Starting phenix.real_space_refine on Tue Jul 29 22:45:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvc_34123/07_2025/7yvc_34123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvc_34123/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvc_34123/07_2025/7yvc_34123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvc_34123/07_2025/7yvc_34123.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvc_34123/07_2025/7yvc_34123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvc_34123/07_2025/7yvc_34123.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.62, per 1000 atoms: 0.65 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: 3.13 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.47 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: 3.70 Time building geometry restraints manager: 3.69 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 577 or resid 701 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: 1.470 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.660 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.430 ------------------------------------------------------------------------------- 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 : 7.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (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 TRP 0.017 0.002 TRP C 564 HIS 0.003 0.001 HIS A 209 PHE 0.015 0.002 PHE C 554 TYR 0.017 0.002 TYR C 448 ARG 0.019 0.001 ARG A 391 Details of bonding type rmsd link_NAG-ASN : bond 0.20792 ( 18) link_NAG-ASN : angle 16.03226 ( 54) link_BETA1-4 : bond 0.00412 ( 12) link_BETA1-4 : angle 1.75779 ( 36) hydrogen bonds : bond 0.14130 ( 561) hydrogen bonds : angle 6.75238 ( 1638) SS BOND : bond 0.00458 ( 18) SS BOND : angle 2.22059 ( 36) covalent geometry : bond 0.00666 (11904) covalent geometry : angle 0.82093 (16104) *********************** 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 : 1.388 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: 1.3216 time to fit residues: 131.9735 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 : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 125 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.115466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075544 restraints weight = 17839.578| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.78 r_work: 0.2848 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1092 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= 0.135 Angle : 0.720 12.790 16230 Z= 0.345 Chirality : 0.047 0.447 1863 Planarity : 0.004 0.040 2037 Dihedral : 7.434 59.555 2154 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.87 % Allowed : 6.33 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1389 helix: 0.70 (0.22), residues: 552 sheet: 0.67 (0.31), residues: 243 loop : -1.18 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 564 HIS 0.002 0.001 HIS A 283 PHE 0.011 0.001 PHE A 222 TYR 0.008 0.001 TYR B 156 ARG 0.007 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.01056 ( 18) link_NAG-ASN : angle 5.09476 ( 54) link_BETA1-4 : bond 0.00357 ( 12) link_BETA1-4 : angle 1.55017 ( 36) hydrogen bonds : bond 0.04226 ( 561) hydrogen bonds : angle 5.46502 ( 1638) SS BOND : bond 0.00296 ( 18) SS BOND : angle 1.67009 ( 36) covalent geometry : bond 0.00290 (11904) covalent geometry : angle 0.65090 (16104) *********************** 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 79 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.287 Fit side-chains REVERT: A 98 MET cc_start: 0.7544 (tpp) cc_final: 0.6994 (tpp) REVERT: B 475 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8361 (mtm) REVERT: B 554 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7446 (t80) REVERT: B 561 LEU cc_start: 0.7387 (mt) cc_final: 0.7037 (mt) REVERT: B 565 MET cc_start: 0.7754 (ppp) cc_final: 0.7505 (ppp) REVERT: C 554 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6520 (t80) outliers start: 11 outliers final: 1 residues processed: 71 average time/residue: 1.4156 time to fit residues: 111.2789 Evaluate side-chains 59 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 15 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.111926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.072103 restraints weight = 18107.696| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.77 r_work: 0.2786 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11952 Z= 0.244 Angle : 0.753 12.437 16230 Z= 0.361 Chirality : 0.049 0.486 1863 Planarity : 0.004 0.044 2037 Dihedral : 7.223 59.193 2154 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.11 % Allowed : 9.66 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.23), residues: 1389 helix: 0.86 (0.23), residues: 552 sheet: 0.69 (0.31), residues: 243 loop : -1.21 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 564 HIS 0.005 0.001 HIS C 283 PHE 0.013 0.002 PHE C 226 TYR 0.019 0.002 TYR B 448 ARG 0.003 0.000 ARG A 391 Details of bonding type rmsd link_NAG-ASN : bond 0.00921 ( 18) link_NAG-ASN : angle 4.92477 ( 54) link_BETA1-4 : bond 0.00283 ( 12) link_BETA1-4 : angle 1.54981 ( 36) hydrogen bonds : bond 0.04661 ( 561) hydrogen bonds : angle 5.22302 ( 1638) SS BOND : bond 0.00423 ( 18) SS BOND : angle 1.82286 ( 36) covalent geometry : bond 0.00577 (11904) covalent geometry : angle 0.69048 (16104) *********************** 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 72 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.364 Fit side-chains REVERT: A 98 MET cc_start: 0.7408 (tpp) cc_final: 0.6814 (tpp) REVERT: B 475 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8506 (mtm) REVERT: B 554 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7335 (t80) REVERT: B 561 LEU cc_start: 0.7406 (mt) cc_final: 0.7005 (mt) REVERT: C 98 MET cc_start: 0.7404 (tpt) cc_final: 0.6892 (tpp) REVERT: C 554 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.6685 (t80) outliers start: 14 outliers final: 4 residues processed: 66 average time/residue: 1.1131 time to fit residues: 81.5885 Evaluate side-chains 60 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 557 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 128 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.115066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.075371 restraints weight = 17917.466| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.78 r_work: 0.2848 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11952 Z= 0.119 Angle : 0.638 10.876 16230 Z= 0.309 Chirality : 0.045 0.436 1863 Planarity : 0.003 0.039 2037 Dihedral : 6.659 57.700 2154 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.63 % Allowed : 11.24 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1389 helix: 1.09 (0.23), residues: 537 sheet: 0.83 (0.31), residues: 243 loop : -0.94 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 564 HIS 0.002 0.000 HIS B 292 PHE 0.010 0.001 PHE C 222 TYR 0.008 0.001 TYR C 156 ARG 0.002 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00969 ( 18) link_NAG-ASN : angle 4.44962 ( 54) link_BETA1-4 : bond 0.00359 ( 12) link_BETA1-4 : angle 1.42724 ( 36) hydrogen bonds : bond 0.03800 ( 561) hydrogen bonds : angle 5.11196 ( 1638) SS BOND : bond 0.00234 ( 18) SS BOND : angle 1.80656 ( 36) covalent geometry : bond 0.00259 (11904) covalent geometry : angle 0.57630 (16104) *********************** 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 72 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.350 Fit side-chains REVERT: A 98 MET cc_start: 0.7567 (tpp) cc_final: 0.6995 (tpp) REVERT: B 475 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8191 (mtm) REVERT: B 554 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7206 (t80) REVERT: B 561 LEU cc_start: 0.7346 (mt) cc_final: 0.6937 (mt) REVERT: C 98 MET cc_start: 0.7370 (tpt) cc_final: 0.6839 (tpp) REVERT: C 333 THR cc_start: 0.8794 (p) cc_final: 0.8444 (t) REVERT: C 554 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.6582 (t80) outliers start: 8 outliers final: 2 residues processed: 66 average time/residue: 1.2854 time to fit residues: 93.7058 Evaluate side-chains 61 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 554 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.114083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.074574 restraints weight = 17908.999| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.76 r_work: 0.2834 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11952 Z= 0.149 Angle : 0.649 10.762 16230 Z= 0.312 Chirality : 0.046 0.446 1863 Planarity : 0.003 0.040 2037 Dihedral : 6.497 57.679 2154 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.43 % Allowed : 12.51 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1389 helix: 1.11 (0.23), residues: 540 sheet: 0.85 (0.31), residues: 243 loop : -0.87 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS B 283 PHE 0.009 0.001 PHE C 226 TYR 0.012 0.001 TYR B 448 ARG 0.002 0.000 ARG A 391 Details of bonding type rmsd link_NAG-ASN : bond 0.00886 ( 18) link_NAG-ASN : angle 4.35017 ( 54) link_BETA1-4 : bond 0.00322 ( 12) link_BETA1-4 : angle 1.44622 ( 36) hydrogen bonds : bond 0.03936 ( 561) hydrogen bonds : angle 5.05254 ( 1638) SS BOND : bond 0.00337 ( 18) SS BOND : angle 1.96522 ( 36) covalent geometry : bond 0.00345 (11904) covalent geometry : angle 0.58979 (16104) *********************** 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 77 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 1.333 Fit side-chains REVERT: A 98 MET cc_start: 0.7607 (tpp) cc_final: 0.7032 (tpp) REVERT: A 411 CYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7618 (t) REVERT: B 98 MET cc_start: 0.7215 (tpp) cc_final: 0.6875 (tpp) REVERT: B 475 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8263 (mtm) REVERT: B 554 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7273 (t80) REVERT: C 98 MET cc_start: 0.7595 (tpt) cc_final: 0.7070 (tpp) REVERT: C 333 THR cc_start: 0.8834 (p) cc_final: 0.8495 (t) REVERT: C 411 CYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7560 (t) REVERT: C 554 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6595 (t80) outliers start: 18 outliers final: 6 residues processed: 71 average time/residue: 1.3783 time to fit residues: 108.7434 Evaluate side-chains 68 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.956 ------------------------------------------------------------------------------- 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 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 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 84 optimal weight: 3.9990 chunk 6 optimal weight: 0.0270 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.6444 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.111795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.073241 restraints weight = 18299.035| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.66 r_work: 0.2805 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11952 Z= 0.192 Angle : 0.671 11.121 16230 Z= 0.324 Chirality : 0.048 0.472 1863 Planarity : 0.004 0.043 2037 Dihedral : 6.507 58.082 2154 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.82 % Allowed : 13.62 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1389 helix: 1.12 (0.23), residues: 540 sheet: 0.85 (0.31), residues: 243 loop : -0.87 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 564 HIS 0.004 0.001 HIS C 283 PHE 0.012 0.001 PHE C 226 TYR 0.015 0.001 TYR B 448 ARG 0.003 0.000 ARG B 423 Details of bonding type rmsd link_NAG-ASN : bond 0.00842 ( 18) link_NAG-ASN : angle 4.28842 ( 54) link_BETA1-4 : bond 0.00235 ( 12) link_BETA1-4 : angle 1.46684 ( 36) hydrogen bonds : bond 0.04129 ( 561) hydrogen bonds : angle 5.02179 ( 1638) SS BOND : bond 0.00345 ( 18) SS BOND : angle 1.63359 ( 36) covalent geometry : bond 0.00452 (11904) covalent geometry : angle 0.61702 (16104) *********************** 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 85 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: A 411 CYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7475 (t) REVERT: B 98 MET cc_start: 0.7283 (tpp) cc_final: 0.7056 (tpp) REVERT: B 411 CYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7448 (t) REVERT: B 475 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8382 (mtm) REVERT: B 554 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7108 (t80) REVERT: C 98 MET cc_start: 0.7481 (tpt) cc_final: 0.7075 (tpp) REVERT: C 333 THR cc_start: 0.8786 (p) cc_final: 0.8462 (t) REVERT: C 411 CYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7498 (t) REVERT: C 554 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.6605 (t80) outliers start: 23 outliers final: 8 residues processed: 80 average time/residue: 1.4300 time to fit residues: 126.0927 Evaluate side-chains 71 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 554 PHE 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 411 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.0870 chunk 7 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.113145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.074819 restraints weight = 18198.615| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.67 r_work: 0.2836 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1841 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= 0.123 Angle : 0.631 10.355 16230 Z= 0.305 Chirality : 0.046 0.442 1863 Planarity : 0.003 0.040 2037 Dihedral : 6.297 56.613 2154 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.66 % Allowed : 14.01 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1389 helix: 1.15 (0.23), residues: 540 sheet: 0.88 (0.32), residues: 243 loop : -0.80 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 564 HIS 0.003 0.001 HIS B 292 PHE 0.009 0.001 PHE C 222 TYR 0.010 0.001 TYR B 448 ARG 0.002 0.000 ARG C 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00891 ( 18) link_NAG-ASN : angle 4.09107 ( 54) link_BETA1-4 : bond 0.00332 ( 12) link_BETA1-4 : angle 1.41672 ( 36) hydrogen bonds : bond 0.03751 ( 561) hydrogen bonds : angle 5.00499 ( 1638) SS BOND : bond 0.00296 ( 18) SS BOND : angle 1.48157 ( 36) covalent geometry : bond 0.00277 (11904) covalent geometry : angle 0.57928 (16104) *********************** 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 84 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 2.212 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7598 (tpp) cc_final: 0.6971 (tpp) REVERT: A 411 CYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7444 (t) REVERT: B 98 MET cc_start: 0.7135 (tpp) cc_final: 0.6689 (tpp) REVERT: B 411 CYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7342 (t) REVERT: B 475 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8265 (mtm) REVERT: B 554 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: C 98 MET cc_start: 0.7500 (tpt) cc_final: 0.7095 (tpp) REVERT: C 333 THR cc_start: 0.8770 (p) cc_final: 0.8436 (t) REVERT: C 411 CYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7486 (t) outliers start: 21 outliers final: 6 residues processed: 78 average time/residue: 1.7096 time to fit residues: 150.4492 Evaluate side-chains 69 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS 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 411 CYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 115 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 75 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.114318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.076213 restraints weight = 18073.110| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.66 r_work: 0.2861 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11952 Z= 0.103 Angle : 0.605 9.937 16230 Z= 0.296 Chirality : 0.045 0.421 1863 Planarity : 0.003 0.039 2037 Dihedral : 6.069 55.576 2154 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.58 % Allowed : 14.73 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1389 helix: 1.19 (0.23), residues: 540 sheet: 0.94 (0.32), residues: 243 loop : -0.72 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 564 HIS 0.003 0.001 HIS B 292 PHE 0.017 0.001 PHE A 554 TYR 0.008 0.001 TYR B 448 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00894 ( 18) link_NAG-ASN : angle 3.94845 ( 54) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.37412 ( 36) hydrogen bonds : bond 0.03605 ( 561) hydrogen bonds : angle 4.98720 ( 1638) SS BOND : bond 0.00246 ( 18) SS BOND : angle 1.40870 ( 36) covalent geometry : bond 0.00218 (11904) covalent geometry : angle 0.55509 (16104) *********************** 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 83 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7431 (tpp) cc_final: 0.6858 (tpp) REVERT: A 411 CYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7423 (t) REVERT: B 98 MET cc_start: 0.7213 (tpp) cc_final: 0.6684 (tpp) REVERT: B 411 CYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7305 (t) REVERT: B 475 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8143 (mtm) REVERT: C 98 MET cc_start: 0.7642 (tpt) cc_final: 0.7229 (tpp) REVERT: C 333 THR cc_start: 0.8795 (p) cc_final: 0.8463 (t) REVERT: C 411 CYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7449 (t) outliers start: 20 outliers final: 11 residues processed: 80 average time/residue: 1.0941 time to fit residues: 97.0099 Evaluate side-chains 74 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 554 PHE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 411 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 82 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 123 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 99 optimal weight: 0.0170 chunk 46 optimal weight: 0.0370 chunk 109 optimal weight: 0.5980 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.116729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.077363 restraints weight = 17955.599| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.78 r_work: 0.2886 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11952 Z= 0.100 Angle : 0.601 9.972 16230 Z= 0.296 Chirality : 0.044 0.411 1863 Planarity : 0.003 0.037 2037 Dihedral : 5.765 55.160 2154 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1389 helix: 1.28 (0.23), residues: 540 sheet: 1.03 (0.32), residues: 243 loop : -0.69 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 564 HIS 0.002 0.001 HIS B 292 PHE 0.014 0.001 PHE A 554 TYR 0.007 0.001 TYR B 448 ARG 0.002 0.000 ARG A 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00867 ( 18) link_NAG-ASN : angle 3.83634 ( 54) link_BETA1-4 : bond 0.00380 ( 12) link_BETA1-4 : angle 1.30406 ( 36) hydrogen bonds : bond 0.03452 ( 561) hydrogen bonds : angle 4.95189 ( 1638) SS BOND : bond 0.00225 ( 18) SS BOND : angle 1.39308 ( 36) covalent geometry : bond 0.00210 (11904) covalent geometry : angle 0.55315 (16104) *********************** 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 88 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7459 (tpp) cc_final: 0.6903 (tpp) REVERT: A 411 CYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7438 (t) REVERT: B 98 MET cc_start: 0.7220 (tpp) cc_final: 0.6648 (tpp) REVERT: B 411 CYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7341 (t) REVERT: B 475 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8129 (mtm) REVERT: C 98 MET cc_start: 0.7606 (tpt) cc_final: 0.7403 (tpp) REVERT: C 333 THR cc_start: 0.8708 (p) cc_final: 0.8406 (t) REVERT: C 411 CYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7448 (t) outliers start: 18 outliers final: 12 residues processed: 86 average time/residue: 1.0489 time to fit residues: 100.1128 Evaluate side-chains 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 111 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 411 CYS 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 16 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 129 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.116128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.076539 restraints weight = 17924.673| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.78 r_work: 0.2868 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11952 Z= 0.123 Angle : 0.630 10.132 16230 Z= 0.310 Chirality : 0.045 0.423 1863 Planarity : 0.003 0.039 2037 Dihedral : 5.771 55.806 2154 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.19 % Allowed : 15.84 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1389 helix: 1.22 (0.23), residues: 540 sheet: 1.10 (0.32), residues: 243 loop : -0.70 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 564 HIS 0.003 0.001 HIS B 292 PHE 0.024 0.001 PHE B 554 TYR 0.009 0.001 TYR B 448 ARG 0.001 0.000 ARG A 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00838 ( 18) link_NAG-ASN : angle 3.84648 ( 54) link_BETA1-4 : bond 0.00326 ( 12) link_BETA1-4 : angle 1.31100 ( 36) hydrogen bonds : bond 0.03543 ( 561) hydrogen bonds : angle 4.90868 ( 1638) SS BOND : bond 0.00226 ( 18) SS BOND : angle 1.43556 ( 36) covalent geometry : bond 0.00272 (11904) covalent geometry : angle 0.58491 (16104) ********************** 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 77 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7452 (tpp) cc_final: 0.6885 (tpp) REVERT: A 411 CYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7389 (t) REVERT: B 98 MET cc_start: 0.7239 (tpp) cc_final: 0.6950 (tpp) REVERT: B 411 CYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7296 (t) REVERT: B 475 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8189 (mtm) REVERT: C 333 THR cc_start: 0.8719 (p) cc_final: 0.8421 (t) REVERT: C 411 CYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7443 (t) outliers start: 15 outliers final: 12 residues processed: 75 average time/residue: 0.9390 time to fit residues: 78.8471 Evaluate side-chains 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 A residue 554 PHE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 411 CYS 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 74 optimal weight: 0.2980 chunk 126 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 114 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.116222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076601 restraints weight = 17902.180| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.78 r_work: 0.2869 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2233 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= 0.116 Angle : 0.623 10.028 16230 Z= 0.307 Chirality : 0.045 0.422 1863 Planarity : 0.003 0.039 2037 Dihedral : 5.753 55.884 2154 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.43 % Allowed : 15.68 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1389 helix: 1.21 (0.23), residues: 540 sheet: 1.12 (0.32), residues: 243 loop : -0.67 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 564 HIS 0.003 0.001 HIS B 292 PHE 0.025 0.001 PHE C 554 TYR 0.009 0.001 TYR B 448 ARG 0.001 0.000 ARG C 153 Details of bonding type rmsd link_NAG-ASN : bond 0.00843 ( 18) link_NAG-ASN : angle 3.82060 ( 54) link_BETA1-4 : bond 0.00328 ( 12) link_BETA1-4 : angle 1.30869 ( 36) hydrogen bonds : bond 0.03525 ( 561) hydrogen bonds : angle 4.90078 ( 1638) SS BOND : bond 0.00224 ( 18) SS BOND : angle 1.39900 ( 36) covalent geometry : bond 0.00256 (11904) covalent geometry : angle 0.57787 (16104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9056.14 seconds wall clock time: 165 minutes 42.94 seconds (9942.94 seconds total)