Starting phenix.real_space_refine on Fri Jul 3 03:00:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yvc_34123/07_2026/7yvc_34123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvc_34123/07_2026/7yvc_34123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yvc_34123/07_2026/7yvc_34123.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yvc_34123/07_2026/7yvc_34123.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvc_34123/07_2026/7yvc_34123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvc_34123/07_2026/7yvc_34123.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvc_34123/07_2026/7yvc_34123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvc_34123/07_2026/7yvc_34123.cif" } resolution = 3.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 78 5.16 5 C 7380 2.51 5 N 1935 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11662 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3747 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 446} Chain breaks: 1 Chain: "B" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3747 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 446} Chain breaks: 1 Chain: "C" Number of atoms: 3747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3747 Classifications: {'peptide': 467} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 446} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.92, per 1000 atoms: 0.25 Number of scatterers: 11662 At special positions: 0 Unit cell: (110.2, 117.16, 136.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 78 16.00 O 2268 8.00 N 1935 7.00 C 7380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 233 " distance=2.04 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 217 " distance=2.04 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 431 " distance=2.04 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 411 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 233 " distance=2.04 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 217 " distance=2.04 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 431 " distance=2.04 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 363 " - pdb=" SG CYS B 411 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 233 " distance=2.04 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 217 " distance=2.04 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 431 " distance=2.04 Simple disulfide: pdb=" SG CYS C 354 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 363 " - pdb=" SG CYS C 411 " distance=2.03 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 381 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM11477 O5 NAG L 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM11603 O5 NAG A 702 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 701 " - " ASN A 401 " " NAG A 702 " - " ASN A 377 " " NAG B 701 " - " ASN B 377 " " NAG B 702 " - " ASN B 401 " " NAG C 701 " - " ASN C 377 " " NAG C 702 " - " ASN C 401 " " NAG D 1 " - " ASN A 393 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 169 " " NAG G 1 " - " ASN A 221 " " NAG H 1 " - " ASN B 393 " " NAG I 1 " - " ASN B 331 " " NAG J 1 " - " ASN B 169 " " NAG K 1 " - " ASN B 221 " " NAG L 1 " - " ASN C 393 " " NAG M 1 " - " ASN C 331 " " NAG N 1 " - " ASN C 169 " " NAG O 1 " - " ASN C 221 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 441.5 milliseconds 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2658 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 44.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 91 through 118 removed outlier: 3.584A pdb=" N TRP A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 102 " --> pdb=" O MET A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 161 through 174 removed outlier: 4.010A pdb=" N LYS A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.697A pdb=" N MET A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 removed outlier: 4.090A pdb=" N PHE A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 346 through 364 Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'A' and resid 406 through 422 removed outlier: 3.530A pdb=" N ALA A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 removed outlier: 4.033A pdb=" N CYS A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.952A pdb=" N MET A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 576 removed outlier: 3.945A pdb=" N GLY A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 118 removed outlier: 3.700A pdb=" N GLY B 102 " --> pdb=" O MET B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 161 through 174 removed outlier: 4.010A pdb=" N LYS B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 174 " --> pdb=" O PHE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.695A pdb=" N MET B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 4.090A pdb=" N PHE B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 346 through 364 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 406 through 422 removed outlier: 3.530A pdb=" N ALA B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 removed outlier: 4.032A pdb=" N CYS B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 475 through 487 Processing helix chain 'B' and resid 510 through 526 removed outlier: 3.952A pdb=" N MET B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 576 removed outlier: 3.945A pdb=" N GLY B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 118 removed outlier: 3.699A pdb=" N GLY C 102 " --> pdb=" O MET C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.011A pdb=" N LYS C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 174 " --> pdb=" O PHE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.696A pdb=" N MET C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 removed outlier: 4.090A pdb=" N PHE C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 346 through 364 Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'C' and resid 406 through 422 removed outlier: 3.530A pdb=" N ALA C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 removed outlier: 4.033A pdb=" N CYS C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 453 No H-bonds generated for 'chain 'C' and resid 451 through 453' Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 475 through 487 Processing helix chain 'C' and resid 510 through 526 removed outlier: 3.951A pdb=" N MET C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 576 removed outlier: 3.945A pdb=" N GLY C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU C 563 " --> pdb=" O GLY C 559 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL A 540 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA A 319 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR A 542 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 321 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN A 544 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 323 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR A 311 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER A 261 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU A 207 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL A 540 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA A 319 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR A 542 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 321 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLN A 544 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 323 " --> pdb=" O GLN A 544 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 135 removed outlier: 4.408A pdb=" N VAL A 134 " --> pdb=" O MET A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 227 removed outlier: 6.307A pdb=" N ASN A 232 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN A 143 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL B 540 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 319 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TYR B 542 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 321 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN B 544 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR B 323 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR B 311 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER B 261 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU B 207 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL B 540 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 319 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TYR B 542 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 321 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN B 544 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR B 323 " --> pdb=" O GLN B 544 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 135 removed outlier: 4.406A pdb=" N VAL B 134 " --> pdb=" O MET B 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 222 through 227 removed outlier: 6.307A pdb=" N ASN B 232 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN B 143 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL C 540 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA C 319 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR C 542 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 321 " --> pdb=" O TYR C 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN C 544 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 323 " --> pdb=" O GLN C 544 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR C 311 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER C 261 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU C 207 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 122 through 129 removed outlier: 9.941A pdb=" N VAL C 540 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA C 319 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR C 542 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 321 " --> pdb=" O TYR C 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLN C 544 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 323 " --> pdb=" O GLN C 544 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 134 through 135 removed outlier: 4.408A pdb=" N VAL C 134 " --> pdb=" O MET C 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 222 through 227 removed outlier: 6.307A pdb=" N ASN C 232 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN C 143 " --> pdb=" O ASN C 232 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3708 1.34 - 1.46: 2811 1.46 - 1.58: 5271 1.58 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 11904 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 ... (remaining 11899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 15661 2.08 - 4.16: 371 4.16 - 6.24: 51 6.24 - 8.32: 12 8.32 - 10.40: 9 Bond angle restraints: 16104 Sorted by residual: angle pdb=" C TYR B 230 " pdb=" N PHE B 231 " pdb=" CA PHE B 231 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C TYR A 230 " pdb=" N PHE A 231 " pdb=" CA PHE A 231 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C TYR C 230 " pdb=" N PHE C 231 " pdb=" CA PHE C 231 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 angle pdb=" CB ARG C 391 " pdb=" CG ARG C 391 " pdb=" CD ARG C 391 " ideal model delta sigma weight residual 111.30 101.30 10.00 2.30e+00 1.89e-01 1.89e+01 angle pdb=" CB ARG B 391 " pdb=" CG ARG B 391 " pdb=" CD ARG B 391 " ideal model delta sigma weight residual 111.30 101.31 9.99 2.30e+00 1.89e-01 1.89e+01 ... (remaining 16099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6303 17.81 - 35.62: 559 35.62 - 53.43: 90 53.43 - 71.24: 20 71.24 - 89.06: 30 Dihedral angle restraints: 7002 sinusoidal: 2892 harmonic: 4110 Sorted by residual: dihedral pdb=" CB CYS B 210 " pdb=" SG CYS B 210 " pdb=" SG CYS B 217 " pdb=" CB CYS B 217 " ideal model delta sinusoidal sigma weight residual -86.00 -20.73 -65.27 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS A 210 " pdb=" SG CYS A 210 " pdb=" SG CYS A 217 " pdb=" CB CYS A 217 " ideal model delta sinusoidal sigma weight residual -86.00 -20.74 -65.26 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS C 210 " pdb=" SG CYS C 210 " pdb=" SG CYS C 217 " pdb=" CB CYS C 217 " ideal model delta sinusoidal sigma weight residual -86.00 -20.76 -65.24 1 1.00e+01 1.00e-02 5.58e+01 ... (remaining 6999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 1847 0.196 - 0.393: 7 0.393 - 0.589: 6 0.589 - 0.785: 1 0.785 - 0.982: 2 Chirality restraints: 1863 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 401 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 169 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.20 0.80 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 221 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.40e+01 ... (remaining 1860 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 221 " -0.003 2.00e-02 2.50e+03 1.36e-01 2.30e+02 pdb=" CG ASN C 221 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 221 " -0.123 2.00e-02 2.50e+03 pdb=" ND2 ASN C 221 " 0.231 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.115 2.00e-02 2.50e+03 1.20e-01 1.81e+02 pdb=" CG ASN C 331 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.174 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 221 " -0.025 2.00e-02 2.50e+03 1.12e-01 1.56e+02 pdb=" CG ASN A 221 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 221 " 0.093 2.00e-02 2.50e+03 pdb=" ND2 ASN A 221 " -0.184 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.137 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 105 2.59 - 3.17: 9651 3.17 - 3.75: 17018 3.75 - 4.32: 24321 4.32 - 4.90: 40463 Nonbonded interactions: 91558 Sorted by model distance: nonbonded pdb=" OD1 ASN C 169 " pdb=" C1 NAG N 1 " model vdw 2.017 2.776 nonbonded pdb=" OD1 ASN C 393 " pdb=" C1 NAG L 1 " model vdw 2.131 2.776 nonbonded pdb=" OD1 ASP A 166 " pdb=" NH1 ARG A 391 " model vdw 2.236 3.120 nonbonded pdb=" OD1 ASP B 166 " pdb=" NH1 ARG B 391 " model vdw 2.236 3.120 nonbonded pdb=" ND2 ASN A 221 " pdb=" N2 NAG G 1 " model vdw 2.236 2.560 ... (remaining 91553 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 91 through 702) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 10.820 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: 0.000 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 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 : 0.010 0.422 11952 Z= 0.498 Angle : 1.242 36.205 16230 Z= 0.530 Chirality : 0.066 0.982 1863 Planarity : 0.004 0.046 2037 Dihedral : 15.100 89.055 4290 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.48 % Allowed : 0.71 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.22), residues: 1389 helix: -0.16 (0.21), residues: 570 sheet: 0.74 (0.31), residues: 231 loop : -1.39 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 391 TYR 0.017 0.002 TYR C 448 PHE 0.015 0.002 PHE C 554 TRP 0.017 0.002 TRP C 564 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.29 (11904) covalent geometry : angle 0.82093 / 0.43 (16104) SS BOND : bond 0.00458 / 0.30 ( 18) SS BOND : angle 2.22059 / 1.57 ( 36) hydrogen bonds : bond 0.14130 / 8.90 ( 561) hydrogen bonds : angle 6.75238 / 4.73 ( 1638) link_BETA1-4 : bond 0.00412 / 0.27 ( 12) link_BETA1-4 : angle 1.75779 / 1.07 ( 36) link_NAG-ASN : bond 0.20792 / 12.09 ( 18) link_NAG-ASN : angle 16.03226 / 11.07 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 561 LEU cc_start: 0.8126 (mt) cc_final: 0.7867 (mt) REVERT: B 247 MET cc_start: 0.9039 (mmm) cc_final: 0.8796 (tpt) REVERT: B 561 LEU cc_start: 0.8082 (mt) cc_final: 0.7394 (mp) REVERT: C 561 LEU cc_start: 0.8134 (mt) cc_final: 0.7767 (mt) outliers start: 6 outliers final: 0 residues processed: 92 average time/residue: 0.5603 time to fit residues: 55.8510 Evaluate side-chains 60 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.114527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.074542 restraints weight = 17931.116| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.79 r_work: 0.2830 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11952 Z= 0.155 Angle : 0.733 12.797 16230 Z= 0.351 Chirality : 0.047 0.436 1863 Planarity : 0.004 0.041 2037 Dihedral : 5.231 24.426 1524 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.87 % Allowed : 6.25 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1389 helix: 0.69 (0.22), residues: 552 sheet: 0.64 (0.31), residues: 243 loop : -1.21 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 391 TYR 0.010 0.001 TYR C 448 PHE 0.011 0.002 PHE C 226 TRP 0.015 0.002 TRP B 564 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (11904) covalent geometry : angle 0.66624 / 0.34 (16104) SS BOND : bond 0.00301 / 0.20 ( 18) SS BOND : angle 1.73511 / 1.25 ( 36) hydrogen bonds : bond 0.04436 / 2.97 ( 561) hydrogen bonds : angle 5.47482 / 3.81 ( 1638) link_BETA1-4 : bond 0.00450 / 0.31 ( 12) link_BETA1-4 : angle 1.41426 / 0.89 ( 36) link_NAG-ASN : bond 0.01010 / 0.63 ( 18) link_NAG-ASN : angle 5.08947 / 3.56 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.384 Fit side-chains REVERT: A 98 MET cc_start: 0.7422 (tpp) cc_final: 0.6892 (tpp) REVERT: B 475 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8348 (mtm) REVERT: B 554 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7453 (t80) REVERT: B 561 LEU cc_start: 0.7378 (mt) cc_final: 0.7037 (mt) REVERT: B 565 MET cc_start: 0.7752 (ppp) cc_final: 0.7506 (ppp) REVERT: C 554 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.6525 (t80) outliers start: 11 outliers final: 1 residues processed: 68 average time/residue: 0.5215 time to fit residues: 38.7957 Evaluate side-chains 57 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.113959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.074128 restraints weight = 18127.844| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.79 r_work: 0.2823 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11952 Z= 0.158 Angle : 0.679 11.790 16230 Z= 0.326 Chirality : 0.046 0.410 1863 Planarity : 0.004 0.041 2037 Dihedral : 5.025 24.424 1524 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.79 % Allowed : 9.18 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.23), residues: 1389 helix: 0.88 (0.23), residues: 558 sheet: 0.79 (0.31), residues: 243 loop : -1.14 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 204 TYR 0.013 0.001 TYR C 448 PHE 0.010 0.001 PHE C 226 TRP 0.014 0.001 TRP B 564 HIS 0.003 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (11904) covalent geometry : angle 0.61807 / 0.31 (16104) SS BOND : bond 0.00320 / 0.21 ( 18) SS BOND : angle 1.61612 / 1.19 ( 36) hydrogen bonds : bond 0.04071 / 2.72 ( 561) hydrogen bonds : angle 5.17220 / 3.60 ( 1638) link_BETA1-4 : bond 0.00272 / 0.18 ( 12) link_BETA1-4 : angle 1.36856 / 0.89 ( 36) link_NAG-ASN : bond 0.00956 / 0.62 ( 18) link_NAG-ASN : angle 4.64263 / 3.28 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.402 Fit side-chains REVERT: A 98 MET cc_start: 0.7490 (tpp) cc_final: 0.6881 (tpp) REVERT: B 475 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8432 (mtm) REVERT: B 554 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7255 (t80) REVERT: B 561 LEU cc_start: 0.7365 (mt) cc_final: 0.6961 (mt) REVERT: C 98 MET cc_start: 0.7234 (tpt) cc_final: 0.6722 (tpp) REVERT: C 333 THR cc_start: 0.8782 (p) cc_final: 0.8425 (t) REVERT: C 554 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.6638 (t80) outliers start: 10 outliers final: 2 residues processed: 68 average time/residue: 0.4313 time to fit residues: 32.5634 Evaluate side-chains 60 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 6 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.114369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.074643 restraints weight = 17978.126| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.78 r_work: 0.2832 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11952 Z= 0.144 Angle : 0.656 10.865 16230 Z= 0.317 Chirality : 0.045 0.410 1863 Planarity : 0.003 0.040 2037 Dihedral : 4.946 27.099 1524 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.79 % Allowed : 11.01 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1389 helix: 1.07 (0.23), residues: 537 sheet: 0.81 (0.31), residues: 243 loop : -0.92 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 204 TYR 0.011 0.001 TYR B 448 PHE 0.009 0.001 PHE C 226 TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (11904) covalent geometry : angle 0.59652 / 0.30 (16104) SS BOND : bond 0.00349 / 0.22 ( 18) SS BOND : angle 2.08205 / 1.36 ( 36) hydrogen bonds : bond 0.03930 / 2.65 ( 561) hydrogen bonds : angle 5.10262 / 3.55 ( 1638) link_BETA1-4 : bond 0.00317 / 0.20 ( 12) link_BETA1-4 : angle 1.35059 / 0.87 ( 36) link_NAG-ASN : bond 0.00914 / 0.58 ( 18) link_NAG-ASN : angle 4.39119 / 3.14 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7531 (tpp) cc_final: 0.7127 (tpp) REVERT: B 475 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8145 (mtm) REVERT: B 554 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7214 (t80) REVERT: B 561 LEU cc_start: 0.7302 (mt) cc_final: 0.6905 (mt) REVERT: C 98 MET cc_start: 0.7356 (tpt) cc_final: 0.6856 (tpp) REVERT: C 333 THR cc_start: 0.8783 (p) cc_final: 0.8430 (t) REVERT: C 554 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.6631 (t80) outliers start: 10 outliers final: 4 residues processed: 68 average time/residue: 0.4802 time to fit residues: 35.7958 Evaluate side-chains 64 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 123 optimal weight: 0.3980 chunk 111 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN ** B 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.115131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075509 restraints weight = 17938.847| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.78 r_work: 0.2850 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11952 Z= 0.124 Angle : 0.621 10.166 16230 Z= 0.300 Chirality : 0.045 0.398 1863 Planarity : 0.003 0.040 2037 Dihedral : 4.760 25.206 1524 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.19 % Allowed : 11.40 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.23), residues: 1389 helix: 1.15 (0.23), residues: 540 sheet: 0.86 (0.31), residues: 243 loop : -0.84 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 524 TYR 0.010 0.001 TYR B 448 PHE 0.009 0.001 PHE C 226 TRP 0.013 0.001 TRP B 564 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11904) covalent geometry : angle 0.56758 / 0.29 (16104) SS BOND : bond 0.00260 / 0.16 ( 18) SS BOND : angle 1.37576 / 0.92 ( 36) hydrogen bonds : bond 0.03656 / 2.47 ( 561) hydrogen bonds : angle 5.01752 / 3.49 ( 1638) link_BETA1-4 : bond 0.00274 / 0.17 ( 12) link_BETA1-4 : angle 1.29296 / 0.84 ( 36) link_NAG-ASN : bond 0.00889 / 0.56 ( 18) link_NAG-ASN : angle 4.17098 / 3.00 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 411 CYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7625 (t) REVERT: B 475 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: B 554 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7250 (t80) REVERT: C 98 MET cc_start: 0.7634 (tpt) cc_final: 0.7073 (tpp) REVERT: C 333 THR cc_start: 0.8782 (p) cc_final: 0.8437 (t) REVERT: C 411 CYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7587 (t) REVERT: C 554 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.6589 (t80) outliers start: 15 outliers final: 4 residues processed: 74 average time/residue: 0.4725 time to fit residues: 38.7565 Evaluate side-chains 67 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 58 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN C 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.115674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.076096 restraints weight = 18015.545| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.79 r_work: 0.2861 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11952 Z= 0.115 Angle : 0.609 9.756 16230 Z= 0.296 Chirality : 0.044 0.391 1863 Planarity : 0.003 0.038 2037 Dihedral : 4.624 24.466 1524 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.27 % Allowed : 12.35 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.23), residues: 1389 helix: 1.22 (0.23), residues: 540 sheet: 0.93 (0.31), residues: 243 loop : -0.77 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 211 TYR 0.009 0.001 TYR B 448 PHE 0.009 0.001 PHE B 226 TRP 0.013 0.001 TRP B 564 HIS 0.002 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (11904) covalent geometry : angle 0.56000 / 0.29 (16104) SS BOND : bond 0.00254 / 0.16 ( 18) SS BOND : angle 1.29811 / 0.90 ( 36) hydrogen bonds : bond 0.03486 / 2.35 ( 561) hydrogen bonds : angle 4.94931 / 3.45 ( 1638) link_BETA1-4 : bond 0.00317 / 0.20 ( 12) link_BETA1-4 : angle 1.24925 / 0.81 ( 36) link_NAG-ASN : bond 0.00860 / 0.54 ( 18) link_NAG-ASN : angle 3.98253 / 2.88 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7568 (tpp) cc_final: 0.6986 (tpp) REVERT: A 411 CYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7511 (t) REVERT: B 98 MET cc_start: 0.7245 (tpp) cc_final: 0.6886 (tpp) REVERT: B 475 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8235 (mtm) REVERT: B 554 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: C 98 MET cc_start: 0.7577 (tpt) cc_final: 0.7046 (tpp) REVERT: C 333 THR cc_start: 0.8794 (p) cc_final: 0.8448 (t) REVERT: C 411 CYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7531 (t) outliers start: 16 outliers final: 8 residues processed: 77 average time/residue: 0.4059 time to fit residues: 34.8704 Evaluate side-chains 70 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 117 optimal weight: 0.0170 chunk 78 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 chunk 63 optimal weight: 0.2980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.117149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.077872 restraints weight = 17956.598| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.79 r_work: 0.2894 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11952 Z= 0.098 Angle : 0.586 9.468 16230 Z= 0.286 Chirality : 0.043 0.370 1863 Planarity : 0.003 0.037 2037 Dihedral : 4.419 22.844 1524 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.66 % Allowed : 13.06 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1389 helix: 1.30 (0.23), residues: 540 sheet: 1.03 (0.32), residues: 243 loop : -0.70 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 211 TYR 0.007 0.001 TYR B 448 PHE 0.008 0.001 PHE A 226 TRP 0.012 0.001 TRP B 564 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (11904) covalent geometry : angle 0.53968 / 0.28 (16104) SS BOND : bond 0.00237 / 0.14 ( 18) SS BOND : angle 1.23812 / 0.83 ( 36) hydrogen bonds : bond 0.03271 / 2.19 ( 561) hydrogen bonds : angle 4.92887 / 3.44 ( 1638) link_BETA1-4 : bond 0.00351 / 0.22 ( 12) link_BETA1-4 : angle 1.18759 / 0.76 ( 36) link_NAG-ASN : bond 0.00865 / 0.55 ( 18) link_NAG-ASN : angle 3.79458 / 2.74 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7366 (tpp) cc_final: 0.7129 (tpp) REVERT: A 411 CYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7443 (t) REVERT: B 98 MET cc_start: 0.7325 (tpp) cc_final: 0.6808 (tpp) REVERT: B 475 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8189 (mtm) REVERT: C 98 MET cc_start: 0.7747 (tpt) cc_final: 0.7270 (tpp) REVERT: C 333 THR cc_start: 0.8697 (p) cc_final: 0.8377 (t) REVERT: C 411 CYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7471 (t) outliers start: 21 outliers final: 6 residues processed: 87 average time/residue: 0.4036 time to fit residues: 38.7675 Evaluate side-chains 70 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 109 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 127 optimal weight: 0.0270 chunk 29 optimal weight: 0.0470 chunk 11 optimal weight: 4.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.116309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.077047 restraints weight = 17911.195| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.77 r_work: 0.2879 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11952 Z= 0.109 Angle : 0.601 9.743 16230 Z= 0.293 Chirality : 0.044 0.385 1863 Planarity : 0.003 0.038 2037 Dihedral : 4.405 23.154 1524 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.43 % Allowed : 13.62 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.23), residues: 1389 helix: 1.27 (0.23), residues: 540 sheet: 1.08 (0.32), residues: 243 loop : -0.67 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 211 TYR 0.008 0.001 TYR B 448 PHE 0.027 0.001 PHE B 554 TRP 0.012 0.001 TRP B 564 HIS 0.002 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (11904) covalent geometry : angle 0.55556 / 0.28 (16104) SS BOND : bond 0.00333 / 0.18 ( 18) SS BOND : angle 1.31283 / 0.87 ( 36) hydrogen bonds : bond 0.03401 / 2.25 ( 561) hydrogen bonds : angle 4.89530 / 3.41 ( 1638) link_BETA1-4 : bond 0.00315 / 0.21 ( 12) link_BETA1-4 : angle 1.20441 / 0.79 ( 36) link_NAG-ASN : bond 0.00835 / 0.53 ( 18) link_NAG-ASN : angle 3.78953 / 2.74 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7423 (tpp) cc_final: 0.7140 (tpp) REVERT: A 411 CYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7438 (t) REVERT: B 98 MET cc_start: 0.7212 (tpp) cc_final: 0.6990 (tpp) REVERT: B 475 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8178 (mtm) REVERT: C 98 MET cc_start: 0.7577 (tpt) cc_final: 0.7350 (tpp) REVERT: C 333 THR cc_start: 0.8698 (p) cc_final: 0.8383 (t) REVERT: C 411 CYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7473 (t) outliers start: 18 outliers final: 10 residues processed: 84 average time/residue: 0.4529 time to fit residues: 41.5307 Evaluate side-chains 73 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 91 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 113 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.076181 restraints weight = 17820.666| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.77 r_work: 0.2864 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11952 Z= 0.134 Angle : 0.619 10.005 16230 Z= 0.303 Chirality : 0.045 0.400 1863 Planarity : 0.003 0.039 2037 Dihedral : 4.446 23.059 1524 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.11 % Allowed : 14.73 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1389 helix: 1.26 (0.23), residues: 540 sheet: 1.09 (0.32), residues: 243 loop : -0.70 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 288 TYR 0.010 0.001 TYR B 448 PHE 0.017 0.001 PHE C 554 TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (11904) covalent geometry : angle 0.57336 / 0.29 (16104) SS BOND : bond 0.00221 / 0.14 ( 18) SS BOND : angle 1.45473 / 0.97 ( 36) hydrogen bonds : bond 0.03537 / 2.35 ( 561) hydrogen bonds : angle 4.88696 / 3.41 ( 1638) link_BETA1-4 : bond 0.00277 / 0.18 ( 12) link_BETA1-4 : angle 1.25208 / 0.82 ( 36) link_NAG-ASN : bond 0.00811 / 0.52 ( 18) link_NAG-ASN : angle 3.80902 / 2.77 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7351 (tpp) cc_final: 0.7071 (tpp) REVERT: A 411 CYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7410 (t) REVERT: B 98 MET cc_start: 0.7226 (tpp) cc_final: 0.6989 (tpp) REVERT: B 475 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8302 (mtm) REVERT: B 554 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7194 (t80) REVERT: C 98 MET cc_start: 0.7506 (tpt) cc_final: 0.7246 (tpp) REVERT: C 333 THR cc_start: 0.8708 (p) cc_final: 0.8392 (t) REVERT: C 411 CYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7467 (t) outliers start: 14 outliers final: 9 residues processed: 72 average time/residue: 0.4876 time to fit residues: 38.8423 Evaluate side-chains 70 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 554 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.115106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075658 restraints weight = 18016.882| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.77 r_work: 0.2854 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11952 Z= 0.142 Angle : 0.625 10.141 16230 Z= 0.305 Chirality : 0.045 0.407 1863 Planarity : 0.003 0.039 2037 Dihedral : 4.491 23.436 1524 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.27 % Allowed : 14.65 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.23), residues: 1389 helix: 1.25 (0.23), residues: 540 sheet: 1.08 (0.32), residues: 243 loop : -0.72 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 288 TYR 0.011 0.001 TYR B 448 PHE 0.009 0.001 PHE C 226 TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (11904) covalent geometry : angle 0.58042 / 0.30 (16104) SS BOND : bond 0.00235 / 0.14 ( 18) SS BOND : angle 1.46452 / 0.97 ( 36) hydrogen bonds : bond 0.03628 / 2.40 ( 561) hydrogen bonds : angle 4.88823 / 3.41 ( 1638) link_BETA1-4 : bond 0.00289 / 0.19 ( 12) link_BETA1-4 : angle 1.26941 / 0.84 ( 36) link_NAG-ASN : bond 0.00809 / 0.51 ( 18) link_NAG-ASN : angle 3.81768 / 2.78 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 CYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7390 (t) REVERT: B 98 MET cc_start: 0.7241 (tpp) cc_final: 0.7010 (tpp) REVERT: B 475 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8321 (mtm) REVERT: B 554 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7069 (t80) REVERT: C 98 MET cc_start: 0.7519 (tpt) cc_final: 0.7280 (tpp) REVERT: C 333 THR cc_start: 0.8818 (p) cc_final: 0.8481 (t) REVERT: C 411 CYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7470 (t) outliers start: 16 outliers final: 10 residues processed: 73 average time/residue: 0.4882 time to fit residues: 39.3432 Evaluate side-chains 72 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.111434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.073306 restraints weight = 18280.805| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.61 r_work: 0.2811 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11952 Z= 0.223 Angle : 0.695 11.031 16230 Z= 0.338 Chirality : 0.048 0.452 1863 Planarity : 0.004 0.043 2037 Dihedral : 4.782 24.816 1524 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.11 % Allowed : 15.04 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.23), residues: 1389 helix: 1.23 (0.23), residues: 540 sheet: 0.97 (0.32), residues: 243 loop : -0.80 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 423 TYR 0.016 0.001 TYR B 448 PHE 0.014 0.002 PHE C 226 TRP 0.011 0.001 TRP B 564 HIS 0.007 0.001 HIS A 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (11904) covalent geometry : angle 0.64950 / 0.33 (16104) SS BOND : bond 0.00301 / 0.18 ( 18) SS BOND : angle 1.76615 / 1.23 ( 36) hydrogen bonds : bond 0.04191 / 2.78 ( 561) hydrogen bonds : angle 4.94090 / 3.44 ( 1638) link_BETA1-4 : bond 0.00210 / 0.14 ( 12) link_BETA1-4 : angle 1.39179 / 0.92 ( 36) link_NAG-ASN : bond 0.00768 / 0.49 ( 18) link_NAG-ASN : angle 3.98029 / 2.92 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3440.11 seconds wall clock time: 59 minutes 23.02 seconds (3563.02 seconds total)