Starting phenix.real_space_refine on Sat Jul 4 02:01:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n16_24114/07_2026/7n16_24114.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n16_24114/07_2026/7n16_24114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n16_24114/07_2026/7n16_24114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n16_24114/07_2026/7n16_24114.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7n16_24114/07_2026/7n16_24114.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n16_24114/07_2026/7n16_24114.cif" model { file = "/net/cci-nas-00/data/ceres_data/7n16_24114/07_2026/7n16_24114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n16_24114/07_2026/7n16_24114.cif" } resolution = 3.2 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= 0.006 sd= 0.092 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 Na 1 4.78 5 C 11300 2.51 5 N 2860 2.21 5 O 3088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17357 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4252 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 15, 'TRANS': 498} Chain breaks: 1 Chain: "A" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4252 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 15, 'TRANS': 498} Chain breaks: 1 Chain: "B" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4252 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 15, 'TRANS': 498} Chain breaks: 1 Chain: "C" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4252 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 15, 'TRANS': 498} Chain breaks: 1 Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'CPL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-3': 4, 'CPL:plan-4': 4, 'CPL:plan-1': 1, 'CPL:plan-2': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 88 Unusual residues: {' NA': 1, 'CPL': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-3': 4, 'CPL:plan-4': 4, 'CPL:plan-1': 1, 'CPL:plan-2': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'CPL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-3': 4, 'CPL:plan-4': 4, 'CPL:plan-1': 1, 'CPL:plan-2': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'CPL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CPL:plan-3': 4, 'CPL:plan-4': 4, 'CPL:plan-1': 1, 'CPL:plan-2': 1} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 3.38, per 1000 atoms: 0.19 Number of scatterers: 17357 At special positions: 0 Unit cell: (133.63, 133.63, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 12 15.00 Na 1 11.00 O 3088 8.00 N 2860 7.00 C 11300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 172 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 509.7 milliseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3896 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 59.2% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'D' and resid 104 through 111 Processing helix chain 'D' and resid 119 through 145 Processing helix chain 'D' and resid 197 through 224 Processing helix chain 'D' and resid 236 through 247 Processing helix chain 'D' and resid 248 through 256 removed outlier: 4.139A pdb=" N ILE D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 removed outlier: 6.114A pdb=" N LEU D 260 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP D 261 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.648A pdb=" N LEU D 279 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 280 " --> pdb=" O PRO D 277 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN D 282 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 283 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE D 285 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 4.067A pdb=" N VAL D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 335 removed outlier: 3.632A pdb=" N GLY D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 375 Processing helix chain 'D' and resid 385 through 418 removed outlier: 3.522A pdb=" N MET D 417 " --> pdb=" O MET D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 439 removed outlier: 3.844A pdb=" N THR D 422 " --> pdb=" O SER D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 458 removed outlier: 3.852A pdb=" N GLU D 445 " --> pdb=" O SER D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 Processing helix chain 'D' and resid 472 through 489 removed outlier: 4.026A pdb=" N VAL D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 507 removed outlier: 3.642A pdb=" N LEU D 502 " --> pdb=" O GLU D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 601 Processing helix chain 'D' and resid 602 through 620 removed outlier: 3.902A pdb=" N ASP D 620 " --> pdb=" O ILE D 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 119 through 145 Processing helix chain 'A' and resid 197 through 224 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 248 through 256 removed outlier: 4.140A pdb=" N ILE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 6.114A pdb=" N LEU A 260 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP A 261 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 removed outlier: 3.648A pdb=" N LEU A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A 280 " --> pdb=" O PRO A 277 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 4.067A pdb=" N VAL A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 335 removed outlier: 3.633A pdb=" N GLY A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 385 through 418 removed outlier: 3.522A pdb=" N MET A 417 " --> pdb=" O MET A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.844A pdb=" N THR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 458 removed outlier: 3.852A pdb=" N GLU A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 Processing helix chain 'A' and resid 472 through 489 removed outlier: 4.026A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 507 removed outlier: 3.642A pdb=" N LEU A 502 " --> pdb=" O GLU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 602 through 620 removed outlier: 3.903A pdb=" N ASP A 620 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 111 Processing helix chain 'B' and resid 119 through 145 Processing helix chain 'B' and resid 197 through 224 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 248 through 256 removed outlier: 4.139A pdb=" N ILE B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 6.113A pdb=" N LEU B 260 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP B 261 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 removed outlier: 3.648A pdb=" N LEU B 279 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 280 " --> pdb=" O PRO B 277 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 4.067A pdb=" N VAL B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 335 removed outlier: 3.632A pdb=" N GLY B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 Processing helix chain 'B' and resid 385 through 418 removed outlier: 3.522A pdb=" N MET B 417 " --> pdb=" O MET B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 439 removed outlier: 3.844A pdb=" N THR B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 458 removed outlier: 3.852A pdb=" N GLU B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 Processing helix chain 'B' and resid 472 through 489 removed outlier: 4.026A pdb=" N VAL B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 507 removed outlier: 3.642A pdb=" N LEU B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 602 through 620 removed outlier: 3.901A pdb=" N ASP B 620 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 111 Processing helix chain 'C' and resid 119 through 145 Processing helix chain 'C' and resid 197 through 224 Processing helix chain 'C' and resid 236 through 247 Processing helix chain 'C' and resid 248 through 256 removed outlier: 4.140A pdb=" N ILE C 252 " --> pdb=" O LYS C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 6.114A pdb=" N LEU C 260 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP C 261 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 285 removed outlier: 3.648A pdb=" N LEU C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 280 " --> pdb=" O PRO C 277 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE C 285 " --> pdb=" O ASN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 removed outlier: 4.068A pdb=" N VAL C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 335 removed outlier: 3.632A pdb=" N GLY C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 375 Processing helix chain 'C' and resid 385 through 418 removed outlier: 3.522A pdb=" N MET C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 439 removed outlier: 3.844A pdb=" N THR C 422 " --> pdb=" O SER C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 458 removed outlier: 3.852A pdb=" N GLU C 445 " --> pdb=" O SER C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 Processing helix chain 'C' and resid 472 through 489 removed outlier: 4.026A pdb=" N VAL C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 507 removed outlier: 3.642A pdb=" N LEU C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 601 Processing helix chain 'C' and resid 602 through 620 removed outlier: 3.903A pdb=" N ASP C 620 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 167 through 171 Processing sheet with id=AA2, first strand: chain 'D' and resid 510 through 514 removed outlier: 3.525A pdb=" N THR D 585 " --> pdb=" O PHE D 514 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 519 through 521 removed outlier: 6.874A pdb=" N VAL D 579 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 540 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL D 550 " --> pdb=" O VAL D 540 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 510 through 514 removed outlier: 3.525A pdb=" N THR A 585 " --> pdb=" O PHE A 514 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.874A pdb=" N VAL A 579 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 540 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL A 550 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 167 through 171 Processing sheet with id=AA8, first strand: chain 'B' and resid 510 through 514 removed outlier: 3.525A pdb=" N THR B 585 " --> pdb=" O PHE B 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 519 through 521 removed outlier: 6.873A pdb=" N VAL B 579 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 540 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B 550 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 167 through 171 Processing sheet with id=AB2, first strand: chain 'C' and resid 510 through 514 removed outlier: 3.524A pdb=" N THR C 585 " --> pdb=" O PHE C 514 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 519 through 521 removed outlier: 6.874A pdb=" N VAL C 579 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 540 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL C 550 " --> pdb=" O VAL C 540 " (cutoff:3.500A) 961 hydrogen bonds defined for protein. 2811 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: 2.18 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2672 1.30 - 1.43: 4990 1.43 - 1.56: 9906 1.56 - 1.68: 32 1.68 - 1.81: 156 Bond restraints: 17756 Sorted by residual: bond pdb=" C11 CPL B1804 " pdb=" O3 CPL B1804 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C11 CPL D 803 " pdb=" O3 CPL D 803 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C11 CPL C1804 " pdb=" O3 CPL C1804 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C11 CPL A1804 " pdb=" O3 CPL A1804 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C11 CPL C1801 " pdb=" O3 CPL C1801 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 17751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 23621 3.59 - 7.19: 359 7.19 - 10.78: 40 10.78 - 14.38: 4 14.38 - 17.97: 12 Bond angle restraints: 24036 Sorted by residual: angle pdb=" O3P CPL B1801 " pdb=" P CPL B1801 " pdb=" O4P CPL B1801 " ideal model delta sigma weight residual 93.29 111.26 -17.97 3.00e+00 1.11e-01 3.59e+01 angle pdb=" O3P CPL C1801 " pdb=" P CPL C1801 " pdb=" O4P CPL C1801 " ideal model delta sigma weight residual 93.29 111.24 -17.95 3.00e+00 1.11e-01 3.58e+01 angle pdb=" O3P CPL A1801 " pdb=" P CPL A1801 " pdb=" O4P CPL A1801 " ideal model delta sigma weight residual 93.29 111.23 -17.94 3.00e+00 1.11e-01 3.57e+01 angle pdb=" O3P CPL D 804 " pdb=" P CPL D 804 " pdb=" O4P CPL D 804 " ideal model delta sigma weight residual 93.29 111.21 -17.92 3.00e+00 1.11e-01 3.57e+01 angle pdb=" O3P CPL C1804 " pdb=" P CPL C1804 " pdb=" O4P CPL C1804 " ideal model delta sigma weight residual 93.29 110.02 -16.73 3.00e+00 1.11e-01 3.11e+01 ... (remaining 24031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 10192 35.11 - 70.23: 240 70.23 - 105.34: 16 105.34 - 140.46: 0 140.46 - 175.57: 4 Dihedral angle restraints: 10452 sinusoidal: 4384 harmonic: 6068 Sorted by residual: dihedral pdb=" CA ASP A 191 " pdb=" C ASP A 191 " pdb=" N LEU A 192 " pdb=" CA LEU A 192 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ASP D 191 " pdb=" C ASP D 191 " pdb=" N LEU D 192 " pdb=" CA LEU D 192 " ideal model delta harmonic sigma weight residual -180.00 -154.32 -25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ASP C 191 " pdb=" C ASP C 191 " pdb=" N LEU C 192 " pdb=" CA LEU C 192 " ideal model delta harmonic sigma weight residual -180.00 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 10449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1685 0.049 - 0.098: 715 0.098 - 0.147: 154 0.147 - 0.196: 33 0.196 - 0.245: 37 Chirality restraints: 2624 Sorted by residual: chirality pdb=" CB VAL A 170 " pdb=" CA VAL A 170 " pdb=" CG1 VAL A 170 " pdb=" CG2 VAL A 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL C 170 " pdb=" CA VAL C 170 " pdb=" CG1 VAL C 170 " pdb=" CG2 VAL C 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB VAL B 170 " pdb=" CA VAL B 170 " pdb=" CG1 VAL B 170 " pdb=" CG2 VAL B 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2621 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 380 " -0.046 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO C 381 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 381 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 381 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 380 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO A 381 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 380 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO B 381 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 381 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 381 " 0.038 5.00e-02 4.00e+02 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3229 2.77 - 3.30: 14769 3.30 - 3.83: 29423 3.83 - 4.37: 33272 4.37 - 4.90: 57909 Nonbonded interactions: 138602 Sorted by model distance: nonbonded pdb=" O ASP A 191 " pdb=" OD1 ASP A 191 " model vdw 2.235 3.040 nonbonded pdb=" O ASP C 191 " pdb=" OD1 ASP C 191 " model vdw 2.235 3.040 nonbonded pdb=" O ASP D 191 " pdb=" OD1 ASP D 191 " model vdw 2.235 3.040 nonbonded pdb=" O ASP B 191 " pdb=" OD1 ASP B 191 " model vdw 2.235 3.040 nonbonded pdb=" O SER B 562 " pdb=" OG SER B 562 " model vdw 2.339 3.040 ... (remaining 138597 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 104 through 1801 or (resid 1803 and (name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17)) or (resid 1804 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name O11 or name O1P or name O2 or name O \ 2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 104 through 1801 or (resid 1803 and (name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17)) or (resid 1804 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name O11 or name O1P or name O2 or name O \ 2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 104 through 1801 or (resid 1803 and (name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17)) or (resid 1804 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name O11 or name O1P or name O2 or name O \ 2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 104 through 620 or (resid 801 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C4 or name C5 or name O11 or name O1P or name O2 \ or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) or (resi \ d 803 and (name C12 or name C13 or name C14 or name C15 or name C16 or name C17) \ ) or (resid 804 and (name C1 or name C11 or name C12 or name C13 or name C14 or \ name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name O11 o \ r name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P \ or name P )))) } 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: 1.430 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.530 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.008 0.079 17760 Z= 0.374 Angle : 1.179 17.974 24044 Z= 0.600 Chirality : 0.061 0.245 2624 Planarity : 0.008 0.068 2948 Dihedral : 16.489 175.569 6544 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.86 % Allowed : 9.87 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.13), residues: 2040 helix: -3.33 (0.09), residues: 1140 sheet: -0.52 (0.45), residues: 120 loop : -2.64 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 447 TYR 0.026 0.003 TYR D 363 PHE 0.028 0.003 PHE B 145 TRP 0.026 0.003 TRP A 266 HIS 0.004 0.001 HIS C 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.37 (17756) covalent geometry : angle 1.17877 / 0.60 (24036) SS BOND : bond 0.00374 / 0.19 ( 4) SS BOND : angle 0.51241 / 0.31 ( 8) hydrogen bonds : bond 0.13344 / 8.43 ( 961) hydrogen bonds : angle 7.06766 / 4.80 ( 2811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 322 time to evaluate : 0.449 Fit side-chains REVERT: D 159 PHE cc_start: 0.8226 (t80) cc_final: 0.7886 (t80) REVERT: D 272 ASN cc_start: 0.8215 (m-40) cc_final: 0.7987 (t0) REVERT: D 424 PHE cc_start: 0.7779 (t80) cc_final: 0.7478 (t80) REVERT: D 525 ASP cc_start: 0.7881 (t0) cc_final: 0.7484 (t0) REVERT: D 535 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7474 (ptp-110) REVERT: D 558 PHE cc_start: 0.6782 (t80) cc_final: 0.6541 (t80) REVERT: A 159 PHE cc_start: 0.8196 (t80) cc_final: 0.7864 (t80) REVERT: A 272 ASN cc_start: 0.8224 (m-40) cc_final: 0.8008 (t0) REVERT: A 458 ASN cc_start: 0.8112 (t0) cc_final: 0.7899 (t0) REVERT: A 525 ASP cc_start: 0.7807 (t0) cc_final: 0.7339 (t0) REVERT: A 535 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7485 (ptp-110) REVERT: A 558 PHE cc_start: 0.6771 (t80) cc_final: 0.6552 (t80) REVERT: B 159 PHE cc_start: 0.8240 (t80) cc_final: 0.7889 (t80) REVERT: B 525 ASP cc_start: 0.7853 (t0) cc_final: 0.7475 (t0) REVERT: B 535 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7481 (ptp-110) REVERT: B 558 PHE cc_start: 0.6843 (t80) cc_final: 0.6567 (t80) REVERT: C 159 PHE cc_start: 0.8188 (t80) cc_final: 0.7870 (t80) REVERT: C 272 ASN cc_start: 0.8251 (m-40) cc_final: 0.8040 (t0) REVERT: C 413 MET cc_start: 0.7802 (tmm) cc_final: 0.7575 (ttp) REVERT: C 421 TRP cc_start: 0.6328 (t-100) cc_final: 0.5977 (t-100) REVERT: C 525 ASP cc_start: 0.7829 (t0) cc_final: 0.7524 (t0) REVERT: C 535 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7464 (ptp-110) outliers start: 16 outliers final: 0 residues processed: 338 average time/residue: 0.1389 time to fit residues: 67.8353 Evaluate side-chains 236 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 114 GLN D 188 GLN D 199 HIS D 416 ASN D 458 ASN D 484 HIS D 510 GLN D 539 GLN A 114 GLN A 188 GLN A 199 HIS A 416 ASN A 484 HIS A 539 GLN B 114 GLN B 188 GLN B 199 HIS B 349 GLN B 416 ASN B 458 ASN B 484 HIS B 510 GLN B 539 GLN C 114 GLN C 188 GLN C 199 HIS C 416 ASN C 458 ASN C 484 HIS C 510 GLN C 539 GLN C 578 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.170001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119323 restraints weight = 23278.521| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.10 r_work: 0.3359 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17760 Z= 0.136 Angle : 0.551 7.249 24044 Z= 0.291 Chirality : 0.040 0.147 2624 Planarity : 0.004 0.040 2948 Dihedral : 10.373 157.986 2460 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.18 % Allowed : 15.18 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.16), residues: 2040 helix: -0.66 (0.14), residues: 1152 sheet: -0.91 (0.44), residues: 108 loop : -2.17 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 280 TYR 0.013 0.001 TYR B 108 PHE 0.013 0.001 PHE B 138 TRP 0.013 0.001 TRP A 421 HIS 0.001 0.000 HIS C 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (17756) covalent geometry : angle 0.55091 / 0.29 (24036) SS BOND : bond 0.00189 / 0.09 ( 4) SS BOND : angle 0.74730 / 0.48 ( 8) hydrogen bonds : bond 0.04406 / 2.79 ( 961) hydrogen bonds : angle 4.77336 / 3.24 ( 2811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 250 time to evaluate : 0.554 Fit side-chains REVERT: D 115 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7792 (p0) REVERT: D 146 ASN cc_start: 0.8533 (t0) cc_final: 0.7981 (t0) REVERT: D 182 GLU cc_start: 0.8877 (pm20) cc_final: 0.8294 (pm20) REVERT: D 272 ASN cc_start: 0.8642 (m-40) cc_final: 0.8144 (t0) REVERT: D 525 ASP cc_start: 0.7872 (t70) cc_final: 0.7308 (t0) REVERT: D 535 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7615 (ptp-110) REVERT: A 115 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7819 (p0) REVERT: A 146 ASN cc_start: 0.8528 (t0) cc_final: 0.7979 (t0) REVERT: A 182 GLU cc_start: 0.8872 (pm20) cc_final: 0.8293 (pm20) REVERT: A 202 MET cc_start: 0.8310 (mmt) cc_final: 0.7974 (mmt) REVERT: A 272 ASN cc_start: 0.8649 (m-40) cc_final: 0.8151 (t0) REVERT: A 525 ASP cc_start: 0.7857 (t70) cc_final: 0.7266 (t0) REVERT: A 535 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7642 (ptp-110) REVERT: A 599 LEU cc_start: 0.7995 (tp) cc_final: 0.7207 (tp) REVERT: B 115 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7800 (p0) REVERT: B 146 ASN cc_start: 0.8575 (t0) cc_final: 0.8045 (t0) REVERT: B 159 PHE cc_start: 0.8095 (t80) cc_final: 0.7842 (t80) REVERT: B 182 GLU cc_start: 0.8837 (pm20) cc_final: 0.8579 (pm20) REVERT: B 272 ASN cc_start: 0.8811 (t0) cc_final: 0.8573 (t0) REVERT: B 507 LEU cc_start: 0.8326 (mm) cc_final: 0.8090 (mm) REVERT: B 525 ASP cc_start: 0.7942 (t70) cc_final: 0.7438 (t0) REVERT: B 535 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7630 (ptp-110) REVERT: C 115 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7774 (p0) REVERT: C 146 ASN cc_start: 0.8546 (t0) cc_final: 0.7991 (t0) REVERT: C 182 GLU cc_start: 0.8863 (pm20) cc_final: 0.8279 (pm20) REVERT: C 272 ASN cc_start: 0.8647 (m-40) cc_final: 0.8198 (t0) REVERT: C 421 TRP cc_start: 0.6341 (t-100) cc_final: 0.6128 (t-100) REVERT: C 507 LEU cc_start: 0.8330 (mm) cc_final: 0.8106 (mm) REVERT: C 525 ASP cc_start: 0.7972 (t70) cc_final: 0.7503 (t0) outliers start: 22 outliers final: 14 residues processed: 267 average time/residue: 0.1369 time to fit residues: 53.6602 Evaluate side-chains 243 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 578 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 2 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 0.0070 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 458 ASN D 510 GLN B 458 ASN C 458 ASN C 510 GLN C 578 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.171627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120438 restraints weight = 23478.310| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.14 r_work: 0.3377 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17760 Z= 0.113 Angle : 0.498 7.118 24044 Z= 0.262 Chirality : 0.039 0.136 2624 Planarity : 0.004 0.040 2948 Dihedral : 9.535 138.885 2460 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.45 % Allowed : 16.26 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.18), residues: 2040 helix: 0.38 (0.15), residues: 1184 sheet: -1.11 (0.41), residues: 116 loop : -1.84 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 535 TYR 0.010 0.001 TYR B 363 PHE 0.020 0.001 PHE D 159 TRP 0.014 0.001 TRP A 421 HIS 0.001 0.001 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (17756) covalent geometry : angle 0.49766 / 0.26 (24036) SS BOND : bond 0.00182 / 0.09 ( 4) SS BOND : angle 0.75364 / 0.48 ( 8) hydrogen bonds : bond 0.03966 / 2.51 ( 961) hydrogen bonds : angle 4.29122 / 2.91 ( 2811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.635 Fit side-chains REVERT: D 115 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7753 (p0) REVERT: D 117 SER cc_start: 0.8497 (m) cc_final: 0.8085 (p) REVERT: D 146 ASN cc_start: 0.8432 (t0) cc_final: 0.7901 (t0) REVERT: D 182 GLU cc_start: 0.8826 (pm20) cc_final: 0.8252 (pm20) REVERT: D 272 ASN cc_start: 0.8629 (m-40) cc_final: 0.8144 (t0) REVERT: D 525 ASP cc_start: 0.7923 (t70) cc_final: 0.7347 (t0) REVERT: D 535 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7672 (ptp-110) REVERT: D 558 PHE cc_start: 0.6713 (t80) cc_final: 0.6342 (t80) REVERT: A 115 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7725 (p0) REVERT: A 117 SER cc_start: 0.8472 (m) cc_final: 0.8085 (p) REVERT: A 146 ASN cc_start: 0.8428 (t0) cc_final: 0.7900 (t0) REVERT: A 182 GLU cc_start: 0.8837 (pm20) cc_final: 0.8262 (pm20) REVERT: A 272 ASN cc_start: 0.8640 (m-40) cc_final: 0.8148 (t0) REVERT: A 507 LEU cc_start: 0.8340 (mm) cc_final: 0.8095 (mm) REVERT: A 525 ASP cc_start: 0.7893 (t70) cc_final: 0.7304 (t0) REVERT: A 535 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7679 (ptp-110) REVERT: A 558 PHE cc_start: 0.6575 (t80) cc_final: 0.6239 (t80) REVERT: B 115 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7987 (p0) REVERT: B 117 SER cc_start: 0.8484 (m) cc_final: 0.8100 (p) REVERT: B 146 ASN cc_start: 0.8450 (t0) cc_final: 0.7908 (t0) REVERT: B 159 PHE cc_start: 0.8045 (t80) cc_final: 0.7795 (t80) REVERT: B 182 GLU cc_start: 0.8817 (pm20) cc_final: 0.8548 (pm20) REVERT: B 272 ASN cc_start: 0.8783 (t0) cc_final: 0.8496 (t0) REVERT: B 507 LEU cc_start: 0.8318 (mm) cc_final: 0.8088 (mm) REVERT: B 525 ASP cc_start: 0.7950 (t70) cc_final: 0.7393 (t0) REVERT: C 115 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7737 (p0) REVERT: C 117 SER cc_start: 0.8520 (m) cc_final: 0.8112 (p) REVERT: C 146 ASN cc_start: 0.8422 (t0) cc_final: 0.7886 (t0) REVERT: C 182 GLU cc_start: 0.8834 (pm20) cc_final: 0.8258 (pm20) REVERT: C 272 ASN cc_start: 0.8683 (m-40) cc_final: 0.8175 (t0) REVERT: C 458 ASN cc_start: 0.7906 (t0) cc_final: 0.7652 (t0) REVERT: C 507 LEU cc_start: 0.8338 (mm) cc_final: 0.8114 (mm) REVERT: C 525 ASP cc_start: 0.7971 (t70) cc_final: 0.7451 (t0) outliers start: 27 outliers final: 18 residues processed: 267 average time/residue: 0.1219 time to fit residues: 49.6497 Evaluate side-chains 249 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 152 optimal weight: 30.0000 chunk 195 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 349 GLN D 458 ASN A 458 ASN B 458 ASN B 510 GLN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.164087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111688 restraints weight = 22919.133| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.19 r_work: 0.3211 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 17760 Z= 0.238 Angle : 0.597 8.756 24044 Z= 0.309 Chirality : 0.043 0.164 2624 Planarity : 0.004 0.037 2948 Dihedral : 9.400 121.576 2460 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.47 % Allowed : 17.76 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2040 helix: 0.65 (0.15), residues: 1160 sheet: -0.63 (0.40), residues: 140 loop : -1.86 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 606 TYR 0.021 0.001 TYR A 363 PHE 0.020 0.002 PHE B 558 TRP 0.010 0.002 TRP D 421 HIS 0.005 0.002 HIS B 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 (17756) covalent geometry : angle 0.59723 / 0.31 (24036) SS BOND : bond 0.00216 / 0.11 ( 4) SS BOND : angle 0.89708 / 0.54 ( 8) hydrogen bonds : bond 0.04728 / 2.98 ( 961) hydrogen bonds : angle 4.47006 / 3.04 ( 2811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8079 (p0) REVERT: D 146 ASN cc_start: 0.8567 (t0) cc_final: 0.8003 (t0) REVERT: D 272 ASN cc_start: 0.8648 (m-40) cc_final: 0.8075 (t0) REVERT: D 525 ASP cc_start: 0.7952 (t70) cc_final: 0.7306 (t0) REVERT: A 115 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8066 (p0) REVERT: A 146 ASN cc_start: 0.8568 (t0) cc_final: 0.8010 (t0) REVERT: A 272 ASN cc_start: 0.8659 (m-40) cc_final: 0.8074 (t0) REVERT: A 507 LEU cc_start: 0.8293 (mm) cc_final: 0.8041 (mm) REVERT: A 525 ASP cc_start: 0.7941 (t70) cc_final: 0.7308 (t0) REVERT: A 558 PHE cc_start: 0.6554 (t80) cc_final: 0.6347 (t80) REVERT: B 115 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8106 (p0) REVERT: B 146 ASN cc_start: 0.8593 (t0) cc_final: 0.8006 (t0) REVERT: B 159 PHE cc_start: 0.7981 (t80) cc_final: 0.7772 (t80) REVERT: B 182 GLU cc_start: 0.8773 (pm20) cc_final: 0.8465 (pm20) REVERT: B 272 ASN cc_start: 0.8913 (t0) cc_final: 0.8605 (t0) REVERT: B 507 LEU cc_start: 0.8305 (mm) cc_final: 0.8065 (mm) REVERT: B 525 ASP cc_start: 0.7956 (t70) cc_final: 0.7340 (t0) REVERT: B 596 TRP cc_start: 0.7625 (m100) cc_final: 0.7225 (m100) REVERT: B 599 LEU cc_start: 0.8140 (tp) cc_final: 0.7669 (tp) REVERT: C 115 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8085 (p0) REVERT: C 146 ASN cc_start: 0.8565 (t0) cc_final: 0.8000 (t0) REVERT: C 272 ASN cc_start: 0.8659 (m-40) cc_final: 0.8095 (t0) REVERT: C 421 TRP cc_start: 0.6549 (t-100) cc_final: 0.6307 (t-100) REVERT: C 507 LEU cc_start: 0.8274 (mm) cc_final: 0.8039 (mm) REVERT: C 525 ASP cc_start: 0.7975 (t70) cc_final: 0.7371 (t0) REVERT: C 606 ARG cc_start: 0.7938 (ttm110) cc_final: 0.7316 (ttm110) outliers start: 46 outliers final: 27 residues processed: 278 average time/residue: 0.1188 time to fit residues: 50.4806 Evaluate side-chains 271 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 63 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 199 optimal weight: 0.4980 chunk 167 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 433 GLN D 458 ASN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN B 433 GLN B 458 ASN C 458 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.171120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.120034 restraints weight = 23084.388| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.11 r_work: 0.3355 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17760 Z= 0.118 Angle : 0.486 7.916 24044 Z= 0.255 Chirality : 0.039 0.136 2624 Planarity : 0.003 0.039 2948 Dihedral : 8.609 108.834 2460 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.25 % Allowed : 17.86 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 2040 helix: 0.94 (0.15), residues: 1180 sheet: -0.54 (0.40), residues: 140 loop : -1.51 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 606 TYR 0.009 0.001 TYR A 365 PHE 0.020 0.001 PHE C 159 TRP 0.016 0.001 TRP D 421 HIS 0.005 0.001 HIS D 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (17756) covalent geometry : angle 0.48541 / 0.25 (24036) SS BOND : bond 0.00162 / 0.08 ( 4) SS BOND : angle 0.76133 / 0.49 ( 8) hydrogen bonds : bond 0.03931 / 2.48 ( 961) hydrogen bonds : angle 4.12441 / 2.81 ( 2811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7984 (p0) REVERT: D 117 SER cc_start: 0.8465 (m) cc_final: 0.8085 (p) REVERT: D 146 ASN cc_start: 0.8343 (t0) cc_final: 0.7811 (t0) REVERT: D 182 GLU cc_start: 0.8829 (pm20) cc_final: 0.8235 (pm20) REVERT: D 272 ASN cc_start: 0.8621 (m-40) cc_final: 0.8155 (t0) REVERT: D 525 ASP cc_start: 0.7896 (t70) cc_final: 0.7310 (t0) REVERT: D 608 LEU cc_start: 0.7823 (mt) cc_final: 0.7353 (pp) REVERT: A 115 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7929 (p0) REVERT: A 117 SER cc_start: 0.8445 (m) cc_final: 0.8065 (p) REVERT: A 146 ASN cc_start: 0.8332 (t0) cc_final: 0.7800 (t0) REVERT: A 182 GLU cc_start: 0.8827 (pm20) cc_final: 0.8235 (pm20) REVERT: A 272 ASN cc_start: 0.8618 (m-40) cc_final: 0.8126 (t0) REVERT: A 458 ASN cc_start: 0.7959 (t0) cc_final: 0.7742 (t0) REVERT: A 507 LEU cc_start: 0.8306 (mm) cc_final: 0.8097 (mm) REVERT: A 508 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8373 (ptpt) REVERT: A 525 ASP cc_start: 0.7866 (t70) cc_final: 0.7267 (t0) REVERT: B 115 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7999 (p0) REVERT: B 117 SER cc_start: 0.8464 (m) cc_final: 0.8069 (p) REVERT: B 146 ASN cc_start: 0.8395 (t0) cc_final: 0.7798 (t0) REVERT: B 182 GLU cc_start: 0.8788 (pm20) cc_final: 0.8426 (pm20) REVERT: B 272 ASN cc_start: 0.8854 (t0) cc_final: 0.8572 (t0) REVERT: B 458 ASN cc_start: 0.7976 (t0) cc_final: 0.7768 (t0) REVERT: B 507 LEU cc_start: 0.8290 (mm) cc_final: 0.8074 (mm) REVERT: B 525 ASP cc_start: 0.7952 (t70) cc_final: 0.7374 (t0) REVERT: B 558 PHE cc_start: 0.6514 (t80) cc_final: 0.6158 (t80) REVERT: B 608 LEU cc_start: 0.7720 (mt) cc_final: 0.7308 (pp) REVERT: C 115 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8010 (p0) REVERT: C 117 SER cc_start: 0.8460 (m) cc_final: 0.8079 (p) REVERT: C 146 ASN cc_start: 0.8351 (t0) cc_final: 0.7820 (t0) REVERT: C 182 GLU cc_start: 0.8828 (pm20) cc_final: 0.8240 (pm20) REVERT: C 272 ASN cc_start: 0.8633 (m-40) cc_final: 0.8180 (t0) REVERT: C 458 ASN cc_start: 0.7852 (t0) cc_final: 0.7639 (t0) REVERT: C 507 LEU cc_start: 0.8265 (mm) cc_final: 0.8049 (mm) REVERT: C 508 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8283 (ptpt) REVERT: C 525 ASP cc_start: 0.7938 (t70) cc_final: 0.7358 (t0) REVERT: C 606 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7377 (ttm110) REVERT: C 608 LEU cc_start: 0.7819 (mt) cc_final: 0.7390 (pp) outliers start: 42 outliers final: 31 residues processed: 279 average time/residue: 0.1213 time to fit residues: 51.7169 Evaluate side-chains 263 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 135 optimal weight: 0.0020 chunk 77 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.166404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113931 restraints weight = 22681.880| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.20 r_work: 0.3233 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17760 Z= 0.178 Angle : 0.533 7.871 24044 Z= 0.278 Chirality : 0.040 0.153 2624 Planarity : 0.003 0.036 2948 Dihedral : 8.458 101.116 2460 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.58 % Allowed : 18.08 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 2040 helix: 0.93 (0.15), residues: 1184 sheet: -1.04 (0.40), residues: 116 loop : -1.34 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 606 TYR 0.015 0.001 TYR A 363 PHE 0.026 0.002 PHE A 558 TRP 0.022 0.001 TRP C 421 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (17756) covalent geometry : angle 0.53281 / 0.28 (24036) SS BOND : bond 0.00172 / 0.09 ( 4) SS BOND : angle 0.83792 / 0.51 ( 8) hydrogen bonds : bond 0.04313 / 2.72 ( 961) hydrogen bonds : angle 4.19336 / 2.86 ( 2811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7988 (p0) REVERT: D 146 ASN cc_start: 0.8440 (t0) cc_final: 0.7895 (t0) REVERT: D 182 GLU cc_start: 0.8839 (pm20) cc_final: 0.8200 (pm20) REVERT: D 272 ASN cc_start: 0.8619 (m-40) cc_final: 0.8056 (t0) REVERT: D 525 ASP cc_start: 0.7961 (t70) cc_final: 0.7353 (t0) REVERT: D 558 PHE cc_start: 0.6368 (t80) cc_final: 0.6030 (t80) REVERT: D 608 LEU cc_start: 0.7754 (mt) cc_final: 0.7360 (pp) REVERT: A 115 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7986 (p0) REVERT: A 117 SER cc_start: 0.8521 (m) cc_final: 0.8095 (p) REVERT: A 146 ASN cc_start: 0.8439 (t0) cc_final: 0.7894 (t0) REVERT: A 182 GLU cc_start: 0.8839 (pm20) cc_final: 0.8200 (pm20) REVERT: A 272 ASN cc_start: 0.8624 (m-40) cc_final: 0.8049 (t0) REVERT: A 507 LEU cc_start: 0.8239 (mm) cc_final: 0.8005 (mm) REVERT: A 525 ASP cc_start: 0.7934 (t70) cc_final: 0.7312 (t0) REVERT: A 558 PHE cc_start: 0.6267 (t80) cc_final: 0.5950 (t80) REVERT: B 115 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7989 (p0) REVERT: B 117 SER cc_start: 0.8511 (m) cc_final: 0.8092 (p) REVERT: B 146 ASN cc_start: 0.8508 (t0) cc_final: 0.7893 (t0) REVERT: B 182 GLU cc_start: 0.8767 (pm20) cc_final: 0.8445 (pm20) REVERT: B 270 TYR cc_start: 0.7764 (m-80) cc_final: 0.7500 (t80) REVERT: B 272 ASN cc_start: 0.8903 (t0) cc_final: 0.8586 (t0) REVERT: B 458 ASN cc_start: 0.7988 (t0) cc_final: 0.7715 (t0) REVERT: B 507 LEU cc_start: 0.8253 (mm) cc_final: 0.8021 (mm) REVERT: B 525 ASP cc_start: 0.7967 (t70) cc_final: 0.7371 (t0) REVERT: B 608 LEU cc_start: 0.7703 (mt) cc_final: 0.7326 (pp) REVERT: C 115 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8048 (p0) REVERT: C 146 ASN cc_start: 0.8454 (t0) cc_final: 0.7900 (t0) REVERT: C 182 GLU cc_start: 0.8830 (pm20) cc_final: 0.8187 (pm20) REVERT: C 272 ASN cc_start: 0.8625 (m-40) cc_final: 0.8064 (t0) REVERT: C 458 ASN cc_start: 0.7870 (t0) cc_final: 0.7579 (t0) REVERT: C 507 LEU cc_start: 0.8242 (mm) cc_final: 0.8009 (mm) REVERT: C 508 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8310 (ptpt) REVERT: C 525 ASP cc_start: 0.7984 (t70) cc_final: 0.7372 (t0) REVERT: C 606 ARG cc_start: 0.7981 (ttm110) cc_final: 0.7342 (ttm110) REVERT: C 608 LEU cc_start: 0.7738 (mt) cc_final: 0.7337 (pp) outliers start: 48 outliers final: 42 residues processed: 274 average time/residue: 0.1150 time to fit residues: 47.7559 Evaluate side-chains 276 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 GLN A 458 ASN A 510 GLN B 305 ASN B 510 GLN C 433 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.170555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119108 restraints weight = 23109.842| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.10 r_work: 0.3350 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17760 Z= 0.123 Angle : 0.485 7.779 24044 Z= 0.255 Chirality : 0.039 0.140 2624 Planarity : 0.003 0.039 2948 Dihedral : 8.157 95.138 2460 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.36 % Allowed : 18.51 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 2040 helix: 1.16 (0.15), residues: 1184 sheet: -0.68 (0.42), residues: 116 loop : -1.17 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 606 TYR 0.010 0.001 TYR C 363 PHE 0.021 0.002 PHE C 159 TRP 0.020 0.001 TRP C 421 HIS 0.002 0.001 HIS B 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (17756) covalent geometry : angle 0.48504 / 0.25 (24036) SS BOND : bond 0.00159 / 0.08 ( 4) SS BOND : angle 0.74363 / 0.47 ( 8) hydrogen bonds : bond 0.03945 / 2.49 ( 961) hydrogen bonds : angle 3.97879 / 2.72 ( 2811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7986 (p0) REVERT: D 117 SER cc_start: 0.8427 (m) cc_final: 0.8044 (p) REVERT: D 146 ASN cc_start: 0.8332 (t0) cc_final: 0.7789 (t0) REVERT: D 182 GLU cc_start: 0.8830 (pm20) cc_final: 0.8220 (pm20) REVERT: D 245 TRP cc_start: 0.8276 (m100) cc_final: 0.7938 (m-10) REVERT: D 272 ASN cc_start: 0.8605 (m-40) cc_final: 0.8084 (t0) REVERT: D 525 ASP cc_start: 0.7930 (t70) cc_final: 0.7361 (t0) REVERT: D 558 PHE cc_start: 0.6381 (t80) cc_final: 0.6056 (t80) REVERT: D 608 LEU cc_start: 0.7832 (mt) cc_final: 0.7429 (pp) REVERT: A 115 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7925 (p0) REVERT: A 117 SER cc_start: 0.8425 (m) cc_final: 0.8038 (p) REVERT: A 146 ASN cc_start: 0.8330 (t0) cc_final: 0.7791 (t0) REVERT: A 245 TRP cc_start: 0.8274 (m100) cc_final: 0.7928 (m-10) REVERT: A 272 ASN cc_start: 0.8602 (m-40) cc_final: 0.8103 (t0) REVERT: A 413 MET cc_start: 0.7690 (ttp) cc_final: 0.7471 (ttp) REVERT: A 525 ASP cc_start: 0.7913 (t70) cc_final: 0.7327 (t0) REVERT: A 558 PHE cc_start: 0.6308 (t80) cc_final: 0.6001 (t80) REVERT: B 115 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7953 (p0) REVERT: B 117 SER cc_start: 0.8431 (m) cc_final: 0.8047 (p) REVERT: B 146 ASN cc_start: 0.8374 (t0) cc_final: 0.7780 (t0) REVERT: B 182 GLU cc_start: 0.8763 (pm20) cc_final: 0.8475 (pm20) REVERT: B 272 ASN cc_start: 0.8851 (t0) cc_final: 0.8475 (t0) REVERT: B 413 MET cc_start: 0.7670 (ttp) cc_final: 0.7457 (ttp) REVERT: B 458 ASN cc_start: 0.8043 (t0) cc_final: 0.7763 (t0) REVERT: B 507 LEU cc_start: 0.8253 (mm) cc_final: 0.8052 (mm) REVERT: B 508 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8344 (ptpt) REVERT: B 525 ASP cc_start: 0.7971 (t70) cc_final: 0.7412 (t0) REVERT: B 558 PHE cc_start: 0.6403 (t80) cc_final: 0.6067 (t80) REVERT: B 588 PHE cc_start: 0.8445 (m-10) cc_final: 0.8235 (m-10) REVERT: B 608 LEU cc_start: 0.7783 (mt) cc_final: 0.7387 (pp) REVERT: C 115 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7989 (p0) REVERT: C 117 SER cc_start: 0.8438 (m) cc_final: 0.8059 (p) REVERT: C 146 ASN cc_start: 0.8351 (t0) cc_final: 0.7815 (t0) REVERT: C 182 GLU cc_start: 0.8814 (pm20) cc_final: 0.8206 (pm20) REVERT: C 245 TRP cc_start: 0.8268 (m100) cc_final: 0.7927 (m-10) REVERT: C 272 ASN cc_start: 0.8601 (m-40) cc_final: 0.8114 (t0) REVERT: C 413 MET cc_start: 0.7693 (ttp) cc_final: 0.7477 (ttp) REVERT: C 458 ASN cc_start: 0.7901 (t0) cc_final: 0.7627 (t0) REVERT: C 525 ASP cc_start: 0.7967 (t70) cc_final: 0.7417 (t0) REVERT: C 558 PHE cc_start: 0.6447 (t80) cc_final: 0.6098 (t80) REVERT: C 588 PHE cc_start: 0.8434 (m-10) cc_final: 0.8232 (m-10) REVERT: C 606 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7443 (ttm110) REVERT: C 608 LEU cc_start: 0.7818 (mt) cc_final: 0.7401 (pp) outliers start: 44 outliers final: 38 residues processed: 271 average time/residue: 0.1135 time to fit residues: 47.2972 Evaluate side-chains 266 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 133 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 510 GLN A 349 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.163246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110300 restraints weight = 23024.375| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.19 r_work: 0.3191 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 17760 Z= 0.290 Angle : 0.632 9.030 24044 Z= 0.325 Chirality : 0.044 0.168 2624 Planarity : 0.004 0.034 2948 Dihedral : 8.512 89.339 2460 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.06 % Allowed : 18.62 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.19), residues: 2040 helix: 0.78 (0.15), residues: 1188 sheet: -0.55 (0.43), residues: 92 loop : -1.31 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 280 TYR 0.018 0.001 TYR A 363 PHE 0.022 0.002 PHE B 159 TRP 0.021 0.002 TRP C 421 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.29 (17756) covalent geometry : angle 0.63181 / 0.33 (24036) SS BOND : bond 0.00166 / 0.08 ( 4) SS BOND : angle 0.91074 / 0.55 ( 8) hydrogen bonds : bond 0.04885 / 3.08 ( 961) hydrogen bonds : angle 4.38774 / 3.00 ( 2811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8066 (p0) REVERT: D 146 ASN cc_start: 0.8587 (t0) cc_final: 0.8004 (t0) REVERT: D 270 TYR cc_start: 0.7756 (m-80) cc_final: 0.7535 (t80) REVERT: D 272 ASN cc_start: 0.8624 (m-40) cc_final: 0.8050 (t0) REVERT: D 525 ASP cc_start: 0.7965 (t70) cc_final: 0.7341 (t0) REVERT: D 558 PHE cc_start: 0.6480 (t80) cc_final: 0.6143 (t80) REVERT: A 115 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8069 (p0) REVERT: A 146 ASN cc_start: 0.8588 (t0) cc_final: 0.8005 (t0) REVERT: A 272 ASN cc_start: 0.8637 (m-40) cc_final: 0.8034 (t0) REVERT: A 525 ASP cc_start: 0.7951 (t70) cc_final: 0.7317 (t0) REVERT: A 558 PHE cc_start: 0.6394 (t80) cc_final: 0.6064 (t80) REVERT: A 607 LYS cc_start: 0.8056 (tttm) cc_final: 0.7735 (mtpp) REVERT: B 115 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8074 (p0) REVERT: B 146 ASN cc_start: 0.8637 (t0) cc_final: 0.7991 (t0) REVERT: B 182 GLU cc_start: 0.8781 (pm20) cc_final: 0.8357 (pm20) REVERT: B 270 TYR cc_start: 0.7806 (m-80) cc_final: 0.7564 (t80) REVERT: B 272 ASN cc_start: 0.8916 (t0) cc_final: 0.8613 (t0) REVERT: B 507 LEU cc_start: 0.8283 (mm) cc_final: 0.8046 (mm) REVERT: B 525 ASP cc_start: 0.7975 (t70) cc_final: 0.7359 (t0) REVERT: C 115 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8053 (p0) REVERT: C 146 ASN cc_start: 0.8582 (t0) cc_final: 0.7993 (t0) REVERT: C 272 ASN cc_start: 0.8624 (m-40) cc_final: 0.8052 (t0) REVERT: C 525 ASP cc_start: 0.7994 (t70) cc_final: 0.7377 (t0) REVERT: C 588 PHE cc_start: 0.8442 (m-10) cc_final: 0.8233 (m-10) REVERT: C 606 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7233 (ttm110) outliers start: 57 outliers final: 45 residues processed: 270 average time/residue: 0.1169 time to fit residues: 48.5889 Evaluate side-chains 280 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 92 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 510 GLN A 458 ASN B 458 ASN C 458 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.171420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120107 restraints weight = 23008.319| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.11 r_work: 0.3357 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17760 Z= 0.112 Angle : 0.493 7.800 24044 Z= 0.257 Chirality : 0.039 0.139 2624 Planarity : 0.003 0.039 2948 Dihedral : 8.025 87.757 2460 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.20 % Allowed : 19.74 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 2040 helix: 1.14 (0.15), residues: 1208 sheet: -0.60 (0.42), residues: 116 loop : -1.06 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 606 TYR 0.011 0.001 TYR C 363 PHE 0.021 0.002 PHE C 159 TRP 0.025 0.001 TRP C 421 HIS 0.002 0.001 HIS B 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17756) covalent geometry : angle 0.49296 / 0.26 (24036) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 0.74496 / 0.48 ( 8) hydrogen bonds : bond 0.03926 / 2.48 ( 961) hydrogen bonds : angle 3.99053 / 2.73 ( 2811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8005 (p0) REVERT: D 117 SER cc_start: 0.8438 (m) cc_final: 0.8029 (p) REVERT: D 146 ASN cc_start: 0.8296 (t0) cc_final: 0.7762 (t0) REVERT: D 245 TRP cc_start: 0.8273 (m100) cc_final: 0.7923 (m-10) REVERT: D 272 ASN cc_start: 0.8595 (m-40) cc_final: 0.8117 (t0) REVERT: D 525 ASP cc_start: 0.7910 (t70) cc_final: 0.7299 (t70) REVERT: D 558 PHE cc_start: 0.6410 (t80) cc_final: 0.6089 (t80) REVERT: A 115 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8005 (p0) REVERT: A 117 SER cc_start: 0.8453 (m) cc_final: 0.8040 (p) REVERT: A 146 ASN cc_start: 0.8288 (t0) cc_final: 0.7752 (t0) REVERT: A 245 TRP cc_start: 0.8287 (m100) cc_final: 0.7930 (m-10) REVERT: A 272 ASN cc_start: 0.8600 (m-40) cc_final: 0.8117 (t0) REVERT: A 525 ASP cc_start: 0.7898 (t70) cc_final: 0.7276 (t70) REVERT: A 558 PHE cc_start: 0.6348 (t80) cc_final: 0.6034 (t80) REVERT: A 607 LYS cc_start: 0.8043 (tttm) cc_final: 0.7689 (mtpp) REVERT: B 115 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7992 (p0) REVERT: B 117 SER cc_start: 0.8418 (m) cc_final: 0.8034 (p) REVERT: B 146 ASN cc_start: 0.8353 (t0) cc_final: 0.7762 (t0) REVERT: B 182 GLU cc_start: 0.8774 (pm20) cc_final: 0.8335 (pm20) REVERT: B 245 TRP cc_start: 0.8274 (m100) cc_final: 0.7889 (m-10) REVERT: B 272 ASN cc_start: 0.8856 (t0) cc_final: 0.8491 (t0) REVERT: B 508 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8443 (ptpt) REVERT: B 525 ASP cc_start: 0.7935 (t70) cc_final: 0.7329 (t70) REVERT: C 115 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8000 (p0) REVERT: C 117 SER cc_start: 0.8443 (m) cc_final: 0.8065 (p) REVERT: C 146 ASN cc_start: 0.8300 (t0) cc_final: 0.7758 (t0) REVERT: C 245 TRP cc_start: 0.8282 (m100) cc_final: 0.7926 (m-10) REVERT: C 272 ASN cc_start: 0.8595 (m-40) cc_final: 0.8116 (t0) REVERT: C 525 ASP cc_start: 0.7935 (t70) cc_final: 0.7324 (t70) REVERT: C 606 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7365 (ttm110) outliers start: 41 outliers final: 36 residues processed: 266 average time/residue: 0.1091 time to fit residues: 45.1400 Evaluate side-chains 265 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 92 optimal weight: 0.4980 chunk 107 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.170275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118642 restraints weight = 22982.195| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.11 r_work: 0.3362 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17760 Z= 0.127 Angle : 0.506 7.698 24044 Z= 0.261 Chirality : 0.039 0.139 2624 Planarity : 0.003 0.037 2948 Dihedral : 7.891 82.363 2460 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.25 % Allowed : 19.80 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 2040 helix: 1.29 (0.15), residues: 1208 sheet: -0.48 (0.42), residues: 116 loop : -1.03 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 606 TYR 0.011 0.001 TYR A 363 PHE 0.022 0.001 PHE B 159 TRP 0.029 0.001 TRP D 421 HIS 0.002 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (17756) covalent geometry : angle 0.50634 / 0.26 (24036) SS BOND : bond 0.00134 / 0.07 ( 4) SS BOND : angle 0.72409 / 0.46 ( 8) hydrogen bonds : bond 0.04009 / 2.53 ( 961) hydrogen bonds : angle 3.96307 / 2.71 ( 2811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8001 (p0) REVERT: D 117 SER cc_start: 0.8434 (m) cc_final: 0.8031 (p) REVERT: D 146 ASN cc_start: 0.8291 (t0) cc_final: 0.7768 (t0) REVERT: D 245 TRP cc_start: 0.8310 (m100) cc_final: 0.7952 (m-10) REVERT: D 272 ASN cc_start: 0.8597 (m-40) cc_final: 0.8112 (t0) REVERT: D 525 ASP cc_start: 0.7933 (t70) cc_final: 0.7363 (t70) REVERT: D 558 PHE cc_start: 0.6371 (t80) cc_final: 0.6067 (t80) REVERT: D 607 LYS cc_start: 0.8030 (tttm) cc_final: 0.7678 (mtpp) REVERT: A 115 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7999 (p0) REVERT: A 117 SER cc_start: 0.8439 (m) cc_final: 0.8036 (p) REVERT: A 146 ASN cc_start: 0.8287 (t0) cc_final: 0.7768 (t0) REVERT: A 245 TRP cc_start: 0.8327 (m100) cc_final: 0.7963 (m-10) REVERT: A 272 ASN cc_start: 0.8600 (m-40) cc_final: 0.8133 (t0) REVERT: A 525 ASP cc_start: 0.7947 (t70) cc_final: 0.7366 (t70) REVERT: A 558 PHE cc_start: 0.6334 (t80) cc_final: 0.6041 (t80) REVERT: A 607 LYS cc_start: 0.8053 (tttm) cc_final: 0.7699 (mtpp) REVERT: B 115 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7987 (p0) REVERT: B 117 SER cc_start: 0.8415 (m) cc_final: 0.8035 (p) REVERT: B 146 ASN cc_start: 0.8309 (t0) cc_final: 0.7746 (t0) REVERT: B 182 GLU cc_start: 0.8777 (pm20) cc_final: 0.8315 (pm20) REVERT: B 245 TRP cc_start: 0.8307 (m100) cc_final: 0.7918 (m-10) REVERT: B 272 ASN cc_start: 0.8841 (t0) cc_final: 0.8476 (t0) REVERT: B 525 ASP cc_start: 0.7966 (t70) cc_final: 0.7415 (t70) REVERT: B 558 PHE cc_start: 0.6463 (t80) cc_final: 0.6181 (t80) REVERT: B 607 LYS cc_start: 0.8034 (tttm) cc_final: 0.7669 (mtpp) REVERT: C 115 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7974 (p0) REVERT: C 117 SER cc_start: 0.8416 (m) cc_final: 0.8044 (p) REVERT: C 146 ASN cc_start: 0.8329 (t0) cc_final: 0.7807 (t0) REVERT: C 245 TRP cc_start: 0.8303 (m100) cc_final: 0.7933 (m-10) REVERT: C 272 ASN cc_start: 0.8602 (m-40) cc_final: 0.8114 (t0) REVERT: C 525 ASP cc_start: 0.8014 (t70) cc_final: 0.7465 (t70) REVERT: C 606 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7453 (ttm110) outliers start: 42 outliers final: 38 residues processed: 268 average time/residue: 0.1148 time to fit residues: 47.6488 Evaluate side-chains 266 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 456 TRP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 549 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 456 TRP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.168873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116931 restraints weight = 23094.226| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.11 r_work: 0.3315 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17760 Z= 0.163 Angle : 0.536 8.005 24044 Z= 0.276 Chirality : 0.040 0.147 2624 Planarity : 0.003 0.037 2948 Dihedral : 7.917 79.134 2460 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.58 % Allowed : 19.85 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 2040 helix: 1.20 (0.15), residues: 1208 sheet: -0.50 (0.43), residues: 116 loop : -1.05 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 606 TYR 0.014 0.001 TYR B 363 PHE 0.022 0.002 PHE C 159 TRP 0.026 0.001 TRP C 421 HIS 0.002 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (17756) covalent geometry : angle 0.53628 / 0.28 (24036) SS BOND : bond 0.00161 / 0.08 ( 4) SS BOND : angle 0.80117 / 0.52 ( 8) hydrogen bonds : bond 0.04251 / 2.67 ( 961) hydrogen bonds : angle 4.05253 / 2.78 ( 2811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4165.45 seconds wall clock time: 71 minutes 54.83 seconds (4314.83 seconds total)