Starting phenix.real_space_refine on Thu Mar 5 00:25:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n16_24114/03_2026/7n16_24114.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n16_24114/03_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_24114/03_2026/7n16_24114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n16_24114/03_2026/7n16_24114.map" model { file = "/net/cci-nas-00/data/ceres_data/7n16_24114/03_2026/7n16_24114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n16_24114/03_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-5986/lib/python3.9/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: 115 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: 115 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: 115 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: 115 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: 3.88, per 1000 atoms: 0.22 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: 1.42 Conformation dependent library (CDL) restraints added in 740.2 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: 0.50 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: 2.51 Time building geometry restraints manager: 1.93 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: 10236 35.11 - 70.23: 272 70.23 - 105.34: 20 105.34 - 140.46: 16 140.46 - 175.57: 12 Dihedral angle restraints: 10556 sinusoidal: 4488 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 10553 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: 1.600 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.720 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 18.872 175.569 6648 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 covalent geometry : bond 0.00831 (17756) covalent geometry : angle 1.17877 (24036) SS BOND : bond 0.00374 ( 4) SS BOND : angle 0.51241 ( 8) hydrogen bonds : bond 0.13344 ( 961) hydrogen bonds : angle 7.06766 ( 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 : 0.546 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: 0.1599 time to fit residues: 77.2225 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 : 0.697 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4133 r_free = 0.4133 target = 0.170202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119445 restraints weight = 23313.616| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.12 r_work: 0.3359 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1807 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= 0.134 Angle : 0.559 7.151 24044 Z= 0.291 Chirality : 0.040 0.144 2624 Planarity : 0.005 0.040 2948 Dihedral : 15.813 176.093 2564 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.23 % Allowed : 15.02 % Favored : 83.74 % 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: -1.90 (0.16), residues: 2040 helix: -0.64 (0.14), residues: 1152 sheet: -0.90 (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 0.014 0.001 PHE B 138 TRP 0.013 0.001 TRP A 421 HIS 0.002 0.000 HIS C 321 Details of bonding type rmsd covalent geometry : bond 0.00291 (17756) covalent geometry : angle 0.55865 (24036) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.70216 ( 8) hydrogen bonds : bond 0.04402 ( 961) hydrogen bonds : angle 4.76058 ( 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 274 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.648 Fit side-chains REVERT: D 115 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7786 (p0) REVERT: D 146 ASN cc_start: 0.8524 (t0) cc_final: 0.7971 (t0) REVERT: D 182 GLU cc_start: 0.8876 (pm20) cc_final: 0.8294 (pm20) REVERT: D 272 ASN cc_start: 0.8639 (m-40) cc_final: 0.8142 (t0) REVERT: D 525 ASP cc_start: 0.7877 (t70) cc_final: 0.7315 (t0) REVERT: D 535 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7597 (ptp-110) REVERT: D 615 GLU cc_start: 0.8461 (tt0) cc_final: 0.8054 (mt-10) REVERT: A 115 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7795 (p0) REVERT: A 146 ASN cc_start: 0.8521 (t0) cc_final: 0.7973 (t0) REVERT: A 182 GLU cc_start: 0.8882 (pm20) cc_final: 0.8302 (pm20) REVERT: A 272 ASN cc_start: 0.8650 (m-40) cc_final: 0.8151 (t0) REVERT: A 525 ASP cc_start: 0.7862 (t70) cc_final: 0.7235 (t0) REVERT: A 535 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7633 (ptp-110) REVERT: A 599 LEU cc_start: 0.8040 (tp) cc_final: 0.7171 (tp) REVERT: B 115 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7799 (p0) REVERT: B 146 ASN cc_start: 0.8561 (t0) cc_final: 0.8024 (t0) REVERT: B 159 PHE cc_start: 0.8093 (t80) cc_final: 0.7840 (t80) REVERT: B 182 GLU cc_start: 0.8835 (pm20) cc_final: 0.8577 (pm20) REVERT: B 272 ASN cc_start: 0.8819 (t0) cc_final: 0.8582 (t0) REVERT: B 507 LEU cc_start: 0.8329 (mm) cc_final: 0.8094 (mm) REVERT: B 525 ASP cc_start: 0.7947 (t70) cc_final: 0.7444 (t0) REVERT: C 115 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7778 (p0) REVERT: C 146 ASN cc_start: 0.8537 (t0) cc_final: 0.7977 (t0) REVERT: C 182 GLU cc_start: 0.8865 (pm20) cc_final: 0.8281 (pm20) REVERT: C 272 ASN cc_start: 0.8649 (m-40) cc_final: 0.8199 (t0) REVERT: C 421 TRP cc_start: 0.6346 (t-100) cc_final: 0.6132 (t-100) REVERT: C 507 LEU cc_start: 0.8333 (mm) cc_final: 0.8111 (mm) REVERT: C 525 ASP cc_start: 0.7980 (t70) cc_final: 0.7511 (t0) outliers start: 23 outliers final: 15 residues processed: 269 average time/residue: 0.1479 time to fit residues: 58.1102 Evaluate side-chains 244 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 138 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 12 optimal weight: 0.0070 chunk 157 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4166 r_free = 0.4166 target = 0.173500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123183 restraints weight = 23498.894| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.15 r_work: 0.3391 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.002 0.026 17760 Z= 0.107 Angle : 0.496 6.935 24044 Z= 0.260 Chirality : 0.038 0.134 2624 Planarity : 0.004 0.041 2948 Dihedral : 13.900 165.427 2564 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.34 % Allowed : 16.36 % 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: -0.75 (0.18), residues: 2040 helix: 0.39 (0.15), residues: 1184 sheet: -1.00 (0.42), residues: 116 loop : -1.82 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 535 TYR 0.009 0.001 TYR C 365 PHE 0.020 0.001 PHE D 159 TRP 0.014 0.001 TRP A 421 HIS 0.002 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00223 (17756) covalent geometry : angle 0.49635 (24036) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.75602 ( 8) hydrogen bonds : bond 0.03867 ( 961) hydrogen bonds : angle 4.25872 ( 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 274 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 0.601 Fit side-chains REVERT: D 115 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7754 (p0) REVERT: D 117 SER cc_start: 0.8470 (m) cc_final: 0.8084 (p) REVERT: D 146 ASN cc_start: 0.8440 (t0) cc_final: 0.7913 (t0) REVERT: D 182 GLU cc_start: 0.8837 (pm20) cc_final: 0.8419 (pm20) REVERT: D 272 ASN cc_start: 0.8659 (m-40) cc_final: 0.8137 (t0) REVERT: D 489 ARG cc_start: 0.7612 (tpp-160) cc_final: 0.7329 (tpt170) REVERT: D 525 ASP cc_start: 0.7941 (t70) cc_final: 0.7371 (t0) REVERT: D 535 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7628 (ptp-110) REVERT: D 558 PHE cc_start: 0.6662 (t80) cc_final: 0.6304 (t80) REVERT: D 608 LEU cc_start: 0.7823 (mt) cc_final: 0.7372 (pp) REVERT: A 115 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7743 (p0) REVERT: A 117 SER cc_start: 0.8474 (m) cc_final: 0.8072 (p) REVERT: A 146 ASN cc_start: 0.8438 (t0) cc_final: 0.7911 (t0) REVERT: A 182 GLU cc_start: 0.8852 (pm20) cc_final: 0.8435 (pm20) REVERT: A 272 ASN cc_start: 0.8645 (m-40) cc_final: 0.8148 (t0) REVERT: A 507 LEU cc_start: 0.8341 (mm) cc_final: 0.8095 (mm) REVERT: A 525 ASP cc_start: 0.7911 (t70) cc_final: 0.7329 (t0) REVERT: A 535 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7693 (ptp-110) REVERT: A 558 PHE cc_start: 0.6541 (t80) cc_final: 0.6213 (t80) REVERT: B 115 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7962 (p0) REVERT: B 117 SER cc_start: 0.8435 (m) cc_final: 0.8042 (p) REVERT: B 146 ASN cc_start: 0.8433 (t0) cc_final: 0.7881 (t0) REVERT: B 159 PHE cc_start: 0.8039 (t80) cc_final: 0.7799 (t80) REVERT: B 182 GLU cc_start: 0.8822 (pm20) cc_final: 0.8560 (pm20) REVERT: B 272 ASN cc_start: 0.8775 (t0) cc_final: 0.8492 (t0) REVERT: B 507 LEU cc_start: 0.8290 (mm) cc_final: 0.8057 (mm) REVERT: B 525 ASP cc_start: 0.7949 (t70) cc_final: 0.7396 (t0) REVERT: C 115 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7726 (p0) REVERT: C 117 SER cc_start: 0.8470 (m) cc_final: 0.8079 (p) REVERT: C 146 ASN cc_start: 0.8435 (t0) cc_final: 0.7896 (t0) REVERT: C 182 GLU cc_start: 0.8840 (pm20) cc_final: 0.8416 (pm20) REVERT: C 272 ASN cc_start: 0.8658 (m-40) cc_final: 0.8185 (t0) REVERT: C 458 ASN cc_start: 0.7902 (t0) cc_final: 0.7653 (t0) REVERT: C 507 LEU cc_start: 0.8308 (mm) cc_final: 0.8083 (mm) REVERT: C 525 ASP cc_start: 0.7946 (t70) cc_final: 0.7450 (t0) outliers start: 25 outliers final: 16 residues processed: 269 average time/residue: 0.1340 time to fit residues: 54.7484 Evaluate side-chains 242 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 168 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 349 GLN D 458 ASN A 349 GLN A 458 ASN B 458 ASN B 510 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108672 restraints weight = 23261.853| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.20 r_work: 0.3171 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 17760 Z= 0.355 Angle : 0.699 9.981 24044 Z= 0.359 Chirality : 0.047 0.178 2624 Planarity : 0.005 0.046 2948 Dihedral : 13.946 171.111 2564 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.63 % Allowed : 18.03 % 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: -0.81 (0.18), residues: 2040 helix: 0.42 (0.15), residues: 1156 sheet: -0.68 (0.42), residues: 116 loop : -1.98 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 606 TYR 0.024 0.002 TYR A 363 PHE 0.025 0.003 PHE D 145 TRP 0.013 0.002 TRP C 451 HIS 0.005 0.002 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00843 (17756) covalent geometry : angle 0.69885 (24036) SS BOND : bond 0.00227 ( 4) SS BOND : angle 1.05014 ( 8) hydrogen bonds : bond 0.05240 ( 961) hydrogen bonds : angle 4.71978 ( 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 290 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.550 Fit side-chains REVERT: D 115 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8172 (p0) REVERT: D 146 ASN cc_start: 0.8687 (t0) cc_final: 0.8118 (t0) REVERT: D 272 ASN cc_start: 0.8644 (m-40) cc_final: 0.8065 (t0) REVERT: D 525 ASP cc_start: 0.7954 (t70) cc_final: 0.7294 (t0) REVERT: D 558 PHE cc_start: 0.6734 (t80) cc_final: 0.6522 (t80) REVERT: A 115 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8146 (p0) REVERT: A 146 ASN cc_start: 0.8687 (t0) cc_final: 0.8120 (t0) REVERT: A 272 ASN cc_start: 0.8650 (m-40) cc_final: 0.8063 (t0) REVERT: A 507 LEU cc_start: 0.8234 (mm) cc_final: 0.8005 (mm) REVERT: A 525 ASP cc_start: 0.7937 (t70) cc_final: 0.7261 (t0) REVERT: A 558 PHE cc_start: 0.6737 (t80) cc_final: 0.6529 (t80) REVERT: B 115 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8150 (p0) REVERT: B 146 ASN cc_start: 0.8694 (t0) cc_final: 0.8107 (t0) REVERT: B 159 PHE cc_start: 0.7985 (t80) cc_final: 0.7773 (t80) REVERT: B 182 GLU cc_start: 0.8801 (pm20) cc_final: 0.8425 (pm20) REVERT: B 272 ASN cc_start: 0.8909 (t0) cc_final: 0.8611 (t0) REVERT: B 507 LEU cc_start: 0.8226 (mm) cc_final: 0.7999 (mm) REVERT: B 525 ASP cc_start: 0.7986 (t70) cc_final: 0.7327 (t0) REVERT: B 558 PHE cc_start: 0.6713 (t80) cc_final: 0.6375 (t80) REVERT: C 115 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8118 (p0) REVERT: C 146 ASN cc_start: 0.8688 (t0) cc_final: 0.8119 (t0) REVERT: C 272 ASN cc_start: 0.8677 (m-40) cc_final: 0.8081 (t0) REVERT: C 507 LEU cc_start: 0.8220 (mm) cc_final: 0.7990 (mm) REVERT: C 525 ASP cc_start: 0.8015 (t70) cc_final: 0.7356 (t0) REVERT: C 606 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7358 (ttm110) outliers start: 49 outliers final: 35 residues processed: 277 average time/residue: 0.1322 time to fit residues: 55.6592 Evaluate side-chains 273 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 185 THR 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 549 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 185 THR 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 185 THR 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 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 185 THR 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: 8.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 458 ASN 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 = 0.4026 r_free = 0.4026 target = 0.165351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112975 restraints weight = 22803.001| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.21 r_work: 0.3230 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17760 Z= 0.180 Angle : 0.545 8.562 24044 Z= 0.284 Chirality : 0.041 0.148 2624 Planarity : 0.004 0.038 2948 Dihedral : 13.355 169.351 2564 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.63 % Allowed : 18.03 % 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: -0.42 (0.19), residues: 2040 helix: 0.66 (0.15), residues: 1180 sheet: -1.33 (0.40), residues: 116 loop : -1.59 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 606 TYR 0.016 0.001 TYR C 363 PHE 0.020 0.002 PHE D 159 TRP 0.015 0.001 TRP D 421 HIS 0.004 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00416 (17756) covalent geometry : angle 0.54442 (24036) SS BOND : bond 0.00178 ( 4) SS BOND : angle 0.84255 ( 8) hydrogen bonds : bond 0.04412 ( 961) hydrogen bonds : angle 4.38101 ( 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 285 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8061 (p0) REVERT: D 146 ASN cc_start: 0.8558 (t0) cc_final: 0.7989 (t0) REVERT: D 272 ASN cc_start: 0.8625 (m-40) cc_final: 0.8073 (t0) REVERT: D 458 ASN cc_start: 0.7981 (t0) cc_final: 0.7763 (t0) REVERT: D 525 ASP cc_start: 0.7940 (t70) cc_final: 0.7323 (t0) REVERT: D 558 PHE cc_start: 0.6520 (t80) cc_final: 0.6264 (t80) REVERT: A 115 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8018 (p0) REVERT: A 146 ASN cc_start: 0.8554 (t0) cc_final: 0.7982 (t0) REVERT: A 272 ASN cc_start: 0.8634 (m-40) cc_final: 0.8074 (t0) REVERT: A 507 LEU cc_start: 0.8268 (mm) cc_final: 0.8034 (mm) REVERT: A 525 ASP cc_start: 0.7925 (t70) cc_final: 0.7296 (t0) REVERT: A 558 PHE cc_start: 0.6448 (t80) cc_final: 0.6203 (t80) REVERT: B 115 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8071 (p0) REVERT: B 146 ASN cc_start: 0.8543 (t0) cc_final: 0.7949 (t0) REVERT: B 159 PHE cc_start: 0.7931 (t80) cc_final: 0.7696 (t80) REVERT: B 182 GLU cc_start: 0.8828 (pm20) cc_final: 0.8435 (pm20) REVERT: B 270 TYR cc_start: 0.7695 (m-80) cc_final: 0.7442 (t80) REVERT: B 272 ASN cc_start: 0.8907 (t0) cc_final: 0.8580 (t0) REVERT: B 458 ASN cc_start: 0.7931 (t0) cc_final: 0.7720 (t0) REVERT: B 507 LEU cc_start: 0.8221 (mm) cc_final: 0.7998 (mm) REVERT: B 525 ASP cc_start: 0.7954 (t70) cc_final: 0.7350 (t0) REVERT: C 115 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8100 (p0) REVERT: C 146 ASN cc_start: 0.8561 (t0) cc_final: 0.7980 (t0) REVERT: C 272 ASN cc_start: 0.8646 (m-40) cc_final: 0.8083 (t0) REVERT: C 507 LEU cc_start: 0.8242 (mm) cc_final: 0.8013 (mm) REVERT: C 525 ASP cc_start: 0.8018 (t70) cc_final: 0.7411 (t0) REVERT: C 606 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7326 (ttm110) outliers start: 49 outliers final: 32 residues processed: 275 average time/residue: 0.1324 time to fit residues: 55.4410 Evaluate side-chains 266 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 431 ILE 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 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 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 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 470 VAL Chi-restraints excluded: chain B residue 488 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 339 ASP 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 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: 6.9990 chunk 100 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN B 510 GLN C 458 ASN C 510 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.168140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115976 restraints weight = 22717.876| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.22 r_work: 0.3271 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2538 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= 0.128 Angle : 0.496 8.004 24044 Z= 0.260 Chirality : 0.039 0.138 2624 Planarity : 0.003 0.038 2948 Dihedral : 12.567 164.072 2564 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.58 % Allowed : 18.35 % Favored : 79.08 % 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: 0.01 (0.19), residues: 2040 helix: 0.98 (0.15), residues: 1180 sheet: -1.16 (0.40), residues: 116 loop : -1.36 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 606 TYR 0.011 0.001 TYR C 363 PHE 0.015 0.001 PHE C 138 TRP 0.027 0.001 TRP C 421 HIS 0.002 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00287 (17756) covalent geometry : angle 0.49624 (24036) SS BOND : bond 0.00174 ( 4) SS BOND : angle 0.78106 ( 8) hydrogen bonds : bond 0.04021 ( 961) hydrogen bonds : angle 4.14132 ( 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 286 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7946 (p0) REVERT: D 117 SER cc_start: 0.8527 (m) cc_final: 0.8101 (p) REVERT: D 146 ASN cc_start: 0.8400 (t0) cc_final: 0.7866 (t0) REVERT: D 272 ASN cc_start: 0.8606 (m-40) cc_final: 0.8058 (t0) REVERT: D 458 ASN cc_start: 0.8023 (t0) cc_final: 0.7729 (t0) REVERT: D 525 ASP cc_start: 0.7943 (t70) cc_final: 0.7360 (t0) REVERT: D 558 PHE cc_start: 0.6362 (t80) cc_final: 0.6137 (t80) REVERT: D 608 LEU cc_start: 0.7710 (mt) cc_final: 0.7278 (pp) REVERT: A 115 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7965 (p0) REVERT: A 117 SER cc_start: 0.8539 (m) cc_final: 0.8097 (p) REVERT: A 146 ASN cc_start: 0.8398 (t0) cc_final: 0.7862 (t0) REVERT: A 272 ASN cc_start: 0.8607 (m-40) cc_final: 0.8060 (t0) REVERT: A 458 ASN cc_start: 0.7922 (t0) cc_final: 0.7713 (t0) REVERT: A 507 LEU cc_start: 0.8256 (mm) cc_final: 0.8021 (mm) REVERT: A 525 ASP cc_start: 0.7915 (t70) cc_final: 0.7257 (t70) REVERT: A 558 PHE cc_start: 0.6351 (t80) cc_final: 0.6096 (t80) REVERT: B 115 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7963 (p0) REVERT: B 117 SER cc_start: 0.8524 (m) cc_final: 0.8088 (p) REVERT: B 146 ASN cc_start: 0.8465 (t0) cc_final: 0.7857 (t0) REVERT: B 182 GLU cc_start: 0.8840 (pm20) cc_final: 0.8544 (pm20) REVERT: B 272 ASN cc_start: 0.8891 (t0) cc_final: 0.8594 (t0) REVERT: B 413 MET cc_start: 0.7528 (ttp) cc_final: 0.7316 (ttp) REVERT: B 458 ASN cc_start: 0.8002 (t0) cc_final: 0.7702 (t0) REVERT: B 507 LEU cc_start: 0.8256 (mm) cc_final: 0.8036 (mm) REVERT: B 508 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8349 (ptpt) REVERT: B 525 ASP cc_start: 0.7970 (t70) cc_final: 0.7398 (t0) REVERT: B 588 PHE cc_start: 0.8491 (m-10) cc_final: 0.8233 (m-10) REVERT: B 606 ARG cc_start: 0.7705 (ttm110) cc_final: 0.6960 (ttm110) REVERT: C 115 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8042 (p0) REVERT: C 146 ASN cc_start: 0.8384 (t0) cc_final: 0.7848 (t0) REVERT: C 272 ASN cc_start: 0.8613 (m-40) cc_final: 0.8051 (t0) REVERT: C 507 LEU cc_start: 0.8254 (mm) cc_final: 0.8037 (mm) REVERT: C 508 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8330 (ptpt) REVERT: C 525 ASP cc_start: 0.7982 (t70) cc_final: 0.7412 (t0) REVERT: C 588 PHE cc_start: 0.8451 (m-10) cc_final: 0.8190 (m-10) outliers start: 48 outliers final: 37 residues processed: 277 average time/residue: 0.1243 time to fit residues: 52.8399 Evaluate side-chains 268 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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 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 481 MET 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 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 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 428 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 64 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 510 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.167080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114620 restraints weight = 22671.383| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.21 r_work: 0.3245 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2599 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= 0.154 Angle : 0.520 7.669 24044 Z= 0.270 Chirality : 0.040 0.146 2624 Planarity : 0.003 0.038 2948 Dihedral : 12.382 161.883 2564 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.36 % Allowed : 18.83 % Favored : 78.81 % 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: 0.15 (0.19), residues: 2040 helix: 1.03 (0.15), residues: 1184 sheet: -0.95 (0.40), residues: 116 loop : -1.21 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 606 TYR 0.014 0.001 TYR C 363 PHE 0.022 0.002 PHE B 159 TRP 0.020 0.001 TRP C 421 HIS 0.006 0.001 HIS D 484 Details of bonding type rmsd covalent geometry : bond 0.00352 (17756) covalent geometry : angle 0.51949 (24036) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.84441 ( 8) hydrogen bonds : bond 0.04183 ( 961) hydrogen bonds : angle 4.13321 ( 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 273 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7989 (p0) REVERT: D 146 ASN cc_start: 0.8395 (t0) cc_final: 0.7860 (t0) REVERT: D 272 ASN cc_start: 0.8609 (m-40) cc_final: 0.8065 (t0) REVERT: D 458 ASN cc_start: 0.7978 (t0) cc_final: 0.7672 (t0) REVERT: D 525 ASP cc_start: 0.7965 (t70) cc_final: 0.7332 (t70) REVERT: D 558 PHE cc_start: 0.6311 (t80) cc_final: 0.6076 (t80) REVERT: D 608 LEU cc_start: 0.7730 (mt) cc_final: 0.7307 (pp) REVERT: A 115 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7981 (p0) REVERT: A 117 SER cc_start: 0.8546 (m) cc_final: 0.8109 (p) REVERT: A 146 ASN cc_start: 0.8395 (t0) cc_final: 0.7858 (t0) REVERT: A 272 ASN cc_start: 0.8618 (m-40) cc_final: 0.8067 (t0) REVERT: A 458 ASN cc_start: 0.7900 (t0) cc_final: 0.7625 (t0) REVERT: A 525 ASP cc_start: 0.7936 (t70) cc_final: 0.7304 (t70) REVERT: A 558 PHE cc_start: 0.6288 (t80) cc_final: 0.6058 (t80) REVERT: B 115 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7993 (p0) REVERT: B 146 ASN cc_start: 0.8465 (t0) cc_final: 0.7859 (t0) REVERT: B 182 GLU cc_start: 0.8839 (pm20) cc_final: 0.8535 (pm20) REVERT: B 270 TYR cc_start: 0.7639 (m-80) cc_final: 0.7386 (t80) REVERT: B 272 ASN cc_start: 0.8903 (t0) cc_final: 0.8619 (t0) REVERT: B 413 MET cc_start: 0.7527 (ttp) cc_final: 0.7310 (ttp) REVERT: B 458 ASN cc_start: 0.7979 (t0) cc_final: 0.7672 (t0) REVERT: B 507 LEU cc_start: 0.8243 (mm) cc_final: 0.8022 (mm) REVERT: B 525 ASP cc_start: 0.7988 (t70) cc_final: 0.7371 (t70) REVERT: B 588 PHE cc_start: 0.8447 (m-10) cc_final: 0.8236 (m-10) REVERT: B 606 ARG cc_start: 0.7562 (ttm110) cc_final: 0.7067 (ttm110) REVERT: C 115 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8017 (p0) REVERT: C 146 ASN cc_start: 0.8392 (t0) cc_final: 0.7846 (t0) REVERT: C 272 ASN cc_start: 0.8616 (m-40) cc_final: 0.8056 (t0) REVERT: C 507 LEU cc_start: 0.8245 (mm) cc_final: 0.8026 (mm) REVERT: C 508 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8324 (ptpt) REVERT: C 525 ASP cc_start: 0.8006 (t70) cc_final: 0.7391 (t70) REVERT: C 588 PHE cc_start: 0.8411 (m-10) cc_final: 0.8167 (m-10) outliers start: 44 outliers final: 38 residues processed: 266 average time/residue: 0.1321 time to fit residues: 53.5128 Evaluate side-chains 269 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 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 511 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 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 488 LEU Chi-restraints excluded: chain B residue 511 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 133 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 141 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 30 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.165201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112414 restraints weight = 22934.206| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.22 r_work: 0.3223 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17760 Z= 0.202 Angle : 0.558 8.119 24044 Z= 0.289 Chirality : 0.041 0.156 2624 Planarity : 0.004 0.040 2948 Dihedral : 12.399 162.754 2564 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.63 % Allowed : 18.62 % Favored : 78.76 % 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: 0.06 (0.19), residues: 2040 helix: 0.83 (0.15), residues: 1212 sheet: -0.87 (0.41), residues: 116 loop : -1.09 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 606 TYR 0.017 0.001 TYR B 363 PHE 0.019 0.002 PHE A 138 TRP 0.021 0.001 TRP C 421 HIS 0.005 0.001 HIS D 484 Details of bonding type rmsd covalent geometry : bond 0.00471 (17756) covalent geometry : angle 0.55829 (24036) SS BOND : bond 0.00189 ( 4) SS BOND : angle 0.89997 ( 8) hydrogen bonds : bond 0.04480 ( 961) hydrogen bonds : angle 4.23115 ( 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 278 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8013 (p0) REVERT: D 146 ASN cc_start: 0.8493 (t0) cc_final: 0.7933 (t0) REVERT: D 272 ASN cc_start: 0.8612 (m-40) cc_final: 0.8050 (t0) REVERT: D 525 ASP cc_start: 0.7970 (t70) cc_final: 0.7334 (t70) REVERT: D 558 PHE cc_start: 0.6326 (t80) cc_final: 0.6087 (t80) REVERT: A 115 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8035 (p0) REVERT: A 146 ASN cc_start: 0.8485 (t0) cc_final: 0.7927 (t0) REVERT: A 272 ASN cc_start: 0.8619 (m-40) cc_final: 0.8049 (t0) REVERT: A 525 ASP cc_start: 0.7941 (t70) cc_final: 0.7463 (t70) REVERT: A 558 PHE cc_start: 0.6337 (t80) cc_final: 0.6088 (t80) REVERT: B 115 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8053 (p0) REVERT: B 146 ASN cc_start: 0.8509 (t0) cc_final: 0.7890 (t0) REVERT: B 182 GLU cc_start: 0.8822 (pm20) cc_final: 0.8405 (pm20) REVERT: B 270 TYR cc_start: 0.7637 (m-80) cc_final: 0.7380 (t80) REVERT: B 272 ASN cc_start: 0.8932 (t0) cc_final: 0.8623 (t0) REVERT: B 525 ASP cc_start: 0.7985 (t70) cc_final: 0.7346 (t70) REVERT: B 588 PHE cc_start: 0.8458 (m-10) cc_final: 0.8243 (m-10) REVERT: B 606 ARG cc_start: 0.7587 (ttm110) cc_final: 0.7140 (ttm110) REVERT: C 115 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8054 (p0) REVERT: C 146 ASN cc_start: 0.8493 (t0) cc_final: 0.7928 (t0) REVERT: C 272 ASN cc_start: 0.8615 (m-40) cc_final: 0.8050 (t0) REVERT: C 507 LEU cc_start: 0.8277 (mm) cc_final: 0.8056 (mm) REVERT: C 525 ASP cc_start: 0.8010 (t70) cc_final: 0.7371 (t70) REVERT: C 588 PHE cc_start: 0.8404 (m-10) cc_final: 0.8194 (m-10) REVERT: C 608 LEU cc_start: 0.7613 (mt) cc_final: 0.7224 (pp) outliers start: 49 outliers final: 43 residues processed: 269 average time/residue: 0.1256 time to fit residues: 52.1993 Evaluate side-chains 275 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 511 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 233 VAL 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 481 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 511 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 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 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 233 VAL Chi-restraints excluded: chain C residue 309 VAL 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 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: 3.9990 chunk 182 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 175 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN D 458 ASN A 433 GLN A 458 ASN B 458 ASN C 433 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.171373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.120118 restraints weight = 23045.965| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.11 r_work: 0.3364 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17760 Z= 0.112 Angle : 0.489 7.345 24044 Z= 0.255 Chirality : 0.038 0.139 2624 Planarity : 0.003 0.039 2948 Dihedral : 11.725 154.799 2564 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.41 % Allowed : 19.15 % Favored : 78.43 % 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: 0.47 (0.19), residues: 2040 helix: 1.21 (0.15), residues: 1208 sheet: -0.63 (0.41), residues: 116 loop : -1.04 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 606 TYR 0.010 0.001 TYR C 363 PHE 0.020 0.001 PHE D 159 TRP 0.025 0.001 TRP C 421 HIS 0.004 0.001 HIS D 484 Details of bonding type rmsd covalent geometry : bond 0.00245 (17756) covalent geometry : angle 0.48907 (24036) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.83954 ( 8) hydrogen bonds : bond 0.03831 ( 961) hydrogen bonds : angle 3.93931 ( 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 286 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7938 (p0) REVERT: D 117 SER cc_start: 0.8454 (m) cc_final: 0.8067 (p) REVERT: D 146 ASN cc_start: 0.8256 (t0) cc_final: 0.7728 (t0) REVERT: D 245 TRP cc_start: 0.8247 (m100) cc_final: 0.7907 (m-10) REVERT: D 272 ASN cc_start: 0.8592 (m-40) cc_final: 0.8111 (t0) REVERT: D 458 ASN cc_start: 0.7844 (t0) cc_final: 0.7625 (t0) REVERT: D 495 GLN cc_start: 0.7246 (tp40) cc_final: 0.7043 (tp40) REVERT: D 505 LEU cc_start: 0.8446 (tp) cc_final: 0.8048 (mp) REVERT: D 525 ASP cc_start: 0.7989 (t70) cc_final: 0.7426 (t70) REVERT: D 558 PHE cc_start: 0.6371 (t80) cc_final: 0.6157 (t80) REVERT: A 115 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7962 (p0) REVERT: A 117 SER cc_start: 0.8471 (m) cc_final: 0.8086 (p) REVERT: A 146 ASN cc_start: 0.8256 (t0) cc_final: 0.7730 (t0) REVERT: A 245 TRP cc_start: 0.8269 (m100) cc_final: 0.7923 (m-10) REVERT: A 272 ASN cc_start: 0.8594 (m-40) cc_final: 0.8111 (t0) REVERT: A 495 GLN cc_start: 0.7167 (tp40) cc_final: 0.6965 (tp40) REVERT: A 525 ASP cc_start: 0.7967 (t70) cc_final: 0.7380 (t70) REVERT: B 115 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7934 (p0) REVERT: B 117 SER cc_start: 0.8441 (m) cc_final: 0.8050 (p) REVERT: B 146 ASN cc_start: 0.8305 (t0) cc_final: 0.7728 (t0) REVERT: B 182 GLU cc_start: 0.8849 (pm20) cc_final: 0.8576 (pm20) REVERT: B 245 TRP cc_start: 0.8268 (m100) cc_final: 0.7868 (m-10) REVERT: B 272 ASN cc_start: 0.8879 (t0) cc_final: 0.8595 (t0) REVERT: B 525 ASP cc_start: 0.7979 (t70) cc_final: 0.7426 (t70) REVERT: B 558 PHE cc_start: 0.6428 (t80) cc_final: 0.6120 (t80) REVERT: B 606 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7155 (ttm110) REVERT: C 115 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7978 (p0) REVERT: C 117 SER cc_start: 0.8458 (m) cc_final: 0.8044 (p) REVERT: C 146 ASN cc_start: 0.8274 (t0) cc_final: 0.7750 (t0) REVERT: C 245 TRP cc_start: 0.8278 (m100) cc_final: 0.7903 (m-10) REVERT: C 272 ASN cc_start: 0.8600 (m-40) cc_final: 0.8114 (t0) REVERT: C 495 GLN cc_start: 0.7209 (tp40) cc_final: 0.7008 (tp40) REVERT: C 525 ASP cc_start: 0.8023 (t70) cc_final: 0.7470 (t70) REVERT: C 608 LEU cc_start: 0.7673 (mt) cc_final: 0.7299 (pp) outliers start: 45 outliers final: 39 residues processed: 277 average time/residue: 0.1335 time to fit residues: 56.4893 Evaluate side-chains 271 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 339 ASP 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 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 511 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 488 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 488 LEU Chi-restraints excluded: chain C residue 511 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 92 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.171079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119630 restraints weight = 23064.203| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.11 r_work: 0.3369 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17760 Z= 0.123 Angle : 0.511 7.710 24044 Z= 0.263 Chirality : 0.039 0.145 2624 Planarity : 0.003 0.037 2948 Dihedral : 11.305 147.709 2564 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.36 % Allowed : 19.69 % 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: 0.60 (0.19), residues: 2040 helix: 1.33 (0.15), residues: 1208 sheet: -0.57 (0.41), residues: 116 loop : -1.01 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 606 TYR 0.011 0.001 TYR B 363 PHE 0.018 0.001 PHE C 558 TRP 0.027 0.001 TRP A 421 HIS 0.004 0.001 HIS D 484 Details of bonding type rmsd covalent geometry : bond 0.00276 (17756) covalent geometry : angle 0.51040 (24036) SS BOND : bond 0.00153 ( 4) SS BOND : angle 0.80148 ( 8) hydrogen bonds : bond 0.03951 ( 961) hydrogen bonds : angle 3.91516 ( 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 274 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7983 (p0) REVERT: D 117 SER cc_start: 0.8442 (m) cc_final: 0.8067 (p) REVERT: D 146 ASN cc_start: 0.8255 (t0) cc_final: 0.7746 (t0) REVERT: D 245 TRP cc_start: 0.8296 (m100) cc_final: 0.7950 (m-10) REVERT: D 272 ASN cc_start: 0.8596 (m-40) cc_final: 0.8124 (t0) REVERT: D 495 GLN cc_start: 0.7207 (tp40) cc_final: 0.6990 (tp40) REVERT: D 505 LEU cc_start: 0.8481 (tp) cc_final: 0.8075 (mp) REVERT: D 525 ASP cc_start: 0.8014 (t70) cc_final: 0.7481 (t70) REVERT: A 115 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7945 (p0) REVERT: A 117 SER cc_start: 0.8449 (m) cc_final: 0.8068 (p) REVERT: A 146 ASN cc_start: 0.8255 (t0) cc_final: 0.7746 (t0) REVERT: A 245 TRP cc_start: 0.8270 (m100) cc_final: 0.7902 (m-10) REVERT: A 272 ASN cc_start: 0.8599 (m-40) cc_final: 0.8130 (t0) REVERT: A 495 GLN cc_start: 0.7141 (tp40) cc_final: 0.6939 (tp40) REVERT: A 525 ASP cc_start: 0.7986 (t70) cc_final: 0.7427 (t70) REVERT: B 115 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7960 (p0) REVERT: B 117 SER cc_start: 0.8428 (m) cc_final: 0.8049 (p) REVERT: B 146 ASN cc_start: 0.8270 (t0) cc_final: 0.7707 (t0) REVERT: B 182 GLU cc_start: 0.8848 (pm20) cc_final: 0.8586 (pm20) REVERT: B 245 TRP cc_start: 0.8285 (m100) cc_final: 0.7868 (m-10) REVERT: B 272 ASN cc_start: 0.8852 (t0) cc_final: 0.8588 (t0) REVERT: B 525 ASP cc_start: 0.8040 (t70) cc_final: 0.7525 (t70) REVERT: B 558 PHE cc_start: 0.6437 (t80) cc_final: 0.6145 (t80) REVERT: B 606 ARG cc_start: 0.7563 (ttm110) cc_final: 0.7182 (ttm110) REVERT: C 115 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8031 (p0) REVERT: C 117 SER cc_start: 0.8399 (m) cc_final: 0.8019 (p) REVERT: C 146 ASN cc_start: 0.8265 (t0) cc_final: 0.7755 (t0) REVERT: C 245 TRP cc_start: 0.8304 (m100) cc_final: 0.7922 (m-10) REVERT: C 272 ASN cc_start: 0.8601 (m-40) cc_final: 0.8109 (t0) REVERT: C 495 GLN cc_start: 0.7188 (tp40) cc_final: 0.6979 (tp40) REVERT: C 525 ASP cc_start: 0.8058 (t70) cc_final: 0.7516 (t70) REVERT: C 558 PHE cc_start: 0.6455 (t80) cc_final: 0.6171 (t80) REVERT: C 607 LYS cc_start: 0.8065 (tttm) cc_final: 0.7697 (mtpp) REVERT: C 608 LEU cc_start: 0.7707 (mt) cc_final: 0.7290 (pp) outliers start: 44 outliers final: 40 residues processed: 266 average time/residue: 0.1256 time to fit residues: 51.6320 Evaluate side-chains 271 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 339 ASP 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 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 511 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 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 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 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 511 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: 5.9990 chunk 167 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 0.0070 chunk 63 optimal weight: 6.9990 chunk 125 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.172517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121271 restraints weight = 23092.133| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.12 r_work: 0.3383 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17760 Z= 0.108 Angle : 0.492 7.518 24044 Z= 0.254 Chirality : 0.038 0.134 2624 Planarity : 0.003 0.040 2948 Dihedral : 10.260 126.120 2564 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.41 % Allowed : 20.01 % 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: 0.77 (0.19), residues: 2040 helix: 1.50 (0.15), residues: 1208 sheet: -0.45 (0.41), residues: 116 loop : -1.02 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 606 TYR 0.009 0.001 TYR C 602 PHE 0.022 0.001 PHE B 159 TRP 0.026 0.001 TRP C 421 HIS 0.004 0.001 HIS D 484 Details of bonding type rmsd covalent geometry : bond 0.00233 (17756) covalent geometry : angle 0.49201 (24036) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.80939 ( 8) hydrogen bonds : bond 0.03753 ( 961) hydrogen bonds : angle 3.80115 ( 2811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4936.91 seconds wall clock time: 84 minutes 51.95 seconds (5091.95 seconds total)