Starting phenix.real_space_refine on Sat Aug 23 11:28:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvc_34123/08_2025/7yvc_34123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvc_34123/08_2025/7yvc_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yvc_34123/08_2025/7yvc_34123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvc_34123/08_2025/7yvc_34123.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvc_34123/08_2025/7yvc_34123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvc_34123/08_2025/7yvc_34123.map" } 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-2.0-5787/lib/python3.9/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 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: 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 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: 3.44, per 1000 atoms: 0.29 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: 1.17 Conformation dependent library (CDL) restraints added in 599.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.42 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: 2.05 Time building geometry restraints manager: 1.52 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: 6858 17.81 - 35.62: 604 35.62 - 53.43: 114 53.43 - 71.24: 26 71.24 - 89.06: 30 Dihedral angle restraints: 7632 sinusoidal: 3522 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 7629 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.290 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:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 14.939 89.055 4920 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 aren 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 covalent geometry : bond 0.00666 (11904) covalent geometry : angle 0.82093 (16104) SS BOND : bond 0.00458 ( 18) SS BOND : angle 2.22059 ( 36) hydrogen bonds : bond 0.14130 ( 561) hydrogen bonds : angle 6.75238 ( 1638) link_BETA1-4 : bond 0.00412 ( 12) link_BETA1-4 : angle 1.75779 ( 36) link_NAG-ASN : bond 0.20792 ( 18) link_NAG-ASN : angle 16.03226 ( 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: 0.7485 (mt) 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: 0.7044 time to fit residues: 69.8224 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 : 0.490 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.114531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.074538 restraints weight = 17935.850| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.79 r_work: 0.2829 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1037 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= 0.156 Angle : 0.736 13.053 16230 Z= 0.352 Chirality : 0.047 0.442 1863 Planarity : 0.004 0.041 2037 Dihedral : 7.508 59.495 2154 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.03 % Allowed : 6.10 % 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 aren not related in a simple way. whole: -0.19 (0.22), residues: 1389 helix: 0.68 (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 0.007 0.000 ARG B 204 TYR 0.010 0.001 TYR B 448 PHE 0.011 0.002 PHE C 226 TRP 0.015 0.002 TRP B 564 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00347 (11904) covalent geometry : angle 0.66600 (16104) SS BOND : bond 0.00303 ( 18) SS BOND : angle 1.73077 ( 36) hydrogen bonds : bond 0.04440 ( 561) hydrogen bonds : angle 5.47338 ( 1638) link_BETA1-4 : bond 0.00479 ( 12) link_BETA1-4 : angle 1.51222 ( 36) link_NAG-ASN : bond 0.01056 ( 18) link_NAG-ASN : angle 5.17978 ( 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 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.513 Fit side-chains REVERT: A 98 MET cc_start: 0.7428 (tpp) cc_final: 0.6882 (tpp) REVERT: B 475 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8441 (mtm) REVERT: B 554 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7475 (t80) REVERT: B 561 LEU cc_start: 0.7379 (mt) cc_final: 0.7038 (mt) REVERT: B 565 MET cc_start: 0.7752 (ppp) cc_final: 0.7504 (ppp) REVERT: C 554 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6526 (t80) outliers start: 13 outliers final: 2 residues processed: 70 average time/residue: 0.6021 time to fit residues: 46.0588 Evaluate side-chains 59 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.7980 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3602 r_free = 0.3602 target = 0.113207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.073342 restraints weight = 18141.054| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.78 r_work: 0.2813 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11952 Z= 0.176 Angle : 0.694 11.632 16230 Z= 0.333 Chirality : 0.047 0.460 1863 Planarity : 0.004 0.042 2037 Dihedral : 7.051 59.223 2154 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.79 % Allowed : 9.03 % Favored : 90.18 % 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 aren not related in a simple way. whole: 0.05 (0.23), residues: 1389 helix: 0.93 (0.23), residues: 552 sheet: 0.76 (0.31), residues: 243 loop : -1.13 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 204 TYR 0.014 0.001 TYR C 448 PHE 0.011 0.001 PHE C 226 TRP 0.014 0.001 TRP B 564 HIS 0.004 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00406 (11904) covalent geometry : angle 0.63071 (16104) SS BOND : bond 0.00348 ( 18) SS BOND : angle 1.64197 ( 36) hydrogen bonds : bond 0.04220 ( 561) hydrogen bonds : angle 5.19208 ( 1638) link_BETA1-4 : bond 0.00276 ( 12) link_BETA1-4 : angle 1.51400 ( 36) link_NAG-ASN : bond 0.00964 ( 18) link_NAG-ASN : angle 4.79245 ( 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 : 0.487 Fit side-chains REVERT: A 98 MET cc_start: 0.7450 (tpp) cc_final: 0.6852 (tpp) REVERT: B 475 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8456 (mtm) REVERT: B 554 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7270 (t80) REVERT: B 561 LEU cc_start: 0.7385 (mt) cc_final: 0.7003 (mt) REVERT: C 98 MET cc_start: 0.7225 (tpt) cc_final: 0.6726 (tpp) REVERT: C 333 THR cc_start: 0.8784 (p) cc_final: 0.8430 (t) REVERT: C 554 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.6644 (t80) outliers start: 10 outliers final: 3 residues processed: 68 average time/residue: 0.5595 time to fit residues: 41.9562 Evaluate side-chains 60 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER 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=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: 0.9980 chunk 83 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 120 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.075372 restraints weight = 17942.331| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.78 r_work: 0.2846 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1537 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= 0.127 Angle : 0.644 10.843 16230 Z= 0.312 Chirality : 0.046 0.439 1863 Planarity : 0.003 0.039 2037 Dihedral : 6.630 57.882 2154 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.48 % Allowed : 11.08 % Favored : 88.44 % 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 aren not related in a simple way. whole: 0.28 (0.23), residues: 1389 helix: 1.13 (0.23), residues: 537 sheet: 0.81 (0.31), residues: 243 loop : -0.93 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 204 TYR 0.009 0.001 TYR B 448 PHE 0.009 0.001 PHE C 222 TRP 0.012 0.001 TRP B 564 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00282 (11904) covalent geometry : angle 0.58141 (16104) SS BOND : bond 0.00287 ( 18) SS BOND : angle 1.93539 ( 36) hydrogen bonds : bond 0.03832 ( 561) hydrogen bonds : angle 5.10619 ( 1638) link_BETA1-4 : bond 0.00357 ( 12) link_BETA1-4 : angle 1.41092 ( 36) link_NAG-ASN : bond 0.00951 ( 18) link_NAG-ASN : angle 4.47496 ( 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 71 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.487 Fit side-chains REVERT: A 98 MET cc_start: 0.7528 (tpp) cc_final: 0.7168 (tpp) REVERT: B 475 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8110 (mtm) REVERT: B 554 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7195 (t80) REVERT: B 561 LEU cc_start: 0.7313 (mt) cc_final: 0.6881 (mt) REVERT: C 98 MET cc_start: 0.7346 (tpt) cc_final: 0.6826 (tpp) REVERT: C 333 THR cc_start: 0.8792 (p) cc_final: 0.8440 (t) REVERT: C 554 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6622 (t80) outliers start: 6 outliers final: 1 residues processed: 67 average time/residue: 0.5480 time to fit residues: 40.4585 Evaluate side-chains 60 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 GLN 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: 0.2980 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 123 optimal weight: 0.0070 chunk 111 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.115764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.076195 restraints weight = 17924.924| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.78 r_work: 0.2863 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1730 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= 0.113 Angle : 0.615 10.161 16230 Z= 0.298 Chirality : 0.045 0.423 1863 Planarity : 0.003 0.038 2037 Dihedral : 6.278 56.860 2154 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.35 % Allowed : 11.88 % Favored : 86.78 % 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 aren not related in a simple way. whole: 0.43 (0.23), residues: 1389 helix: 1.24 (0.23), residues: 537 sheet: 0.91 (0.32), residues: 243 loop : -0.83 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 C 564 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00249 (11904) covalent geometry : angle 0.55943 (16104) SS BOND : bond 0.00273 ( 18) SS BOND : angle 1.33571 ( 36) hydrogen bonds : bond 0.03533 ( 561) hydrogen bonds : angle 4.99914 ( 1638) link_BETA1-4 : bond 0.00347 ( 12) link_BETA1-4 : angle 1.35990 ( 36) link_NAG-ASN : bond 0.00909 ( 18) link_NAG-ASN : angle 4.23491 ( 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 81 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 411 CYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7521 (t) REVERT: B 98 MET cc_start: 0.7250 (tpp) cc_final: 0.6876 (tpp) REVERT: B 475 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8206 (mtm) REVERT: B 554 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7237 (t80) REVERT: C 98 MET cc_start: 0.7525 (tpt) cc_final: 0.6942 (tpp) REVERT: C 333 THR cc_start: 0.8782 (p) cc_final: 0.8447 (t) REVERT: C 411 CYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7567 (t) REVERT: C 554 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7587 (m-80) outliers start: 17 outliers final: 4 residues processed: 76 average time/residue: 0.4934 time to fit residues: 41.6676 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 : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER 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 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: 1.9990 chunk 91 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3622 r_free = 0.3622 target = 0.114313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.074446 restraints weight = 18079.450| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.79 r_work: 0.2827 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11952 Z= 0.162 Angle : 0.644 10.841 16230 Z= 0.311 Chirality : 0.046 0.455 1863 Planarity : 0.003 0.041 2037 Dihedral : 6.282 57.569 2154 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.74 % Allowed : 12.91 % Favored : 85.35 % 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 aren not related in a simple way. whole: 0.42 (0.23), residues: 1389 helix: 1.21 (0.23), residues: 540 sheet: 0.90 (0.32), residues: 243 loop : -0.80 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 423 TYR 0.014 0.001 TYR B 448 PHE 0.010 0.001 PHE C 226 TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00377 (11904) covalent geometry : angle 0.59082 (16104) SS BOND : bond 0.00286 ( 18) SS BOND : angle 1.52069 ( 36) hydrogen bonds : bond 0.03880 ( 561) hydrogen bonds : angle 4.96731 ( 1638) link_BETA1-4 : bond 0.00284 ( 12) link_BETA1-4 : angle 1.39315 ( 36) link_NAG-ASN : bond 0.00849 ( 18) link_NAG-ASN : angle 4.20830 ( 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 82 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7563 (tpp) cc_final: 0.7028 (tpp) REVERT: A 411 CYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7504 (t) REVERT: B 98 MET cc_start: 0.7364 (tpp) cc_final: 0.6860 (tpp) REVERT: B 475 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8238 (mtm) REVERT: B 554 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: C 98 MET cc_start: 0.7569 (tpt) cc_final: 0.7125 (tpp) REVERT: C 333 THR cc_start: 0.8814 (p) cc_final: 0.8485 (t) REVERT: C 411 CYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7551 (t) outliers start: 22 outliers final: 10 residues processed: 77 average time/residue: 0.5039 time to fit residues: 43.2774 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 : 0.494 ------------------------------------------------------------------------------- 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 554 PHE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 152 ILE 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 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: 0.9980 chunk 125 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 63 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: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.076062 restraints weight = 17979.985| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.78 r_work: 0.2860 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11952 Z= 0.114 Angle : 0.606 10.083 16230 Z= 0.294 Chirality : 0.045 0.427 1863 Planarity : 0.003 0.039 2037 Dihedral : 6.036 55.814 2154 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.82 % Allowed : 13.54 % Favored : 84.64 % 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 aren not related in a simple way. whole: 0.53 (0.23), residues: 1389 helix: 1.26 (0.23), residues: 540 sheet: 0.99 (0.32), residues: 243 loop : -0.73 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 288 TYR 0.009 0.001 TYR B 448 PHE 0.009 0.001 PHE A 226 TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00252 (11904) covalent geometry : angle 0.55604 (16104) SS BOND : bond 0.00254 ( 18) SS BOND : angle 1.29403 ( 36) hydrogen bonds : bond 0.03576 ( 561) hydrogen bonds : angle 4.93215 ( 1638) link_BETA1-4 : bond 0.00348 ( 12) link_BETA1-4 : angle 1.35063 ( 36) link_NAG-ASN : bond 0.00885 ( 18) link_NAG-ASN : angle 3.98021 ( 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 91 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7566 (tpp) cc_final: 0.6979 (tpp) REVERT: A 411 CYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7488 (t) REVERT: B 98 MET cc_start: 0.7297 (tpp) cc_final: 0.6721 (tpp) REVERT: B 475 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8224 (mtm) REVERT: C 98 MET cc_start: 0.7720 (tpt) cc_final: 0.7255 (tpp) REVERT: C 333 THR cc_start: 0.8816 (p) cc_final: 0.8490 (t) REVERT: C 411 CYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7497 (t) outliers start: 23 outliers final: 9 residues processed: 87 average time/residue: 0.5017 time to fit residues: 48.4967 Evaluate side-chains 72 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 142 CYS 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 B residue 111 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET 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: 2.9990 chunk 129 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 0.0070 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.115346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075878 restraints weight = 17910.463| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.77 r_work: 0.2856 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11952 Z= 0.119 Angle : 0.612 10.191 16230 Z= 0.296 Chirality : 0.045 0.427 1863 Planarity : 0.003 0.039 2037 Dihedral : 5.939 55.947 2154 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.43 % Allowed : 14.96 % Favored : 83.61 % 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 aren not related in a simple way. whole: 0.58 (0.23), residues: 1389 helix: 1.29 (0.23), residues: 540 sheet: 1.04 (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 A 211 TYR 0.010 0.001 TYR B 448 PHE 0.008 0.001 PHE C 226 TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00265 (11904) covalent geometry : angle 0.56295 (16104) SS BOND : bond 0.00218 ( 18) SS BOND : angle 1.39792 ( 36) hydrogen bonds : bond 0.03591 ( 561) hydrogen bonds : angle 4.91918 ( 1638) link_BETA1-4 : bond 0.00302 ( 12) link_BETA1-4 : angle 1.34859 ( 36) link_NAG-ASN : bond 0.00858 ( 18) link_NAG-ASN : angle 3.94927 ( 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 82 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7552 (tpp) cc_final: 0.7006 (tpp) REVERT: A 411 CYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7434 (t) REVERT: B 98 MET cc_start: 0.7224 (tpp) cc_final: 0.6684 (tpp) REVERT: B 475 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8362 (mtm) REVERT: C 98 MET cc_start: 0.7700 (tpt) cc_final: 0.7469 (tpp) REVERT: C 333 THR cc_start: 0.8811 (p) cc_final: 0.8492 (t) REVERT: C 411 CYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7483 (t) outliers start: 18 outliers final: 14 residues processed: 81 average time/residue: 0.5165 time to fit residues: 46.2306 Evaluate side-chains 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 142 CYS 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 152 ILE 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 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: 6.9990 chunk 88 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.114802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075294 restraints weight = 17876.576| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.77 r_work: 0.2850 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2060 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= 0.139 Angle : 0.625 10.396 16230 Z= 0.303 Chirality : 0.046 0.437 1863 Planarity : 0.003 0.040 2037 Dihedral : 5.937 56.292 2154 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.50 % Allowed : 15.20 % Favored : 83.29 % 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 aren not related in a simple way. whole: 0.54 (0.23), residues: 1389 helix: 1.25 (0.23), residues: 540 sheet: 1.03 (0.32), residues: 243 loop : -0.73 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 423 TYR 0.011 0.001 TYR B 448 PHE 0.021 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 covalent geometry : bond 0.00319 (11904) covalent geometry : angle 0.57669 (16104) SS BOND : bond 0.00228 ( 18) SS BOND : angle 1.51471 ( 36) hydrogen bonds : bond 0.03692 ( 561) hydrogen bonds : angle 4.92375 ( 1638) link_BETA1-4 : bond 0.00301 ( 12) link_BETA1-4 : angle 1.35815 ( 36) link_NAG-ASN : bond 0.00839 ( 18) link_NAG-ASN : angle 3.95059 ( 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 83 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7579 (tpp) cc_final: 0.7017 (tpp) REVERT: A 411 CYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7414 (t) REVERT: B 98 MET cc_start: 0.7242 (tpp) cc_final: 0.6705 (tpp) REVERT: B 475 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8215 (mtm) REVERT: C 98 MET cc_start: 0.7507 (tpt) cc_final: 0.7253 (tpp) REVERT: C 333 THR cc_start: 0.8843 (p) cc_final: 0.8521 (t) REVERT: C 411 CYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7471 (t) outliers start: 19 outliers final: 14 residues processed: 81 average time/residue: 0.5334 time to fit residues: 47.7584 Evaluate side-chains 79 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 142 CYS 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 152 ILE 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 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: 2.9990 chunk 66 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 117 optimal weight: 0.0970 chunk 81 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.8298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.115110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.075554 restraints weight = 18037.117| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.78 r_work: 0.2851 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2099 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= 0.125 Angle : 0.622 10.260 16230 Z= 0.302 Chirality : 0.045 0.433 1863 Planarity : 0.003 0.039 2037 Dihedral : 5.894 56.160 2154 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.27 % Allowed : 15.44 % Favored : 83.29 % 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 aren not related in a simple way. whole: 0.55 (0.23), residues: 1389 helix: 1.25 (0.23), residues: 540 sheet: 1.04 (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 A 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 B 292 Details of bonding type rmsd covalent geometry : bond 0.00281 (11904) covalent geometry : angle 0.57437 (16104) SS BOND : bond 0.00223 ( 18) SS BOND : angle 1.44018 ( 36) hydrogen bonds : bond 0.03641 ( 561) hydrogen bonds : angle 4.91899 ( 1638) link_BETA1-4 : bond 0.00307 ( 12) link_BETA1-4 : angle 1.33440 ( 36) link_NAG-ASN : bond 0.00851 ( 18) link_NAG-ASN : angle 3.90107 ( 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 81 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7420 (tpp) cc_final: 0.6881 (tpp) REVERT: A 411 CYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7416 (t) REVERT: B 98 MET cc_start: 0.7219 (tpp) cc_final: 0.6983 (tpp) REVERT: B 475 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8392 (mtm) REVERT: C 333 THR cc_start: 0.8851 (p) cc_final: 0.8527 (t) REVERT: C 411 CYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7487 (t) outliers start: 16 outliers final: 12 residues processed: 79 average time/residue: 0.5187 time to fit residues: 45.3672 Evaluate side-chains 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 142 CYS 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 152 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 475 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.0020 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.111922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.073694 restraints weight = 18298.649| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.66 r_work: 0.2816 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11952 Z= 0.187 Angle : 0.665 10.969 16230 Z= 0.322 Chirality : 0.048 0.467 1863 Planarity : 0.003 0.042 2037 Dihedral : 6.093 57.603 2154 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.19 % Allowed : 15.68 % Favored : 83.14 % 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 aren not related in a simple way. whole: 0.50 (0.23), residues: 1389 helix: 1.26 (0.23), residues: 540 sheet: 0.98 (0.32), residues: 243 loop : -0.77 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 423 TYR 0.015 0.001 TYR B 448 PHE 0.011 0.001 PHE C 226 TRP 0.012 0.001 TRP B 564 HIS 0.004 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00439 (11904) covalent geometry : angle 0.61796 (16104) SS BOND : bond 0.00262 ( 18) SS BOND : angle 1.64399 ( 36) hydrogen bonds : bond 0.04053 ( 561) hydrogen bonds : angle 4.95826 ( 1638) link_BETA1-4 : bond 0.00248 ( 12) link_BETA1-4 : angle 1.41931 ( 36) link_NAG-ASN : bond 0.00804 ( 18) link_NAG-ASN : angle 4.00612 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4342.99 seconds wall clock time: 74 minutes 58.24 seconds (4498.24 seconds total)