Starting phenix.real_space_refine on Sat Sep 28 00:34:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n16_24114/09_2024/7n16_24114.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n16_24114/09_2024/7n16_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n16_24114/09_2024/7n16_24114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n16_24114/09_2024/7n16_24114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n16_24114/09_2024/7n16_24114.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n16_24114/09_2024/7n16_24114.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17357 Number of models: 1 Model: "" Number of chains: 4 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: "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-4': 4, 'CPL:plan-3': 4, 'CPL:plan-2': 1, 'CPL:plan-1': 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-4': 4, 'CPL:plan-3': 4, 'CPL:plan-2': 1, 'CPL:plan-1': 1} Unresolved non-hydrogen planarities: 38 Restraints were copied for chains: B, C Time building chain proxies: 11.38, per 1000 atoms: 0.66 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=2, 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 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: 4.17 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.65 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: 4.89 Time building geometry restraints manager: 4.86 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: 10230 35.11 - 70.23: 272 70.23 - 105.34: 20 105.34 - 140.46: 16 140.46 - 175.57: 12 Dihedral angle restraints: 10550 sinusoidal: 4482 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 10547 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: 2.03 - 2.60: 134 2.60 - 3.18: 13352 3.18 - 3.75: 27108 3.75 - 4.33: 36826 4.33 - 4.90: 61188 Nonbonded interactions: 138608 Sorted by model distance: nonbonded pdb=" SG CYS B 157 " pdb=" SG CYS B 172 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS C 157 " pdb=" SG CYS C 172 " model vdw 2.028 3.760 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 ... (remaining 138603 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 620 or resid 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 an \ d (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 O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 104 through 620 or resid 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 an \ d (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 O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 104 through 620 or resid 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 an \ d (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 O2P 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: 1.110 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 38.280 Find NCS groups from input model: 0.920 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.820 ------------------------------------------------------------------------------- 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 17756 Z= 0.522 Angle : 1.179 17.974 24036 Z= 0.601 Chirality : 0.061 0.245 2624 Planarity : 0.008 0.068 2948 Dihedral : 18.872 175.569 6648 Min Nonbonded Distance : 2.027 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.003 TRP A 266 HIS 0.004 0.001 HIS C 321 PHE 0.028 0.003 PHE B 145 TYR 0.026 0.003 TYR D 363 ARG 0.005 0.001 ARG B 447 *********************** 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 fitting. rotamer outliers: 16 poor density : 322 time to evaluate : 2.036 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: 0.3440 time to fit residues: 165.4107 Evaluate side-chains 236 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 349 GLN 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: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17756 Z= 0.187 Angle : 0.560 7.133 24036 Z= 0.292 Chirality : 0.040 0.144 2624 Planarity : 0.004 0.040 2948 Dihedral : 15.857 176.356 2564 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.23 % Allowed : 15.29 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.16), residues: 2040 helix: -0.67 (0.14), residues: 1152 sheet: -0.97 (0.44), residues: 108 loop : -2.18 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 421 HIS 0.002 0.001 HIS C 321 PHE 0.014 0.001 PHE B 138 TYR 0.014 0.001 TYR B 108 ARG 0.004 0.000 ARG C 280 *********************** 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 276 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 1.932 Fit side-chains REVERT: D 115 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7685 (p0) REVERT: D 146 ASN cc_start: 0.8117 (t0) cc_final: 0.7519 (t0) REVERT: D 182 GLU cc_start: 0.8316 (pm20) cc_final: 0.7787 (pm20) REVERT: D 272 ASN cc_start: 0.8234 (m-40) cc_final: 0.8016 (t0) REVERT: D 525 ASP cc_start: 0.7748 (t70) cc_final: 0.7256 (t0) REVERT: D 528 ARG cc_start: 0.6943 (ptt90) cc_final: 0.6739 (ptt90) REVERT: D 535 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7314 (ptp-110) REVERT: A 115 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7696 (p0) REVERT: A 146 ASN cc_start: 0.8114 (t0) cc_final: 0.7518 (t0) REVERT: A 182 GLU cc_start: 0.8314 (pm20) cc_final: 0.7786 (pm20) REVERT: A 202 MET cc_start: 0.7552 (mmt) cc_final: 0.7165 (mmt) REVERT: A 272 ASN cc_start: 0.8229 (m-40) cc_final: 0.8020 (t0) REVERT: A 525 ASP cc_start: 0.7749 (t70) cc_final: 0.7186 (t0) REVERT: A 535 ARG cc_start: 0.7802 (ttm110) cc_final: 0.7342 (ptp-110) REVERT: A 558 PHE cc_start: 0.6591 (t80) cc_final: 0.6329 (t80) REVERT: A 599 LEU cc_start: 0.8015 (tp) cc_final: 0.7105 (tp) REVERT: B 115 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7684 (p0) REVERT: B 146 ASN cc_start: 0.8189 (t0) cc_final: 0.7566 (t0) REVERT: B 272 ASN cc_start: 0.8488 (t0) cc_final: 0.8280 (t0) REVERT: B 507 LEU cc_start: 0.8256 (mm) cc_final: 0.8041 (mm) REVERT: B 525 ASP cc_start: 0.7818 (t70) cc_final: 0.7386 (t0) REVERT: B 528 ARG cc_start: 0.6854 (ptt90) cc_final: 0.6647 (ptt90) REVERT: C 115 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7684 (p0) REVERT: C 146 ASN cc_start: 0.8145 (t0) cc_final: 0.7540 (t0) REVERT: C 182 GLU cc_start: 0.8326 (pm20) cc_final: 0.7782 (pm20) REVERT: C 507 LEU cc_start: 0.8262 (mm) cc_final: 0.8060 (mm) REVERT: C 525 ASP cc_start: 0.7837 (t70) cc_final: 0.7443 (t0) REVERT: C 528 ARG cc_start: 0.6875 (ptt90) cc_final: 0.6666 (ptt90) outliers start: 23 outliers final: 15 residues processed: 271 average time/residue: 0.3206 time to fit residues: 126.6143 Evaluate side-chains 244 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 225 time to evaluate : 1.999 ------------------------------------------------------------------------------- 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 102 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 165 optimal weight: 0.0000 chunk 184 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 overall best weight: 3.9992 ------------------------------------------------------------------------------- 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 B 458 ASN C 349 GLN C 458 ASN C 578 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 17756 Z= 0.428 Angle : 0.651 9.220 24036 Z= 0.337 Chirality : 0.044 0.168 2624 Planarity : 0.004 0.042 2948 Dihedral : 14.975 175.976 2564 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.15 % Allowed : 17.60 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2040 helix: 0.06 (0.15), residues: 1160 sheet: -1.67 (0.44), residues: 92 loop : -2.14 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 421 HIS 0.003 0.001 HIS B 199 PHE 0.021 0.002 PHE D 145 TYR 0.022 0.001 TYR A 363 ARG 0.005 0.001 ARG C 274 *********************** 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 281 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 241 time to evaluate : 1.823 Fit side-chains REVERT: D 115 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7918 (p0) REVERT: D 146 ASN cc_start: 0.8299 (t0) cc_final: 0.7705 (t0) REVERT: D 272 ASN cc_start: 0.8256 (m-40) cc_final: 0.8004 (t0) REVERT: D 525 ASP cc_start: 0.7827 (t70) cc_final: 0.7261 (t0) REVERT: A 115 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7920 (p0) REVERT: A 146 ASN cc_start: 0.8300 (t0) cc_final: 0.7708 (t0) REVERT: A 202 MET cc_start: 0.7606 (mmt) cc_final: 0.7241 (mmt) REVERT: A 272 ASN cc_start: 0.8254 (m-40) cc_final: 0.8005 (t0) REVERT: A 507 LEU cc_start: 0.8240 (mm) cc_final: 0.8029 (mm) REVERT: A 525 ASP cc_start: 0.7781 (t70) cc_final: 0.7200 (t0) REVERT: B 115 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7942 (p0) REVERT: B 146 ASN cc_start: 0.8344 (t0) cc_final: 0.7699 (t0) REVERT: B 272 ASN cc_start: 0.8545 (t0) cc_final: 0.8317 (t0) REVERT: B 507 LEU cc_start: 0.8241 (mm) cc_final: 0.8031 (mm) REVERT: B 525 ASP cc_start: 0.7883 (t70) cc_final: 0.7313 (t0) REVERT: C 115 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7940 (p0) REVERT: C 146 ASN cc_start: 0.8319 (t0) cc_final: 0.7718 (t0) REVERT: C 423 GLU cc_start: 0.7701 (tp30) cc_final: 0.7428 (tp30) REVERT: C 507 LEU cc_start: 0.8197 (mm) cc_final: 0.7995 (mm) REVERT: C 525 ASP cc_start: 0.7872 (t70) cc_final: 0.7319 (t0) outliers start: 40 outliers final: 29 residues processed: 271 average time/residue: 0.2894 time to fit residues: 118.1029 Evaluate side-chains 267 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 234 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 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 511 LEU 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 511 LEU 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 422 THR Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 511 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 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 458 ASN A 458 ASN B 458 ASN C 458 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17756 Z= 0.157 Angle : 0.505 8.033 24036 Z= 0.264 Chirality : 0.039 0.135 2624 Planarity : 0.003 0.040 2948 Dihedral : 13.495 168.849 2564 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.77 % Allowed : 17.92 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2040 helix: 0.82 (0.15), residues: 1156 sheet: -1.33 (0.42), residues: 116 loop : -1.87 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 421 HIS 0.006 0.001 HIS A 484 PHE 0.019 0.001 PHE B 159 TYR 0.010 0.001 TYR A 363 ARG 0.005 0.000 ARG B 535 *********************** 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 270 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 237 time to evaluate : 1.890 Fit side-chains REVERT: D 115 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7790 (p0) REVERT: D 146 ASN cc_start: 0.8009 (t0) cc_final: 0.7421 (t0) REVERT: D 458 ASN cc_start: 0.7831 (t0) cc_final: 0.7602 (t0) REVERT: D 525 ASP cc_start: 0.7828 (t70) cc_final: 0.7326 (t0) REVERT: D 535 ARG cc_start: 0.7871 (ptp-110) cc_final: 0.7591 (ptp-110) REVERT: D 558 PHE cc_start: 0.6380 (t80) cc_final: 0.5981 (t80) REVERT: A 115 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7778 (p0) REVERT: A 117 SER cc_start: 0.8309 (m) cc_final: 0.7893 (p) REVERT: A 146 ASN cc_start: 0.8009 (t0) cc_final: 0.7423 (t0) REVERT: A 507 LEU cc_start: 0.8247 (mm) cc_final: 0.8039 (mm) REVERT: A 525 ASP cc_start: 0.7790 (t70) cc_final: 0.7247 (t0) REVERT: A 535 ARG cc_start: 0.7860 (ptp-110) cc_final: 0.7552 (ptp-110) REVERT: B 115 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7822 (p0) REVERT: B 146 ASN cc_start: 0.8121 (t0) cc_final: 0.7477 (t0) REVERT: B 272 ASN cc_start: 0.8499 (t0) cc_final: 0.8267 (t0) REVERT: B 458 ASN cc_start: 0.7788 (t0) cc_final: 0.7568 (t0) REVERT: B 507 LEU cc_start: 0.8281 (mm) cc_final: 0.8069 (mm) REVERT: B 525 ASP cc_start: 0.7826 (t70) cc_final: 0.7320 (t0) REVERT: B 558 PHE cc_start: 0.6431 (t80) cc_final: 0.6003 (t80) REVERT: C 115 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7820 (p0) REVERT: C 146 ASN cc_start: 0.8017 (t0) cc_final: 0.7436 (t0) REVERT: C 272 ASN cc_start: 0.8249 (t0) cc_final: 0.8012 (t0) REVERT: C 458 ASN cc_start: 0.7825 (t0) cc_final: 0.7599 (t0) REVERT: C 525 ASP cc_start: 0.7821 (t70) cc_final: 0.7331 (t0) outliers start: 33 outliers final: 20 residues processed: 266 average time/residue: 0.3040 time to fit residues: 121.1807 Evaluate side-chains 250 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 226 time to evaluate : 1.945 ------------------------------------------------------------------------------- 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 470 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 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 617 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 0.0670 chunk 49 optimal weight: 5.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17756 Z= 0.294 Angle : 0.564 8.379 24036 Z= 0.293 Chirality : 0.041 0.160 2624 Planarity : 0.004 0.036 2948 Dihedral : 13.188 168.658 2564 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.17 % Allowed : 17.33 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2040 helix: 0.86 (0.15), residues: 1160 sheet: -1.39 (0.43), residues: 92 loop : -1.76 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 421 HIS 0.004 0.001 HIS B 484 PHE 0.022 0.002 PHE A 558 TYR 0.018 0.001 TYR A 363 ARG 0.007 0.000 ARG C 606 *********************** 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 295 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 236 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7806 (p0) REVERT: D 146 ASN cc_start: 0.8116 (t0) cc_final: 0.7535 (t0) REVERT: D 525 ASP cc_start: 0.7838 (t70) cc_final: 0.7306 (t0) REVERT: D 608 LEU cc_start: 0.7808 (mt) cc_final: 0.7378 (pp) REVERT: A 115 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7790 (p0) REVERT: A 146 ASN cc_start: 0.8120 (t0) cc_final: 0.7539 (t0) REVERT: A 458 ASN cc_start: 0.7965 (t0) cc_final: 0.7759 (t0) REVERT: A 507 LEU cc_start: 0.8268 (mm) cc_final: 0.8045 (mm) REVERT: A 525 ASP cc_start: 0.7804 (t70) cc_final: 0.7261 (t0) REVERT: A 558 PHE cc_start: 0.6409 (t80) cc_final: 0.6089 (t80) REVERT: B 115 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7845 (p0) REVERT: B 146 ASN cc_start: 0.8208 (t0) cc_final: 0.7546 (t0) REVERT: B 272 ASN cc_start: 0.8532 (t0) cc_final: 0.8262 (t0) REVERT: B 507 LEU cc_start: 0.8255 (mm) cc_final: 0.8039 (mm) REVERT: B 525 ASP cc_start: 0.7834 (t70) cc_final: 0.7317 (t0) REVERT: B 608 LEU cc_start: 0.7810 (mt) cc_final: 0.7389 (pp) REVERT: C 115 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7827 (p0) REVERT: C 146 ASN cc_start: 0.8128 (t0) cc_final: 0.7553 (t0) REVERT: C 272 ASN cc_start: 0.8403 (t0) cc_final: 0.8137 (t0) REVERT: C 421 TRP cc_start: 0.6709 (t-100) cc_final: 0.6364 (t-100) REVERT: C 458 ASN cc_start: 0.7881 (t0) cc_final: 0.7607 (t0) REVERT: C 525 ASP cc_start: 0.7856 (t70) cc_final: 0.7340 (t0) REVERT: C 608 LEU cc_start: 0.7796 (mt) cc_final: 0.7361 (pp) outliers start: 59 outliers final: 44 residues processed: 284 average time/residue: 0.2936 time to fit residues: 125.5880 Evaluate side-chains 278 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 230 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 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 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 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 481 MET 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 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 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 330 ILE 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 511 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 197 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 458 ASN B 458 ASN C 510 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17756 Z= 0.191 Angle : 0.509 7.855 24036 Z= 0.266 Chirality : 0.039 0.141 2624 Planarity : 0.003 0.038 2948 Dihedral : 12.641 164.873 2564 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.47 % Allowed : 18.56 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.19), residues: 2040 helix: 0.95 (0.15), residues: 1184 sheet: -1.20 (0.41), residues: 116 loop : -1.43 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 421 HIS 0.003 0.001 HIS D 484 PHE 0.021 0.001 PHE B 159 TYR 0.012 0.001 TYR D 363 ARG 0.009 0.000 ARG B 606 *********************** 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 280 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 234 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7758 (p0) REVERT: D 146 ASN cc_start: 0.7952 (t0) cc_final: 0.7402 (t0) REVERT: D 525 ASP cc_start: 0.7818 (t70) cc_final: 0.7317 (t0) REVERT: D 558 PHE cc_start: 0.6280 (t80) cc_final: 0.5918 (t80) REVERT: D 606 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7516 (ttm110) REVERT: D 608 LEU cc_start: 0.7829 (mt) cc_final: 0.7396 (pp) REVERT: A 115 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7751 (p0) REVERT: A 146 ASN cc_start: 0.7948 (t0) cc_final: 0.7402 (t0) REVERT: A 458 ASN cc_start: 0.7999 (t0) cc_final: 0.7727 (t0) REVERT: A 507 LEU cc_start: 0.8225 (mm) cc_final: 0.8014 (mm) REVERT: A 525 ASP cc_start: 0.7820 (t70) cc_final: 0.7307 (t0) REVERT: A 558 PHE cc_start: 0.6324 (t80) cc_final: 0.5977 (t80) REVERT: A 588 PHE cc_start: 0.8295 (m-10) cc_final: 0.7992 (m-10) REVERT: B 115 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7787 (p0) REVERT: B 146 ASN cc_start: 0.8086 (t0) cc_final: 0.7440 (t0) REVERT: B 272 ASN cc_start: 0.8510 (t0) cc_final: 0.8262 (t0) REVERT: B 421 TRP cc_start: 0.6937 (t-100) cc_final: 0.6547 (t-100) REVERT: B 507 LEU cc_start: 0.8224 (mm) cc_final: 0.8024 (mm) REVERT: B 508 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8345 (ptpt) REVERT: B 525 ASP cc_start: 0.7880 (t70) cc_final: 0.7374 (t0) REVERT: B 558 PHE cc_start: 0.6286 (t80) cc_final: 0.5908 (t80) REVERT: B 606 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7510 (ttm110) REVERT: B 608 LEU cc_start: 0.7823 (mt) cc_final: 0.7396 (pp) REVERT: C 115 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7732 (p0) REVERT: C 146 ASN cc_start: 0.7954 (t0) cc_final: 0.7414 (t0) REVERT: C 182 GLU cc_start: 0.8290 (pm20) cc_final: 0.7739 (pm20) REVERT: C 272 ASN cc_start: 0.8366 (t0) cc_final: 0.8070 (t0) REVERT: C 421 TRP cc_start: 0.6834 (t-100) cc_final: 0.6463 (t-100) REVERT: C 458 ASN cc_start: 0.7934 (t0) cc_final: 0.7640 (t0) REVERT: C 525 ASP cc_start: 0.7875 (t70) cc_final: 0.7370 (t0) REVERT: C 558 PHE cc_start: 0.6274 (t80) cc_final: 0.5897 (t80) REVERT: C 608 LEU cc_start: 0.7847 (mt) cc_final: 0.7407 (pp) outliers start: 46 outliers final: 41 residues processed: 273 average time/residue: 0.2898 time to fit residues: 118.9705 Evaluate side-chains 265 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 220 time to evaluate : 1.875 ------------------------------------------------------------------------------- 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 511 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 481 MET 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 540 VAL Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 456 TRP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 540 VAL 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 190 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 GLN C 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17756 Z= 0.214 Angle : 0.523 7.520 24036 Z= 0.272 Chirality : 0.040 0.146 2624 Planarity : 0.003 0.036 2948 Dihedral : 12.391 161.809 2564 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.74 % Allowed : 18.56 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 2040 helix: 1.20 (0.15), residues: 1160 sheet: -1.00 (0.41), residues: 116 loop : -1.41 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.006 0.001 HIS C 484 PHE 0.022 0.002 PHE C 159 TYR 0.013 0.001 TYR D 363 ARG 0.012 0.000 ARG A 606 *********************** 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 282 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 231 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7755 (p0) REVERT: D 146 ASN cc_start: 0.7913 (t0) cc_final: 0.7390 (t0) REVERT: D 182 GLU cc_start: 0.8290 (pm20) cc_final: 0.7881 (pm20) REVERT: D 525 ASP cc_start: 0.7826 (t70) cc_final: 0.7277 (t70) REVERT: D 608 LEU cc_start: 0.7847 (mt) cc_final: 0.7415 (pp) REVERT: A 115 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7776 (p0) REVERT: A 146 ASN cc_start: 0.7950 (t0) cc_final: 0.7423 (t0) REVERT: A 525 ASP cc_start: 0.7793 (t70) cc_final: 0.7250 (t70) REVERT: A 558 PHE cc_start: 0.6244 (t80) cc_final: 0.5914 (t80) REVERT: A 588 PHE cc_start: 0.8222 (m-10) cc_final: 0.7969 (m-10) REVERT: B 115 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7798 (p0) REVERT: B 117 SER cc_start: 0.8297 (m) cc_final: 0.7870 (p) REVERT: B 146 ASN cc_start: 0.8083 (t0) cc_final: 0.7440 (t0) REVERT: B 272 ASN cc_start: 0.8520 (t0) cc_final: 0.8274 (t0) REVERT: B 507 LEU cc_start: 0.8233 (mm) cc_final: 0.8018 (mm) REVERT: B 525 ASP cc_start: 0.7871 (t70) cc_final: 0.7378 (t0) REVERT: B 558 PHE cc_start: 0.6246 (t80) cc_final: 0.5877 (t80) REVERT: B 608 LEU cc_start: 0.7834 (mt) cc_final: 0.7405 (pp) REVERT: C 115 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7763 (p0) REVERT: C 117 SER cc_start: 0.8282 (m) cc_final: 0.7880 (p) REVERT: C 146 ASN cc_start: 0.7958 (t0) cc_final: 0.7420 (t0) REVERT: C 182 GLU cc_start: 0.8297 (pm20) cc_final: 0.7878 (pm20) REVERT: C 272 ASN cc_start: 0.8396 (t0) cc_final: 0.8100 (t0) REVERT: C 458 ASN cc_start: 0.7933 (t0) cc_final: 0.7628 (t0) REVERT: C 525 ASP cc_start: 0.7886 (t70) cc_final: 0.7393 (t0) REVERT: C 558 PHE cc_start: 0.6217 (t80) cc_final: 0.5846 (t80) REVERT: C 608 LEU cc_start: 0.7871 (mt) cc_final: 0.7431 (pp) outliers start: 51 outliers final: 45 residues processed: 275 average time/residue: 0.3131 time to fit residues: 128.6658 Evaluate side-chains 273 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 224 time to evaluate : 2.252 ------------------------------------------------------------------------------- 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 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 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 540 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9980 chunk 78 optimal weight: 0.0670 chunk 117 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 433 GLN D 510 GLN A 458 ASN C 510 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17756 Z= 0.208 Angle : 0.528 8.364 24036 Z= 0.273 Chirality : 0.039 0.145 2624 Planarity : 0.003 0.041 2948 Dihedral : 12.172 158.853 2564 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.17 % Allowed : 18.45 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 2040 helix: 1.04 (0.15), residues: 1208 sheet: -0.88 (0.40), residues: 116 loop : -1.20 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 421 HIS 0.006 0.001 HIS C 484 PHE 0.022 0.001 PHE B 159 TYR 0.013 0.001 TYR D 363 ARG 0.011 0.000 ARG C 606 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 228 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7738 (p0) REVERT: D 146 ASN cc_start: 0.7895 (t0) cc_final: 0.7360 (t0) REVERT: D 182 GLU cc_start: 0.8259 (pm20) cc_final: 0.7864 (pm20) REVERT: D 245 TRP cc_start: 0.8270 (m100) cc_final: 0.8014 (m-10) REVERT: D 525 ASP cc_start: 0.7798 (t70) cc_final: 0.7285 (t70) REVERT: D 558 PHE cc_start: 0.6246 (t80) cc_final: 0.5919 (t80) REVERT: D 608 LEU cc_start: 0.7864 (mt) cc_final: 0.7443 (pp) REVERT: A 115 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7747 (p0) REVERT: A 117 SER cc_start: 0.8262 (m) cc_final: 0.7843 (p) REVERT: A 146 ASN cc_start: 0.7913 (t0) cc_final: 0.7375 (t0) REVERT: A 182 GLU cc_start: 0.8263 (pm20) cc_final: 0.7855 (pm20) REVERT: A 245 TRP cc_start: 0.8277 (m100) cc_final: 0.8034 (m-10) REVERT: A 525 ASP cc_start: 0.7806 (t70) cc_final: 0.7289 (t70) REVERT: A 558 PHE cc_start: 0.6228 (t80) cc_final: 0.5885 (t80) REVERT: A 588 PHE cc_start: 0.8182 (m-10) cc_final: 0.7967 (m-10) REVERT: B 115 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7778 (p0) REVERT: B 117 SER cc_start: 0.8282 (m) cc_final: 0.7865 (p) REVERT: B 146 ASN cc_start: 0.8049 (t0) cc_final: 0.7407 (t0) REVERT: B 272 ASN cc_start: 0.8526 (t0) cc_final: 0.8277 (t0) REVERT: B 525 ASP cc_start: 0.7862 (t70) cc_final: 0.7390 (t0) REVERT: B 608 LEU cc_start: 0.7847 (mt) cc_final: 0.7432 (pp) REVERT: C 115 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7748 (p0) REVERT: C 117 SER cc_start: 0.8273 (m) cc_final: 0.7868 (p) REVERT: C 146 ASN cc_start: 0.7905 (t0) cc_final: 0.7367 (t0) REVERT: C 272 ASN cc_start: 0.8442 (t0) cc_final: 0.8136 (t0) REVERT: C 525 ASP cc_start: 0.7869 (t70) cc_final: 0.7401 (t0) REVERT: C 608 LEU cc_start: 0.7853 (mt) cc_final: 0.7423 (pp) outliers start: 59 outliers final: 48 residues processed: 281 average time/residue: 0.2964 time to fit residues: 125.8845 Evaluate side-chains 278 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 226 time to evaluate : 1.892 ------------------------------------------------------------------------------- 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 511 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 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 504 GLU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 143 optimal weight: 0.3980 chunk 56 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN C 433 GLN C 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17756 Z= 0.212 Angle : 0.534 7.607 24036 Z= 0.276 Chirality : 0.040 0.145 2624 Planarity : 0.003 0.043 2948 Dihedral : 11.872 154.196 2564 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.90 % Allowed : 19.05 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 2040 helix: 1.09 (0.15), residues: 1208 sheet: -0.81 (0.41), residues: 116 loop : -1.17 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 421 HIS 0.006 0.001 HIS C 484 PHE 0.030 0.002 PHE C 558 TYR 0.013 0.001 TYR D 363 ARG 0.013 0.000 ARG A 606 *********************** 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 281 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 227 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7761 (p0) REVERT: D 146 ASN cc_start: 0.7877 (t0) cc_final: 0.7354 (t0) REVERT: D 245 TRP cc_start: 0.8295 (m100) cc_final: 0.8025 (m-10) REVERT: D 505 LEU cc_start: 0.8469 (tp) cc_final: 0.8080 (mp) REVERT: D 525 ASP cc_start: 0.7827 (t70) cc_final: 0.7327 (t70) REVERT: D 558 PHE cc_start: 0.6226 (t80) cc_final: 0.5920 (t80) REVERT: D 608 LEU cc_start: 0.7826 (mt) cc_final: 0.7405 (pp) REVERT: A 115 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7730 (p0) REVERT: A 117 SER cc_start: 0.8257 (m) cc_final: 0.7834 (p) REVERT: A 146 ASN cc_start: 0.7879 (t0) cc_final: 0.7357 (t0) REVERT: A 245 TRP cc_start: 0.8284 (m100) cc_final: 0.8025 (m-10) REVERT: A 525 ASP cc_start: 0.7812 (t70) cc_final: 0.7302 (t70) REVERT: A 558 PHE cc_start: 0.6214 (t80) cc_final: 0.5890 (t80) REVERT: A 588 PHE cc_start: 0.8166 (m-10) cc_final: 0.7964 (m-10) REVERT: B 115 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7765 (p0) REVERT: B 117 SER cc_start: 0.8282 (m) cc_final: 0.7868 (p) REVERT: B 146 ASN cc_start: 0.8031 (t0) cc_final: 0.7397 (t0) REVERT: B 272 ASN cc_start: 0.8531 (t0) cc_final: 0.8293 (t0) REVERT: B 525 ASP cc_start: 0.7852 (t70) cc_final: 0.7403 (t0) REVERT: B 558 PHE cc_start: 0.6274 (t80) cc_final: 0.5957 (t80) REVERT: B 608 LEU cc_start: 0.7830 (mt) cc_final: 0.7417 (pp) REVERT: C 115 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7753 (p0) REVERT: C 117 SER cc_start: 0.8268 (m) cc_final: 0.7857 (p) REVERT: C 146 ASN cc_start: 0.7878 (t0) cc_final: 0.7353 (t0) REVERT: C 182 GLU cc_start: 0.8290 (pm20) cc_final: 0.7907 (pm20) REVERT: C 272 ASN cc_start: 0.8455 (t0) cc_final: 0.8135 (t0) REVERT: C 525 ASP cc_start: 0.7867 (t70) cc_final: 0.7429 (t0) REVERT: C 558 PHE cc_start: 0.6206 (t80) cc_final: 0.5949 (t80) REVERT: C 608 LEU cc_start: 0.7808 (mt) cc_final: 0.7400 (pp) outliers start: 54 outliers final: 48 residues processed: 274 average time/residue: 0.3009 time to fit residues: 122.0985 Evaluate side-chains 276 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 224 time to evaluate : 1.793 ------------------------------------------------------------------------------- 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 511 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 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 540 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 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 504 GLU Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 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 504 GLU 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 193 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17756 Z= 0.188 Angle : 0.527 7.751 24036 Z= 0.273 Chirality : 0.039 0.141 2624 Planarity : 0.003 0.047 2948 Dihedral : 11.326 144.175 2564 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.74 % Allowed : 19.26 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2040 helix: 1.22 (0.15), residues: 1208 sheet: -0.73 (0.40), residues: 116 loop : -1.15 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 421 HIS 0.008 0.001 HIS D 484 PHE 0.027 0.002 PHE C 558 TYR 0.011 0.001 TYR C 363 ARG 0.015 0.000 ARG D 606 ********************** 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 281 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 230 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7750 (p0) REVERT: D 117 SER cc_start: 0.8231 (m) cc_final: 0.7844 (p) REVERT: D 146 ASN cc_start: 0.7895 (t0) cc_final: 0.7361 (t0) REVERT: D 245 TRP cc_start: 0.8295 (m100) cc_final: 0.8009 (m-10) REVERT: D 505 LEU cc_start: 0.8438 (tp) cc_final: 0.8054 (mp) REVERT: D 525 ASP cc_start: 0.7870 (t70) cc_final: 0.7409 (t70) REVERT: D 558 PHE cc_start: 0.6211 (t80) cc_final: 0.5909 (t80) REVERT: D 608 LEU cc_start: 0.7799 (mt) cc_final: 0.7365 (pp) REVERT: A 115 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7763 (p0) REVERT: A 117 SER cc_start: 0.8227 (m) cc_final: 0.7835 (p) REVERT: A 146 ASN cc_start: 0.7898 (t0) cc_final: 0.7364 (t0) REVERT: A 245 TRP cc_start: 0.8295 (m100) cc_final: 0.8007 (m-10) REVERT: A 525 ASP cc_start: 0.7821 (t70) cc_final: 0.7339 (t70) REVERT: A 558 PHE cc_start: 0.6177 (t80) cc_final: 0.5871 (t80) REVERT: A 588 PHE cc_start: 0.8168 (m-10) cc_final: 0.7949 (m-10) REVERT: B 115 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7750 (p0) REVERT: B 117 SER cc_start: 0.8244 (m) cc_final: 0.7862 (p) REVERT: B 146 ASN cc_start: 0.7955 (t0) cc_final: 0.7330 (t0) REVERT: B 245 TRP cc_start: 0.8260 (m100) cc_final: 0.7931 (m-10) REVERT: B 272 ASN cc_start: 0.8512 (t0) cc_final: 0.8279 (t0) REVERT: B 525 ASP cc_start: 0.7876 (t70) cc_final: 0.7456 (t0) REVERT: B 608 LEU cc_start: 0.7793 (mt) cc_final: 0.7393 (pp) REVERT: C 115 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7724 (p0) REVERT: C 117 SER cc_start: 0.8221 (m) cc_final: 0.7837 (p) REVERT: C 146 ASN cc_start: 0.7892 (t0) cc_final: 0.7352 (t0) REVERT: C 182 GLU cc_start: 0.8266 (pm20) cc_final: 0.7889 (pm20) REVERT: C 245 TRP cc_start: 0.8253 (m100) cc_final: 0.7933 (m-10) REVERT: C 272 ASN cc_start: 0.8463 (t0) cc_final: 0.8167 (t0) REVERT: C 525 ASP cc_start: 0.7898 (t70) cc_final: 0.7472 (t0) REVERT: C 558 PHE cc_start: 0.6147 (t80) cc_final: 0.5912 (t80) REVERT: C 608 LEU cc_start: 0.7795 (mt) cc_final: 0.7382 (pp) outliers start: 51 outliers final: 47 residues processed: 274 average time/residue: 0.3111 time to fit residues: 127.6272 Evaluate side-chains 275 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 224 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 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 540 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 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 549 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 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 504 GLU 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 172 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 162 optimal weight: 0.0470 chunk 67 optimal weight: 0.0470 chunk 166 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.173973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.126521 restraints weight = 23133.552| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.12 r_work: 0.3421 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17756 Z= 0.137 Angle : 0.499 7.459 24036 Z= 0.258 Chirality : 0.038 0.130 2624 Planarity : 0.003 0.049 2948 Dihedral : 9.946 113.055 2564 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.09 % Allowed : 20.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 2040 helix: 1.55 (0.15), residues: 1208 sheet: -0.49 (0.40), residues: 116 loop : -1.13 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 421 HIS 0.006 0.001 HIS C 484 PHE 0.026 0.001 PHE B 159 TYR 0.010 0.001 TYR B 365 ARG 0.015 0.000 ARG B 606 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.59 seconds wall clock time: 68 minutes 2.95 seconds (4082.95 seconds total)