " 0.016 2.00e-02 2.50e+03 1.96e-02 6.76e+00 pdb=" CG PHE C 462 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 462 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 462 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE C 462 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 462 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 462 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 462 " 0.016 2.00e-02 2.50e+03 1.95e-02 6.69e+00 pdb=" CG PHE A 462 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 462 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 462 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 462 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 462 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 462 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 462 " -0.016 2.00e-02 2.50e+03 1.95e-02 6.67e+00 pdb=" CG PHE B 462 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 462 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 462 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE B 462 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 462 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 462 " -0.001 2.00e-02 2.50e+03 ... (remaining 2091 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1802 2.75 - 3.29: 11735 3.29 - 3.83: 20550 3.83 - 4.36: 24642 4.36 - 4.90: 41705 Nonbonded interactions: 100434 Sorted by model distance: nonbonded pdb=" OG SER A 284 " pdb=" OG SER B 447 " model vdw 2.215 3.040 nonbonded pdb=" OG SER A 447 " pdb=" OG SER C 284 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 284 " pdb=" OG SER C 447 " model vdw 2.215 3.040 nonbonded pdb=" O GLY C 295 " pdb=" N ARG C 344 " model vdw 2.225 3.120 nonbonded pdb=" O GLY A 295 " pdb=" N ARG A 344 " model vdw 2.225 3.120 ... (remaining 100429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.280 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.147 12183 Z= 0.376 Angle : 0.798 9.219 16533 Z= 0.444 Chirality : 0.048 0.220 1890 Planarity : 0.005 0.063 2076 Dihedral : 14.818 88.463 4998 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.17 % Allowed : 1.40 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00684 (12138) covalent geometry : angle 0.78370 (16413) SS BOND : bond 0.00552 ( 15) SS BOND : angle 1.54217 ( 30) hydrogen bonds : bond 0.12707 ( 598) hydrogen bonds : angle 6.07902 ( 1758) link_BETA1-4 : bond 0.00257 ( 12) link_BETA1-4 : angle 1.36385 ( 36) link_NAG-ASN : bond 0.00475 ( 18) link_NAG-ASN : angle 2.42651 ( 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 : 0.397 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: 0.6849 time to fit residues: 117.6754 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 : 0.463 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 322 HIS B 191 ASN B 322 HIS C 172 GLN C 191 ASN C 322 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.094003 restraints weight = 15113.652| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.22 r_work: 0.2930 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12183 Z= 0.141 Angle : 0.644 9.342 16533 Z= 0.324 Chirality : 0.044 0.268 1890 Planarity : 0.004 0.058 2076 Dihedral : 8.182 57.170 2188 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.56 % Allowed : 8.96 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.22), residues: 1404 helix: 0.91 (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 0.009 0.001 ARG C 484 TYR 0.014 0.001 TYR C 432 PHE 0.030 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 covalent geometry : bond 0.00302 (12138) covalent geometry : angle 0.63008 (16413) SS BOND : bond 0.00361 ( 15) SS BOND : angle 1.19574 ( 30) hydrogen bonds : bond 0.03893 ( 598) hydrogen bonds : angle 4.63911 ( 1758) link_BETA1-4 : bond 0.00367 ( 12) link_BETA1-4 : angle 1.53602 ( 36) link_NAG-ASN : bond 0.00264 ( 18) link_NAG-ASN : angle 1.97671 ( 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 140 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.513 Fit side-chains REVERT: A 121 GLN cc_start: 0.8314 (mm110) cc_final: 0.7973 (mp10) REVERT: A 182 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8206 (mmm) REVERT: A 341 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7772 (pt0) REVERT: A 515 MET cc_start: 0.8708 (mtm) cc_final: 0.8499 (mtm) REVERT: B 337 LEU cc_start: 0.8863 (mt) cc_final: 0.8578 (mt) REVERT: B 477 ILE cc_start: 0.8511 (mt) cc_final: 0.8264 (mm) REVERT: B 515 MET cc_start: 0.8959 (mtm) cc_final: 0.8746 (mtm) REVERT: B 535 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8005 (mt-10) REVERT: C 98 MET cc_start: 0.5602 (ptt) cc_final: 0.5297 (ptm) REVERT: C 121 GLN cc_start: 0.8431 (mm110) cc_final: 0.8036 (mp10) REVERT: C 163 ASN cc_start: 0.8382 (m-40) cc_final: 0.8179 (t0) REVERT: C 182 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8296 (mtt) REVERT: C 543 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7970 (mtp-110) REVERT: R 3 ARG cc_start: 0.8657 (mtt-85) cc_final: 0.8362 (mtt90) outliers start: 20 outliers final: 2 residues processed: 126 average time/residue: 0.6460 time to fit residues: 87.8463 Evaluate side-chains 102 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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: 4.9990 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.090054 restraints weight = 15424.345| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.23 r_work: 0.2856 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12183 Z= 0.263 Angle : 0.684 9.221 16533 Z= 0.342 Chirality : 0.046 0.246 1890 Planarity : 0.004 0.053 2076 Dihedral : 7.818 58.358 2184 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.18 % Allowed : 11.45 % Favored : 86.37 % 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 aren not related in a simple way. whole: 0.03 (0.22), residues: 1404 helix: 0.91 (0.21), residues: 600 sheet: -0.10 (0.31), residues: 231 loop : -0.81 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 242 TYR 0.022 0.002 TYR B 448 PHE 0.023 0.002 PHE B 462 TRP 0.011 0.001 TRP C 564 HIS 0.006 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00592 (12138) covalent geometry : angle 0.66857 (16413) SS BOND : bond 0.00414 ( 15) SS BOND : angle 1.49266 ( 30) hydrogen bonds : bond 0.04011 ( 598) hydrogen bonds : angle 4.59406 ( 1758) link_BETA1-4 : bond 0.00305 ( 12) link_BETA1-4 : angle 1.57474 ( 36) link_NAG-ASN : bond 0.00540 ( 18) link_NAG-ASN : angle 2.12629 ( 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 143 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.480 Fit side-chains REVERT: A 121 GLN cc_start: 0.8344 (mm110) cc_final: 0.7871 (mm110) REVERT: A 132 MET cc_start: 0.8721 (ptm) cc_final: 0.8503 (ptp) REVERT: A 163 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.7978 (t0) REVERT: A 341 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7851 (pt0) REVERT: A 515 MET cc_start: 0.8728 (mtm) cc_final: 0.8524 (mtm) REVERT: A 535 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 121 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7738 (mm110) REVERT: B 307 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8904 (mt) REVERT: B 337 LEU cc_start: 0.8916 (mt) cc_final: 0.8580 (mt) REVERT: B 477 ILE cc_start: 0.8607 (mt) cc_final: 0.8399 (mm) REVERT: B 515 MET cc_start: 0.9006 (mtm) cc_final: 0.8717 (mtm) REVERT: C 98 MET cc_start: 0.5750 (ptt) cc_final: 0.5418 (ptm) REVERT: C 121 GLN cc_start: 0.8496 (mm110) cc_final: 0.7927 (mm110) REVERT: C 192 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8406 (pt) REVERT: C 543 ARG cc_start: 0.8244 (ttp-110) cc_final: 0.7853 (ttp-110) REVERT: C 576 MET cc_start: 0.3720 (pmm) cc_final: 0.3355 (pmm) REVERT: R 3 ARG cc_start: 0.8659 (mtt-85) cc_final: 0.8427 (mtt-85) outliers start: 28 outliers final: 10 residues processed: 128 average time/residue: 0.6317 time to fit residues: 87.5954 Evaluate side-chains 117 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 359 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: 2.9990 chunk 54 optimal weight: 0.7980 chunk 100 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN B 183 ASN C 119 GLN C 191 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.092100 restraints weight = 15321.291| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.21 r_work: 0.2889 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1663 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= 0.173 Angle : 0.613 9.287 16533 Z= 0.306 Chirality : 0.043 0.251 1890 Planarity : 0.004 0.053 2076 Dihedral : 7.479 57.396 2184 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.87 % Allowed : 13.63 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1404 helix: 1.01 (0.22), residues: 603 sheet: -0.14 (0.31), residues: 228 loop : -0.63 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 242 TYR 0.016 0.001 TYR B 448 PHE 0.015 0.002 PHE B 462 TRP 0.012 0.002 TRP C 564 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00385 (12138) covalent geometry : angle 0.59927 (16413) SS BOND : bond 0.00335 ( 15) SS BOND : angle 1.21100 ( 30) hydrogen bonds : bond 0.03582 ( 598) hydrogen bonds : angle 4.40663 ( 1758) link_BETA1-4 : bond 0.00352 ( 12) link_BETA1-4 : angle 1.46977 ( 36) link_NAG-ASN : bond 0.00347 ( 18) link_NAG-ASN : angle 1.93735 ( 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 139 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.340 Fit side-chains REVERT: A 121 GLN cc_start: 0.8292 (mm110) cc_final: 0.7861 (mm110) REVERT: A 132 MET cc_start: 0.8615 (ptm) cc_final: 0.8404 (ptp) REVERT: A 163 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.7953 (t0) REVERT: A 179 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8433 (mmm) REVERT: A 346 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8619 (p) REVERT: A 515 MET cc_start: 0.8721 (mtm) cc_final: 0.8509 (mtm) REVERT: A 535 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8023 (mt-10) REVERT: B 121 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: B 337 LEU cc_start: 0.8915 (mt) cc_final: 0.8648 (mt) REVERT: B 515 MET cc_start: 0.8954 (mtm) cc_final: 0.8647 (mtm) REVERT: C 98 MET cc_start: 0.5848 (ptt) cc_final: 0.5499 (ptm) REVERT: C 121 GLN cc_start: 0.8464 (mm110) cc_final: 0.7929 (mm110) REVERT: C 192 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8301 (pt) REVERT: C 518 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7725 (tt0) REVERT: C 543 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7913 (ttp80) REVERT: R 3 ARG cc_start: 0.8598 (mtt-85) cc_final: 0.8368 (mtt-85) outliers start: 24 outliers final: 7 residues processed: 127 average time/residue: 0.5100 time to fit residues: 70.6778 Evaluate side-chains 113 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 MET 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 B residue 550 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091864 restraints weight = 15290.460| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.23 r_work: 0.2901 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1800 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= 0.157 Angle : 0.604 9.275 16533 Z= 0.299 Chirality : 0.043 0.250 1890 Planarity : 0.004 0.050 2076 Dihedral : 7.254 57.568 2184 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.49 % Allowed : 13.63 % 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 aren not related in a simple way. whole: 0.32 (0.23), residues: 1404 helix: 1.13 (0.22), residues: 600 sheet: -0.15 (0.31), residues: 228 loop : -0.53 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 242 TYR 0.015 0.001 TYR B 448 PHE 0.012 0.001 PHE C 277 TRP 0.012 0.001 TRP A 564 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00351 (12138) covalent geometry : angle 0.59010 (16413) SS BOND : bond 0.00308 ( 15) SS BOND : angle 1.14956 ( 30) hydrogen bonds : bond 0.03490 ( 598) hydrogen bonds : angle 4.35768 ( 1758) link_BETA1-4 : bond 0.00350 ( 12) link_BETA1-4 : angle 1.44043 ( 36) link_NAG-ASN : bond 0.00305 ( 18) link_NAG-ASN : angle 1.88805 ( 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 146 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.522 Fit side-chains REVERT: A 121 GLN cc_start: 0.8339 (mm110) cc_final: 0.7927 (mm110) REVERT: A 132 MET cc_start: 0.8600 (ptm) cc_final: 0.8352 (ptp) REVERT: A 160 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: A 163 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.7994 (t0) REVERT: A 182 MET cc_start: 0.8989 (mmm) cc_final: 0.8674 (mmt) REVERT: A 400 MET cc_start: 0.8464 (tpp) cc_final: 0.8209 (tpt) REVERT: A 535 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 121 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: B 307 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8576 (pt) REVERT: B 320 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8172 (mt) REVERT: B 337 LEU cc_start: 0.8897 (mt) cc_final: 0.8637 (mt) REVERT: B 515 MET cc_start: 0.8945 (mtm) cc_final: 0.8675 (mtm) REVERT: C 98 MET cc_start: 0.5854 (ptt) cc_final: 0.5503 (ptm) REVERT: C 121 GLN cc_start: 0.8429 (mm110) cc_final: 0.7918 (mm110) REVERT: C 192 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8416 (pt) REVERT: C 265 ASP cc_start: 0.8434 (t0) cc_final: 0.8153 (t70) REVERT: C 518 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7721 (tt0) REVERT: C 543 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7837 (ttp80) REVERT: R 2 MET cc_start: 0.9361 (ptt) cc_final: 0.9122 (ptm) REVERT: R 3 ARG cc_start: 0.8598 (mtt-85) cc_final: 0.8298 (mtt-85) outliers start: 32 outliers final: 13 residues processed: 131 average time/residue: 0.5819 time to fit residues: 83.2860 Evaluate side-chains 122 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 340 ILE 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: 8.9990 chunk 138 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.091573 restraints weight = 15382.425| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.22 r_work: 0.2881 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1857 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= 0.194 Angle : 0.624 9.220 16533 Z= 0.310 Chirality : 0.044 0.246 1890 Planarity : 0.004 0.050 2076 Dihedral : 7.162 57.901 2184 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.80 % Allowed : 14.80 % Favored : 82.40 % 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 aren not related in a simple way. whole: 0.29 (0.22), residues: 1404 helix: 1.10 (0.22), residues: 597 sheet: -0.16 (0.31), residues: 228 loop : -0.53 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 242 TYR 0.017 0.001 TYR B 448 PHE 0.013 0.002 PHE B 554 TRP 0.011 0.001 TRP C 564 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00439 (12138) covalent geometry : angle 0.61030 (16413) SS BOND : bond 0.00324 ( 15) SS BOND : angle 1.20494 ( 30) hydrogen bonds : bond 0.03588 ( 598) hydrogen bonds : angle 4.36626 ( 1758) link_BETA1-4 : bond 0.00325 ( 12) link_BETA1-4 : angle 1.46645 ( 36) link_NAG-ASN : bond 0.00385 ( 18) link_NAG-ASN : angle 1.93029 ( 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 152 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.533 Fit side-chains REVERT: A 121 GLN cc_start: 0.8338 (mm110) cc_final: 0.7948 (mm110) REVERT: A 132 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8373 (ptp) REVERT: A 163 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.7972 (t0) REVERT: A 341 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7756 (pt0) REVERT: A 346 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 535 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7960 (mt-10) REVERT: B 121 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7764 (mp10) REVERT: B 307 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8822 (mt) REVERT: B 337 LEU cc_start: 0.8910 (mt) cc_final: 0.8618 (mt) REVERT: B 515 MET cc_start: 0.8945 (mtm) cc_final: 0.8678 (mtm) REVERT: C 121 GLN cc_start: 0.8463 (mm110) cc_final: 0.7959 (mm110) REVERT: C 192 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8371 (pt) REVERT: C 265 ASP cc_start: 0.8448 (t70) cc_final: 0.8166 (t70) REVERT: C 518 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7719 (tt0) REVERT: C 543 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7816 (ttp80) REVERT: R 2 MET cc_start: 0.9347 (ptt) cc_final: 0.9117 (ptm) REVERT: R 3 ARG cc_start: 0.8591 (mtt-85) cc_final: 0.8294 (mtt-85) outliers start: 36 outliers final: 18 residues processed: 137 average time/residue: 0.5783 time to fit residues: 86.6451 Evaluate side-chains 129 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 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 359 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 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: 0.9990 chunk 111 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 172 GLN C 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.093070 restraints weight = 15249.040| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.21 r_work: 0.2906 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1964 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 : 0.612 9.251 16533 Z= 0.302 Chirality : 0.043 0.252 1890 Planarity : 0.004 0.050 2076 Dihedral : 6.976 57.346 2184 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.18 % Allowed : 15.58 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.23), residues: 1404 helix: 1.17 (0.22), residues: 597 sheet: -0.29 (0.31), residues: 237 loop : -0.51 (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 0.013 0.001 PHE A 554 TRP 0.011 0.001 TRP A 564 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00337 (12138) covalent geometry : angle 0.59900 (16413) SS BOND : bond 0.00291 ( 15) SS BOND : angle 1.18297 ( 30) hydrogen bonds : bond 0.03425 ( 598) hydrogen bonds : angle 4.32037 ( 1758) link_BETA1-4 : bond 0.00353 ( 12) link_BETA1-4 : angle 1.42456 ( 36) link_NAG-ASN : bond 0.00284 ( 18) link_NAG-ASN : angle 1.82944 ( 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 145 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.465 Fit side-chains REVERT: A 121 GLN cc_start: 0.8331 (mm110) cc_final: 0.7957 (mm110) REVERT: A 132 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8315 (ptp) REVERT: A 163 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.7970 (t0) REVERT: A 265 ASP cc_start: 0.8572 (t0) cc_final: 0.8306 (t70) REVERT: A 346 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8609 (p) REVERT: A 535 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7990 (mt-10) REVERT: B 121 GLN cc_start: 0.8050 (mp10) cc_final: 0.7800 (mp10) REVERT: B 307 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8588 (pt) REVERT: B 320 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8123 (mt) REVERT: B 337 LEU cc_start: 0.8883 (mt) cc_final: 0.8627 (mt) REVERT: B 515 MET cc_start: 0.8915 (mtm) cc_final: 0.8645 (mtm) REVERT: B 543 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7846 (ttp80) REVERT: C 98 MET cc_start: 0.5685 (ptt) cc_final: 0.5297 (ptm) REVERT: C 121 GLN cc_start: 0.8458 (mm110) cc_final: 0.7954 (mm110) REVERT: C 192 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8397 (pt) REVERT: C 265 ASP cc_start: 0.8437 (t70) cc_final: 0.8159 (t70) REVERT: C 518 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7707 (tt0) REVERT: C 543 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7776 (ttp80) REVERT: R 3 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8257 (mtt-85) outliers start: 28 outliers final: 18 residues processed: 133 average time/residue: 0.5829 time to fit residues: 84.4970 Evaluate side-chains 131 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 297 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 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 C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 29 optimal weight: 0.0470 chunk 90 optimal weight: 6.9990 chunk 12 optimal weight: 0.0030 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.4888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094721 restraints weight = 15231.756| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.22 r_work: 0.2931 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12183 Z= 0.124 Angle : 0.611 9.291 16533 Z= 0.301 Chirality : 0.042 0.253 1890 Planarity : 0.004 0.057 2076 Dihedral : 6.851 57.342 2184 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.95 % Allowed : 15.89 % Favored : 82.17 % 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 aren not related in a simple way. whole: 0.35 (0.23), residues: 1404 helix: 1.21 (0.22), residues: 597 sheet: -0.31 (0.31), residues: 237 loop : -0.47 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 242 TYR 0.013 0.001 TYR A 448 PHE 0.017 0.001 PHE B 554 TRP 0.012 0.001 TRP C 564 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00276 (12138) covalent geometry : angle 0.59712 (16413) SS BOND : bond 0.00359 ( 15) SS BOND : angle 1.80469 ( 30) hydrogen bonds : bond 0.03295 ( 598) hydrogen bonds : angle 4.29034 ( 1758) link_BETA1-4 : bond 0.00387 ( 12) link_BETA1-4 : angle 1.37431 ( 36) link_NAG-ASN : bond 0.00223 ( 18) link_NAG-ASN : angle 1.72387 ( 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 149 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.457 Fit side-chains REVERT: A 121 GLN cc_start: 0.8305 (mm110) cc_final: 0.7929 (mm110) REVERT: A 132 MET cc_start: 0.8488 (ptm) cc_final: 0.8231 (ptp) REVERT: A 163 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.7905 (t0) REVERT: A 265 ASP cc_start: 0.8516 (t0) cc_final: 0.8022 (t0) REVERT: A 346 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8625 (p) REVERT: A 535 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 121 GLN cc_start: 0.8057 (mp10) cc_final: 0.7782 (mp10) REVERT: B 320 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8199 (mt) REVERT: B 337 LEU cc_start: 0.8837 (mt) cc_final: 0.8614 (mt) REVERT: B 515 MET cc_start: 0.8859 (mtm) cc_final: 0.8582 (mtm) REVERT: B 543 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7862 (ttp80) REVERT: C 98 MET cc_start: 0.5653 (ptt) cc_final: 0.5283 (ptm) REVERT: C 121 GLN cc_start: 0.8363 (mm110) cc_final: 0.7883 (mm110) REVERT: C 192 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8348 (pt) REVERT: C 265 ASP cc_start: 0.8449 (t70) cc_final: 0.8155 (t70) REVERT: C 518 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7729 (tt0) REVERT: C 543 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7866 (ttp80) REVERT: R 3 ARG cc_start: 0.8578 (mtt-85) cc_final: 0.7972 (mtt-85) outliers start: 25 outliers final: 14 residues processed: 140 average time/residue: 0.5350 time to fit residues: 82.0476 Evaluate side-chains 125 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 313 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 354 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 94 optimal weight: 0.0980 chunk 110 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 127 optimal weight: 0.0070 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 0.0020 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.135898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100296 restraints weight = 15080.729| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.35 r_work: 0.2920 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2255 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= 0.120 Angle : 0.613 9.310 16533 Z= 0.302 Chirality : 0.042 0.254 1890 Planarity : 0.004 0.059 2076 Dihedral : 6.662 57.343 2184 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.56 % Allowed : 17.06 % Favored : 81.39 % 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 aren not related in a simple way. whole: 0.39 (0.23), residues: 1404 helix: 1.25 (0.22), residues: 597 sheet: -0.31 (0.31), residues: 237 loop : -0.45 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 242 TYR 0.012 0.001 TYR A 448 PHE 0.018 0.001 PHE A 554 TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00265 (12138) covalent geometry : angle 0.60023 (16413) SS BOND : bond 0.00246 ( 15) SS BOND : angle 1.82837 ( 30) hydrogen bonds : bond 0.03243 ( 598) hydrogen bonds : angle 4.25670 ( 1758) link_BETA1-4 : bond 0.00392 ( 12) link_BETA1-4 : angle 1.33339 ( 36) link_NAG-ASN : bond 0.00191 ( 18) link_NAG-ASN : angle 1.63282 ( 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 137 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.529 Fit side-chains REVERT: A 121 GLN cc_start: 0.8349 (mm110) cc_final: 0.7983 (mm110) REVERT: A 132 MET cc_start: 0.8495 (ptm) cc_final: 0.8233 (ptp) REVERT: A 163 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8011 (t0) REVERT: A 265 ASP cc_start: 0.8517 (t0) cc_final: 0.8027 (t0) REVERT: A 346 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8675 (p) REVERT: A 535 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8083 (mt-10) REVERT: B 121 GLN cc_start: 0.8130 (mp10) cc_final: 0.7844 (mp10) REVERT: B 515 MET cc_start: 0.8894 (mtm) cc_final: 0.8664 (mtm) REVERT: B 543 ARG cc_start: 0.8308 (ttp-110) cc_final: 0.7962 (ttp80) REVERT: C 98 MET cc_start: 0.5705 (ptt) cc_final: 0.5316 (ptm) REVERT: C 121 GLN cc_start: 0.8356 (mm110) cc_final: 0.7872 (mm110) REVERT: C 265 ASP cc_start: 0.8402 (t70) cc_final: 0.8133 (t70) REVERT: C 543 ARG cc_start: 0.8244 (ttp-110) cc_final: 0.7934 (mtp-110) outliers start: 20 outliers final: 14 residues processed: 132 average time/residue: 0.6072 time to fit residues: 87.1113 Evaluate side-chains 121 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 244 GLN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 483 SER 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 19 optimal weight: 0.0770 chunk 132 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 109 optimal weight: 0.0010 chunk 84 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.5546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100591 restraints weight = 15346.307| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.38 r_work: 0.2909 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2309 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 : 0.636 9.857 16533 Z= 0.311 Chirality : 0.043 0.254 1890 Planarity : 0.004 0.062 2076 Dihedral : 6.663 57.441 2184 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.56 % Allowed : 17.45 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: 0.39 (0.23), residues: 1404 helix: 1.23 (0.22), residues: 597 sheet: -0.27 (0.31), residues: 237 loop : -0.46 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 242 TYR 0.012 0.001 TYR A 448 PHE 0.020 0.001 PHE B 554 TRP 0.011 0.001 TRP C 564 HIS 0.005 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00288 (12138) covalent geometry : angle 0.62056 (16413) SS BOND : bond 0.00408 ( 15) SS BOND : angle 2.36171 ( 30) hydrogen bonds : bond 0.03286 ( 598) hydrogen bonds : angle 4.25827 ( 1758) link_BETA1-4 : bond 0.00381 ( 12) link_BETA1-4 : angle 1.33780 ( 36) link_NAG-ASN : bond 0.00217 ( 18) link_NAG-ASN : angle 1.63600 ( 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 128 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.483 Fit side-chains REVERT: A 121 GLN cc_start: 0.8365 (mm110) cc_final: 0.7999 (mm110) REVERT: A 132 MET cc_start: 0.8510 (ptm) cc_final: 0.8253 (ptp) REVERT: A 163 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8018 (t0) REVERT: A 265 ASP cc_start: 0.8545 (t0) cc_final: 0.8082 (t0) REVERT: A 346 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8675 (p) REVERT: A 535 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8098 (mt-10) REVERT: B 121 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: B 515 MET cc_start: 0.8896 (mtm) cc_final: 0.8651 (mtm) REVERT: B 543 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.7985 (ttp80) REVERT: C 98 MET cc_start: 0.5860 (ptt) cc_final: 0.5449 (ptm) REVERT: C 121 GLN cc_start: 0.8355 (mm110) cc_final: 0.7932 (mm110) REVERT: C 192 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8418 (pt) REVERT: C 265 ASP cc_start: 0.8423 (t70) cc_final: 0.8143 (t70) REVERT: C 543 ARG cc_start: 0.8263 (ttp-110) cc_final: 0.7953 (mtp-110) REVERT: R 3 ARG cc_start: 0.8546 (mtt-85) cc_final: 0.8033 (mtt-85) outliers start: 20 outliers final: 12 residues processed: 122 average time/residue: 0.6337 time to fit residues: 83.9472 Evaluate side-chains 121 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 313 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 354 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 66 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.135841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099902 restraints weight = 15337.162| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.40 r_work: 0.2890 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2344 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= 0.138 Angle : 0.639 10.740 16533 Z= 0.313 Chirality : 0.043 0.251 1890 Planarity : 0.004 0.057 2076 Dihedral : 6.647 57.464 2184 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.25 % Allowed : 18.22 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: 0.59 (0.23), residues: 1404 helix: 1.43 (0.22), residues: 579 sheet: -0.25 (0.31), residues: 237 loop : -0.27 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 242 TYR 0.014 0.001 TYR B 117 PHE 0.020 0.002 PHE A 554 TRP 0.011 0.001 TRP B 564 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00310 (12138) covalent geometry : angle 0.62314 (16413) SS BOND : bond 0.00324 ( 15) SS BOND : angle 2.32867 ( 30) hydrogen bonds : bond 0.03311 ( 598) hydrogen bonds : angle 4.26695 ( 1758) link_BETA1-4 : bond 0.00364 ( 12) link_BETA1-4 : angle 1.32797 ( 36) link_NAG-ASN : bond 0.00242 ( 18) link_NAG-ASN : angle 1.64969 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4586.16 seconds wall clock time: 79 minutes 6.02 seconds (4746.02 seconds total)