Starting phenix.real_space_refine on Sun May 11 09:05:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afm_15402/05_2025/8afm_15402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afm_15402/05_2025/8afm_15402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8afm_15402/05_2025/8afm_15402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afm_15402/05_2025/8afm_15402.map" model { file = "/net/cci-nas-00/data/ceres_data/8afm_15402/05_2025/8afm_15402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afm_15402/05_2025/8afm_15402.cif" } resolution = 4.8 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= 0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4754 2.51 5 N 1492 2.21 5 O 1568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7842 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "B" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "E" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 455 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "G" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "I" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "K" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "L" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 455 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Time building chain proxies: 4.87, per 1000 atoms: 0.62 Number of scatterers: 7842 At special positions: 0 Unit cell: (212.544, 98.496, 86.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1568 8.00 N 1492 7.00 C 4754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 795 " - pdb=" SG CYS D 868 " distance=2.03 Simple disulfide: pdb=" SG CYS C 795 " - pdb=" SG CYS C 868 " distance=2.04 Simple disulfide: pdb=" SG CYS J 795 " - pdb=" SG CYS J 868 " distance=2.03 Simple disulfide: pdb=" SG CYS I 795 " - pdb=" SG CYS I 868 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 975.1 milliseconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 58.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 369 through 419 removed outlier: 3.537A pdb=" N LYS A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.766A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 removed outlier: 4.228A pdb=" N LEU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.846A pdb=" N LYS B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 391 " --> pdb=" O GLN B 387 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 429 removed outlier: 3.517A pdb=" N ALA B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 410 " --> pdb=" O HIS B 406 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.606A pdb=" N ALA B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'D' and resid 833 through 837 removed outlier: 3.505A pdb=" N LYS D 837 " --> pdb=" O ASP D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 863 removed outlier: 4.111A pdb=" N THR D 863 " --> pdb=" O PRO D 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 863 removed outlier: 3.537A pdb=" N THR C 863 " --> pdb=" O PRO C 860 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 155 removed outlier: 3.911A pdb=" N GLN E 105 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 155 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 160 removed outlier: 3.631A pdb=" N SER E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'F' and resid 97 through 139 removed outlier: 3.522A pdb=" N LEU F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F 106 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU F 124 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN F 139 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 154 removed outlier: 3.894A pdb=" N ILE F 143 " --> pdb=" O ASN F 139 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN F 148 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 419 removed outlier: 3.537A pdb=" N LYS G 376 " --> pdb=" O VAL G 372 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA G 377 " --> pdb=" O ALA G 373 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 378 " --> pdb=" O GLN G 374 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU G 382 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA G 390 " --> pdb=" O GLN G 386 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG G 391 " --> pdb=" O GLN G 387 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN G 396 " --> pdb=" O LEU G 392 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU G 407 " --> pdb=" O ARG G 403 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 408 " --> pdb=" O ARG G 404 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE G 410 " --> pdb=" O HIS G 406 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G 411 " --> pdb=" O GLU G 407 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR G 416 " --> pdb=" O GLU G 412 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 434 removed outlier: 3.766A pdb=" N LEU G 426 " --> pdb=" O SER G 422 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU G 428 " --> pdb=" O ALA G 424 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA G 430 " --> pdb=" O LEU G 426 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU G 431 " --> pdb=" O ALA G 427 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA G 434 " --> pdb=" O ALA G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 443 removed outlier: 4.228A pdb=" N LEU G 441 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 401 removed outlier: 3.846A pdb=" N LYS H 379 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG H 380 " --> pdb=" O LYS H 376 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA H 381 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU H 383 " --> pdb=" O LYS H 379 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN H 386 " --> pdb=" O GLU H 382 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG H 391 " --> pdb=" O GLN H 387 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU H 392 " --> pdb=" O LEU H 388 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN H 399 " --> pdb=" O MET H 395 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP H 400 " --> pdb=" O GLN H 396 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN H 401 " --> pdb=" O GLU H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 429 removed outlier: 3.516A pdb=" N ALA H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE H 410 " --> pdb=" O HIS H 406 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 411 " --> pdb=" O GLU H 407 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR H 416 " --> pdb=" O GLU H 412 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE H 417 " --> pdb=" O LEU H 413 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU H 418 " --> pdb=" O GLN H 414 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR H 421 " --> pdb=" O ILE H 417 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H 426 " --> pdb=" O SER H 422 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY H 429 " --> pdb=" O ALA H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 434 removed outlier: 3.606A pdb=" N ALA H 434 " --> pdb=" O ALA H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 439 Processing helix chain 'H' and resid 440 through 443 Processing helix chain 'J' and resid 833 through 837 removed outlier: 3.505A pdb=" N LYS J 837 " --> pdb=" O ASP J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 859 through 863 removed outlier: 4.111A pdb=" N THR J 863 " --> pdb=" O PRO J 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 859 through 863 removed outlier: 3.536A pdb=" N THR I 863 " --> pdb=" O PRO I 860 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 155 removed outlier: 3.911A pdb=" N GLN K 105 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA K 106 " --> pdb=" O ALA K 102 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA K 116 " --> pdb=" O SER K 112 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU K 137 " --> pdb=" O ASP K 133 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG K 145 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU K 146 " --> pdb=" O GLU K 142 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU K 155 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 160 removed outlier: 3.631A pdb=" N SER K 159 " --> pdb=" O LEU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'L' and resid 97 through 139 removed outlier: 3.523A pdb=" N LEU L 103 " --> pdb=" O ARG L 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA L 106 " --> pdb=" O ALA L 102 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU L 124 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN L 139 " --> pdb=" O ALA L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 154 removed outlier: 3.893A pdb=" N ILE L 143 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN L 148 " --> pdb=" O ASP L 144 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER L 153 " --> pdb=" O ALA L 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7 removed outlier: 4.036A pdb=" N CYS D 795 " --> pdb=" O VAL D 851 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL D 851 " --> pdb=" O CYS D 795 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 841 " --> pdb=" O GLN D 854 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 818 through 824 removed outlier: 3.561A pdb=" N GLY D 819 " --> pdb=" O ARG D 811 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP D 809 " --> pdb=" O VAL D 821 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL D 823 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N MET D 807 " --> pdb=" O VAL D 823 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 869 through 872 removed outlier: 3.693A pdb=" N ALA D 870 " --> pdb=" O TYR D 877 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 790 through 795 removed outlier: 3.516A pdb=" N CYS C 795 " --> pdb=" O VAL C 851 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN C 831 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 823 " --> pdb=" O ASN C 831 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 821 " --> pdb=" O TRP C 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 870 " --> pdb=" O TYR C 877 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN C 831 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 823 " --> pdb=" O ASN C 831 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 821 " --> pdb=" O TRP C 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 5 through 7 removed outlier: 4.036A pdb=" N CYS J 795 " --> pdb=" O VAL J 851 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL J 851 " --> pdb=" O CYS J 795 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE J 841 " --> pdb=" O GLN J 854 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 818 through 824 removed outlier: 3.562A pdb=" N GLY J 819 " --> pdb=" O ARG J 811 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP J 809 " --> pdb=" O VAL J 821 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL J 823 " --> pdb=" O MET J 807 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N MET J 807 " --> pdb=" O VAL J 823 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 869 through 872 removed outlier: 3.694A pdb=" N ALA J 870 " --> pdb=" O TYR J 877 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 790 through 795 removed outlier: 3.515A pdb=" N CYS I 795 " --> pdb=" O VAL I 851 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN I 831 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL I 823 " --> pdb=" O ASN I 831 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 821 " --> pdb=" O TRP I 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA I 870 " --> pdb=" O TYR I 877 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN I 831 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL I 823 " --> pdb=" O ASN I 831 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 821 " --> pdb=" O TRP I 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2844 1.34 - 1.46: 1129 1.46 - 1.58: 3873 1.58 - 1.70: 0 1.70 - 1.81: 48 Bond restraints: 7894 Sorted by residual: bond pdb=" N LEU E 115 " pdb=" CA LEU E 115 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.78e+00 bond pdb=" N LEU K 115 " pdb=" CA LEU K 115 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.74e+00 bond pdb=" N ARG K 114 " pdb=" CA ARG K 114 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.71e+00 bond pdb=" N ARG E 114 " pdb=" CA ARG E 114 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.46e+00 bond pdb=" N ALA K 113 " pdb=" CA ALA K 113 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.69e+00 ... (remaining 7889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 10187 1.72 - 3.44: 371 3.44 - 5.17: 39 5.17 - 6.89: 5 6.89 - 8.61: 4 Bond angle restraints: 10606 Sorted by residual: angle pdb=" N GLY I 803 " pdb=" CA GLY I 803 " pdb=" C GLY I 803 " ideal model delta sigma weight residual 113.18 106.21 6.97 2.37e+00 1.78e-01 8.65e+00 angle pdb=" N GLY C 803 " pdb=" CA GLY C 803 " pdb=" C GLY C 803 " ideal model delta sigma weight residual 113.18 106.25 6.93 2.37e+00 1.78e-01 8.55e+00 angle pdb=" N ALA C 864 " pdb=" CA ALA C 864 " pdb=" C ALA C 864 " ideal model delta sigma weight residual 107.88 111.58 -3.70 1.41e+00 5.03e-01 6.88e+00 angle pdb=" CA ARG K 99 " pdb=" CB ARG K 99 " pdb=" CG ARG K 99 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.85e+00 angle pdb=" N ALA I 864 " pdb=" CA ALA I 864 " pdb=" C ALA I 864 " ideal model delta sigma weight residual 107.88 111.56 -3.68 1.41e+00 5.03e-01 6.82e+00 ... (remaining 10601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4412 17.76 - 35.52: 412 35.52 - 53.27: 88 53.27 - 71.03: 12 71.03 - 88.79: 18 Dihedral angle restraints: 4942 sinusoidal: 2012 harmonic: 2930 Sorted by residual: dihedral pdb=" CB CYS I 795 " pdb=" SG CYS I 795 " pdb=" SG CYS I 868 " pdb=" CB CYS I 868 " ideal model delta sinusoidal sigma weight residual 93.00 47.66 45.34 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS C 795 " pdb=" SG CYS C 795 " pdb=" SG CYS C 868 " pdb=" CB CYS C 868 " ideal model delta sinusoidal sigma weight residual 93.00 47.67 45.33 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CA ILE D 804 " pdb=" C ILE D 804 " pdb=" N ASN D 805 " pdb=" CA ASN D 805 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 4939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 683 0.028 - 0.057: 311 0.057 - 0.085: 126 0.085 - 0.114: 46 0.114 - 0.142: 26 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA LEU E 115 " pdb=" N LEU E 115 " pdb=" C LEU E 115 " pdb=" CB LEU E 115 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ASN J 857 " pdb=" N ASN J 857 " pdb=" C ASN J 857 " pdb=" CB ASN J 857 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA LEU K 115 " pdb=" N LEU K 115 " pdb=" C LEU K 115 " pdb=" CB LEU K 115 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1189 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 827 " -0.015 2.00e-02 2.50e+03 9.58e-03 2.29e+00 pdb=" CG TRP D 827 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP D 827 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 827 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 827 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 827 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 827 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 827 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 827 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 827 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 827 " 0.015 2.00e-02 2.50e+03 9.38e-03 2.20e+00 pdb=" CG TRP J 827 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP J 827 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP J 827 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 827 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 827 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 827 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 827 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 827 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 827 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 809 " -0.013 2.00e-02 2.50e+03 9.04e-03 2.04e+00 pdb=" CG TRP I 809 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP I 809 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP I 809 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 809 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 809 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I 809 " 0.001 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 309 2.70 - 3.25: 8455 3.25 - 3.80: 11709 3.80 - 4.35: 15177 4.35 - 4.90: 23284 Nonbonded interactions: 58934 Sorted by model distance: nonbonded pdb=" OE1 GLN J 883 " pdb=" OG1 THR J 885 " model vdw 2.153 3.040 nonbonded pdb=" OE1 GLN D 883 " pdb=" OG1 THR D 885 " model vdw 2.153 3.040 nonbonded pdb=" O LEU C 791 " pdb=" NE2 GLN C 854 " model vdw 2.157 3.120 nonbonded pdb=" O LEU I 791 " pdb=" NE2 GLN I 854 " model vdw 2.157 3.120 nonbonded pdb=" O LEU K 160 " pdb=" OG SER K 163 " model vdw 2.157 3.040 ... (remaining 58929 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'E' and resid 96 through 154) selection = chain 'F' selection = (chain 'K' and resid 96 through 154) selection = chain 'L' } 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 group one per residue 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.850 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5120 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 : 0.004 0.033 7898 Z= 0.214 Angle : 0.744 8.610 10614 Z= 0.446 Chirality : 0.042 0.142 1192 Planarity : 0.003 0.029 1416 Dihedral : 15.273 88.790 3022 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.25 % Allowed : 0.25 % Favored : 99.50 % 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: -3.48 (0.24), residues: 978 helix: -2.28 (0.20), residues: 504 sheet: -2.15 (0.40), residues: 166 loop : -1.97 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP D 827 HIS 0.002 0.001 HIS H 406 PHE 0.010 0.003 PHE D 840 TYR 0.019 0.002 TYR C 872 ARG 0.020 0.001 ARG B 380 Details of bonding type rmsd hydrogen bonds : bond 0.30317 ( 418) hydrogen bonds : angle 11.34145 ( 1236) SS BOND : bond 0.00658 ( 4) SS BOND : angle 1.33673 ( 8) covalent geometry : bond 0.00411 ( 7894) covalent geometry : angle 0.74289 (10606) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 256 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 GLU cc_start: 0.6981 (mm-30) cc_final: 0.5861 (mt-10) REVERT: B 419 ARG cc_start: 0.4921 (tpp80) cc_final: 0.4551 (tpp80) REVERT: D 820 MET cc_start: 0.5763 (mpp) cc_final: 0.5553 (mpp) REVERT: D 877 TYR cc_start: 0.5320 (m-80) cc_final: 0.4962 (m-80) REVERT: C 6 GLU cc_start: 0.6366 (tm-30) cc_final: 0.5971 (pt0) REVERT: C 798 SER cc_start: 0.8393 (t) cc_final: 0.7858 (m) REVERT: C 806 ILE cc_start: 0.7215 (tp) cc_final: 0.7013 (tp) REVERT: C 827 TRP cc_start: 0.6154 (m-90) cc_final: 0.4380 (m-90) REVERT: C 841 ILE cc_start: 0.7607 (mp) cc_final: 0.7345 (mm) REVERT: E 148 ASN cc_start: 0.8067 (m-40) cc_final: 0.7745 (t0) REVERT: F 108 GLU cc_start: 0.6685 (tp30) cc_final: 0.6201 (tp30) REVERT: F 133 ASP cc_start: 0.8257 (m-30) cc_final: 0.7702 (m-30) REVERT: F 136 LEU cc_start: 0.6453 (tp) cc_final: 0.6159 (mt) REVERT: F 139 ASN cc_start: 0.7392 (p0) cc_final: 0.7136 (p0) REVERT: G 395 MET cc_start: 0.5819 (mmm) cc_final: 0.5346 (ttt) REVERT: G 423 GLU cc_start: 0.7778 (tt0) cc_final: 0.7129 (tm-30) REVERT: G 438 ARG cc_start: 0.5662 (ptt-90) cc_final: 0.3368 (mmp-170) REVERT: J 807 MET cc_start: 0.3696 (ppp) cc_final: 0.2786 (ppp) REVERT: J 820 MET cc_start: 0.5423 (mpp) cc_final: 0.4849 (mpp) REVERT: I 807 MET cc_start: 0.6350 (ppp) cc_final: 0.5998 (ppp) REVERT: I 884 VAL cc_start: 0.7868 (t) cc_final: 0.5549 (t) REVERT: L 107 GLU cc_start: 0.7886 (tp30) cc_final: 0.7665 (mm-30) outliers start: 2 outliers final: 0 residues processed: 256 average time/residue: 0.3166 time to fit residues: 97.5787 Evaluate side-chains 191 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 0.0030 chunk 85 optimal weight: 5.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN C 805 ASN F 96 GLN F 130 GLN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 805 ASN L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.207801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.185239 restraints weight = 12799.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 82)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.183567 restraints weight = 14269.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.183373 restraints weight = 13976.335| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7898 Z= 0.186 Angle : 0.733 9.169 10614 Z= 0.382 Chirality : 0.045 0.153 1192 Planarity : 0.006 0.068 1416 Dihedral : 5.760 25.092 1126 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.12 % Allowed : 6.84 % Favored : 93.03 % 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: -2.18 (0.26), residues: 978 helix: -0.94 (0.22), residues: 520 sheet: -2.65 (0.42), residues: 138 loop : -1.37 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP J 827 HIS 0.007 0.004 HIS B 406 PHE 0.011 0.002 PHE J 840 TYR 0.019 0.002 TYR I 872 ARG 0.007 0.001 ARG L 145 Details of bonding type rmsd hydrogen bonds : bond 0.04962 ( 418) hydrogen bonds : angle 5.69050 ( 1236) SS BOND : bond 0.01273 ( 4) SS BOND : angle 0.90144 ( 8) covalent geometry : bond 0.00382 ( 7894) covalent geometry : angle 0.73331 (10606) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6146 (mm-30) REVERT: A 393 ASP cc_start: 0.6291 (m-30) cc_final: 0.6038 (m-30) REVERT: D 802 ASP cc_start: 0.3934 (t0) cc_final: 0.3485 (t0) REVERT: D 812 GLN cc_start: 0.5204 (mp10) cc_final: 0.3735 (mp10) REVERT: D 850 THR cc_start: 0.6572 (m) cc_final: 0.6125 (t) REVERT: D 873 ARG cc_start: 0.5967 (mpp-170) cc_final: 0.5735 (mpp-170) REVERT: D 877 TYR cc_start: 0.5865 (m-80) cc_final: 0.5172 (m-80) REVERT: C 798 SER cc_start: 0.8415 (t) cc_final: 0.8210 (m) REVERT: C 806 ILE cc_start: 0.7758 (tp) cc_final: 0.7486 (tp) REVERT: C 811 ARG cc_start: 0.5391 (ptt180) cc_final: 0.5091 (ttp80) REVERT: C 825 THR cc_start: 0.6820 (OUTLIER) cc_final: 0.6143 (m) REVERT: C 856 ASN cc_start: 0.8175 (t0) cc_final: 0.7920 (t0) REVERT: F 108 GLU cc_start: 0.6970 (tp30) cc_final: 0.6314 (tp30) REVERT: F 115 LEU cc_start: 0.8286 (mm) cc_final: 0.7992 (mm) REVERT: F 133 ASP cc_start: 0.7812 (m-30) cc_final: 0.7429 (m-30) REVERT: F 142 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6305 (tp30) REVERT: F 144 ASP cc_start: 0.6268 (m-30) cc_final: 0.5824 (m-30) REVERT: H 370 SER cc_start: 0.6847 (t) cc_final: 0.6536 (m) REVERT: J 808 ARG cc_start: 0.6041 (ptt-90) cc_final: 0.5615 (ptt90) REVERT: J 820 MET cc_start: 0.6058 (mpp) cc_final: 0.5357 (mpp) REVERT: I 802 ASP cc_start: 0.5418 (t70) cc_final: 0.5023 (t0) REVERT: I 807 MET cc_start: 0.6537 (ppp) cc_final: 0.6017 (ppp) REVERT: I 884 VAL cc_start: 0.7786 (t) cc_final: 0.6117 (t) REVERT: K 148 ASN cc_start: 0.7609 (t0) cc_final: 0.7377 (t0) REVERT: L 115 LEU cc_start: 0.8613 (mm) cc_final: 0.8145 (mm) REVERT: L 132 GLN cc_start: 0.8281 (mp-120) cc_final: 0.7891 (pp30) REVERT: L 142 GLU cc_start: 0.5487 (tm-30) cc_final: 0.4662 (tm-30) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.2982 time to fit residues: 83.8925 Evaluate side-chains 198 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.0070 chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 GLN H 387 GLN L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.202736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.175877 restraints weight = 12806.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.171702 restraints weight = 11062.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.172490 restraints weight = 9392.893| |-----------------------------------------------------------------------------| r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7898 Z= 0.138 Angle : 0.633 7.392 10614 Z= 0.332 Chirality : 0.042 0.181 1192 Planarity : 0.005 0.056 1416 Dihedral : 5.180 22.273 1126 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.12 % Allowed : 4.73 % Favored : 95.15 % 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: -1.52 (0.27), residues: 978 helix: -0.46 (0.22), residues: 508 sheet: -2.00 (0.40), residues: 168 loop : -0.97 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 878 HIS 0.005 0.002 HIS H 406 PHE 0.005 0.001 PHE J 840 TYR 0.009 0.001 TYR I 832 ARG 0.015 0.001 ARG B 435 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 418) hydrogen bonds : angle 4.97032 ( 1236) SS BOND : bond 0.00365 ( 4) SS BOND : angle 0.55393 ( 8) covalent geometry : bond 0.00285 ( 7894) covalent geometry : angle 0.63281 (10606) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ARG cc_start: 0.5008 (ptp-170) cc_final: 0.4714 (ptp-170) REVERT: D 812 GLN cc_start: 0.5081 (mp10) cc_final: 0.4596 (mt0) REVERT: D 850 THR cc_start: 0.6328 (m) cc_final: 0.5651 (t) REVERT: D 865 VAL cc_start: 0.5797 (t) cc_final: 0.4379 (p) REVERT: D 877 TYR cc_start: 0.5985 (m-80) cc_final: 0.5454 (m-80) REVERT: C 811 ARG cc_start: 0.5740 (ptt180) cc_final: 0.4947 (ttp80) REVERT: C 827 TRP cc_start: 0.6852 (m-90) cc_final: 0.4973 (m-90) REVERT: F 104 ILE cc_start: 0.7353 (tt) cc_final: 0.6891 (tt) REVERT: F 107 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6779 (mm-30) REVERT: F 108 GLU cc_start: 0.7336 (tp30) cc_final: 0.6778 (tp30) REVERT: F 129 ARG cc_start: 0.7672 (tpt-90) cc_final: 0.7467 (tpt-90) REVERT: F 133 ASP cc_start: 0.7795 (m-30) cc_final: 0.7418 (m-30) REVERT: F 139 ASN cc_start: 0.7326 (p0) cc_final: 0.6899 (p0) REVERT: F 142 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7417 (tm-30) REVERT: F 144 ASP cc_start: 0.6804 (m-30) cc_final: 0.6531 (m-30) REVERT: G 375 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6301 (mt-10) REVERT: H 370 SER cc_start: 0.6664 (t) cc_final: 0.6451 (m) REVERT: J 807 MET cc_start: 0.3158 (ppp) cc_final: 0.2079 (ppp) REVERT: J 808 ARG cc_start: 0.4765 (ptt-90) cc_final: 0.4136 (ptt180) REVERT: J 848 LYS cc_start: 0.7067 (tptp) cc_final: 0.6797 (tptp) REVERT: I 793 LEU cc_start: 0.4938 (mt) cc_final: 0.4619 (mt) REVERT: I 802 ASP cc_start: 0.5671 (t70) cc_final: 0.4621 (t0) REVERT: I 807 MET cc_start: 0.6825 (ppp) cc_final: 0.6191 (ppp) REVERT: I 823 VAL cc_start: 0.7507 (p) cc_final: 0.7249 (p) REVERT: I 853 LEU cc_start: 0.6586 (tp) cc_final: 0.6137 (tp) REVERT: I 855 MET cc_start: 0.6035 (mmp) cc_final: 0.5756 (mmm) REVERT: I 884 VAL cc_start: 0.7764 (t) cc_final: 0.6285 (t) REVERT: K 126 ASP cc_start: 0.7605 (m-30) cc_final: 0.6707 (p0) REVERT: K 148 ASN cc_start: 0.7994 (t0) cc_final: 0.7755 (m-40) REVERT: K 156 LYS cc_start: 0.7644 (mppt) cc_final: 0.7416 (mppt) REVERT: L 107 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7519 (mm-30) REVERT: L 115 LEU cc_start: 0.8743 (mm) cc_final: 0.8347 (mm) REVERT: L 132 GLN cc_start: 0.8513 (mp-120) cc_final: 0.8132 (pp30) REVERT: L 142 GLU cc_start: 0.6513 (tm-30) cc_final: 0.6278 (tm-30) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.2914 time to fit residues: 79.3886 Evaluate side-chains 200 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.8980 chunk 13 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 52 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN H 387 GLN L 100 GLN L 130 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.204093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.174976 restraints weight = 12417.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.173133 restraints weight = 10461.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.174336 restraints weight = 8259.012| |-----------------------------------------------------------------------------| r_work (final): 0.4495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7898 Z= 0.119 Angle : 0.588 7.272 10614 Z= 0.306 Chirality : 0.040 0.147 1192 Planarity : 0.004 0.047 1416 Dihedral : 4.810 20.425 1126 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.00 (0.27), residues: 978 helix: -0.01 (0.23), residues: 498 sheet: -1.75 (0.41), residues: 168 loop : -0.78 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 827 HIS 0.003 0.002 HIS H 406 PHE 0.006 0.001 PHE J 840 TYR 0.010 0.001 TYR C 866 ARG 0.007 0.001 ARG D 818 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 418) hydrogen bonds : angle 4.57710 ( 1236) SS BOND : bond 0.00555 ( 4) SS BOND : angle 0.61913 ( 8) covalent geometry : bond 0.00240 ( 7894) covalent geometry : angle 0.58767 (10606) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.6124 (mm-30) cc_final: 0.5920 (mm-30) REVERT: A 389 ARG cc_start: 0.4652 (ptp-170) cc_final: 0.4323 (ptp-170) REVERT: D 812 GLN cc_start: 0.5170 (mp10) cc_final: 0.4351 (mt0) REVERT: D 850 THR cc_start: 0.6327 (m) cc_final: 0.5469 (t) REVERT: D 865 VAL cc_start: 0.5505 (t) cc_final: 0.3598 (p) REVERT: D 877 TYR cc_start: 0.6068 (m-80) cc_final: 0.5462 (m-80) REVERT: C 806 ILE cc_start: 0.7707 (tp) cc_final: 0.7381 (tp) REVERT: C 811 ARG cc_start: 0.5859 (ptt180) cc_final: 0.5048 (ttp80) REVERT: C 820 MET cc_start: 0.6832 (ptt) cc_final: 0.6627 (ppp) REVERT: C 825 THR cc_start: 0.7649 (OUTLIER) cc_final: 0.7100 (t) REVERT: C 861 GLU cc_start: 0.7919 (tp30) cc_final: 0.7657 (tp30) REVERT: E 119 GLU cc_start: 0.7106 (pp20) cc_final: 0.6726 (mm-30) REVERT: E 120 THR cc_start: 0.7207 (m) cc_final: 0.6294 (m) REVERT: E 145 ARG cc_start: 0.7477 (mtt180) cc_final: 0.7131 (mtt180) REVERT: F 107 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7051 (mm-30) REVERT: F 108 GLU cc_start: 0.7243 (tp30) cc_final: 0.6834 (tp30) REVERT: F 115 LEU cc_start: 0.8490 (mm) cc_final: 0.8190 (mm) REVERT: F 142 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7514 (tm-30) REVERT: F 144 ASP cc_start: 0.7005 (m-30) cc_final: 0.6669 (m-30) REVERT: H 389 ARG cc_start: 0.6468 (tpp-160) cc_final: 0.6068 (tpt170) REVERT: J 807 MET cc_start: 0.3297 (ppp) cc_final: 0.2018 (ppp) REVERT: J 808 ARG cc_start: 0.4922 (ptt-90) cc_final: 0.4163 (ptt180) REVERT: I 793 LEU cc_start: 0.4967 (mt) cc_final: 0.4712 (mt) REVERT: I 802 ASP cc_start: 0.4609 (t70) cc_final: 0.3981 (t70) REVERT: I 807 MET cc_start: 0.6902 (ppp) cc_final: 0.6604 (ppp) REVERT: I 823 VAL cc_start: 0.7527 (p) cc_final: 0.7271 (p) REVERT: I 853 LEU cc_start: 0.6859 (tp) cc_final: 0.6436 (tp) REVERT: I 855 MET cc_start: 0.6312 (mmp) cc_final: 0.5936 (mmm) REVERT: I 884 VAL cc_start: 0.7828 (t) cc_final: 0.6635 (t) REVERT: K 126 ASP cc_start: 0.7795 (m-30) cc_final: 0.7549 (p0) REVERT: K 129 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7934 (tmm-80) REVERT: K 156 LYS cc_start: 0.7598 (mppt) cc_final: 0.7392 (mppt) REVERT: L 105 GLN cc_start: 0.6879 (tm-30) cc_final: 0.6414 (tm-30) REVERT: L 107 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7847 (mm-30) REVERT: L 115 LEU cc_start: 0.8772 (mm) cc_final: 0.8376 (mm) REVERT: L 119 GLU cc_start: 0.8583 (pp20) cc_final: 0.8306 (pp20) REVERT: L 131 THR cc_start: 0.8064 (p) cc_final: 0.7736 (p) REVERT: L 132 GLN cc_start: 0.8606 (mp-120) cc_final: 0.8021 (pp30) REVERT: L 142 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6550 (tm-30) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.2875 time to fit residues: 78.7555 Evaluate side-chains 199 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN H 387 GLN I 857 ASN L 100 GLN L 130 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.199025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.175739 restraints weight = 12763.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.175967 restraints weight = 14960.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.176385 restraints weight = 12134.322| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7898 Z= 0.147 Angle : 0.639 9.212 10614 Z= 0.333 Chirality : 0.042 0.170 1192 Planarity : 0.005 0.058 1416 Dihedral : 4.950 20.074 1126 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.12 % Allowed : 3.86 % Favored : 96.02 % 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: -0.97 (0.28), residues: 978 helix: -0.01 (0.23), residues: 508 sheet: -1.69 (0.41), residues: 168 loop : -0.78 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 827 HIS 0.006 0.003 HIS H 406 PHE 0.005 0.001 PHE J 840 TYR 0.012 0.001 TYR C 866 ARG 0.013 0.001 ARG K 128 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 418) hydrogen bonds : angle 4.60023 ( 1236) SS BOND : bond 0.00513 ( 4) SS BOND : angle 0.74386 ( 8) covalent geometry : bond 0.00309 ( 7894) covalent geometry : angle 0.63933 (10606) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 812 GLN cc_start: 0.5324 (mp10) cc_final: 0.4621 (mt0) REVERT: D 850 THR cc_start: 0.6031 (m) cc_final: 0.5321 (t) REVERT: D 865 VAL cc_start: 0.6459 (t) cc_final: 0.4316 (p) REVERT: C 806 ILE cc_start: 0.7788 (tp) cc_final: 0.7515 (tp) REVERT: C 811 ARG cc_start: 0.5786 (ptt180) cc_final: 0.5027 (ttp80) REVERT: C 823 VAL cc_start: 0.7175 (p) cc_final: 0.6870 (p) REVERT: C 827 TRP cc_start: 0.5673 (m-90) cc_final: 0.4713 (m-90) REVERT: C 861 GLU cc_start: 0.8251 (tp30) cc_final: 0.7691 (tp30) REVERT: E 119 GLU cc_start: 0.6656 (pp20) cc_final: 0.6423 (pp20) REVERT: E 145 ARG cc_start: 0.6270 (mtt180) cc_final: 0.6040 (mtt180) REVERT: F 107 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7043 (mm-30) REVERT: F 108 GLU cc_start: 0.7146 (tp30) cc_final: 0.6527 (tp30) REVERT: F 115 LEU cc_start: 0.8371 (mm) cc_final: 0.8069 (mm) REVERT: F 129 ARG cc_start: 0.7363 (tpt-90) cc_final: 0.7114 (tpt90) REVERT: F 133 ASP cc_start: 0.7876 (m-30) cc_final: 0.7151 (m-30) REVERT: F 142 GLU cc_start: 0.6896 (tm-30) cc_final: 0.6595 (tp30) REVERT: F 144 ASP cc_start: 0.6481 (m-30) cc_final: 0.6075 (m-30) REVERT: G 389 ARG cc_start: 0.6030 (ptm160) cc_final: 0.5619 (ptm-80) REVERT: G 422 SER cc_start: 0.3627 (p) cc_final: 0.3291 (p) REVERT: H 443 MET cc_start: 0.1717 (ptt) cc_final: 0.1312 (ptt) REVERT: J 807 MET cc_start: 0.3611 (ppp) cc_final: 0.1960 (ppp) REVERT: J 808 ARG cc_start: 0.5424 (ptt-90) cc_final: 0.3445 (mtm180) REVERT: I 802 ASP cc_start: 0.5409 (t70) cc_final: 0.4650 (t70) REVERT: I 807 MET cc_start: 0.6907 (ppp) cc_final: 0.6462 (ppp) REVERT: I 823 VAL cc_start: 0.7556 (p) cc_final: 0.7264 (p) REVERT: I 884 VAL cc_start: 0.7840 (t) cc_final: 0.6552 (t) REVERT: K 114 ARG cc_start: 0.8002 (ptt-90) cc_final: 0.7795 (ptt-90) REVERT: K 150 LEU cc_start: 0.7982 (tp) cc_final: 0.7780 (tt) REVERT: K 156 LYS cc_start: 0.7909 (mppt) cc_final: 0.7220 (mppt) REVERT: L 105 GLN cc_start: 0.6972 (tm-30) cc_final: 0.6373 (tm-30) REVERT: L 107 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7602 (mm-30) REVERT: L 115 LEU cc_start: 0.8594 (mm) cc_final: 0.8211 (mm) REVERT: L 132 GLN cc_start: 0.8210 (mp-120) cc_final: 0.7947 (pp30) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.2949 time to fit residues: 78.9286 Evaluate side-chains 195 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 83 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 5 optimal weight: 0.0370 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.4520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN I 805 ASN L 100 GLN L 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.201490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 126)---------------| | r_work = 0.4484 r_free = 0.4484 target = 0.172941 restraints weight = 12615.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.172770 restraints weight = 10170.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.173270 restraints weight = 8303.436| |-----------------------------------------------------------------------------| r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5621 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7898 Z= 0.127 Angle : 0.601 7.537 10614 Z= 0.317 Chirality : 0.041 0.156 1192 Planarity : 0.004 0.051 1416 Dihedral : 4.704 20.185 1126 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.93 (0.27), residues: 978 helix: 0.08 (0.23), residues: 514 sheet: -1.57 (0.41), residues: 172 loop : -0.96 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 827 HIS 0.004 0.002 HIS G 406 PHE 0.005 0.001 PHE I 840 TYR 0.010 0.001 TYR J 832 ARG 0.005 0.000 ARG I 799 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 418) hydrogen bonds : angle 4.38584 ( 1236) SS BOND : bond 0.00762 ( 4) SS BOND : angle 1.41416 ( 8) covalent geometry : bond 0.00260 ( 7894) covalent geometry : angle 0.59968 (10606) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ARG cc_start: 0.4572 (ptp-170) cc_final: 0.4221 (ptt-90) REVERT: D 812 GLN cc_start: 0.5144 (mp10) cc_final: 0.4474 (mt0) REVERT: D 865 VAL cc_start: 0.5848 (t) cc_final: 0.4011 (p) REVERT: C 806 ILE cc_start: 0.7839 (tp) cc_final: 0.7613 (tp) REVERT: C 811 ARG cc_start: 0.5871 (ptt180) cc_final: 0.5503 (ttp-170) REVERT: C 825 THR cc_start: 0.7807 (t) cc_final: 0.7378 (t) REVERT: C 827 TRP cc_start: 0.6113 (m-90) cc_final: 0.4448 (m-90) REVERT: C 861 GLU cc_start: 0.8407 (tp30) cc_final: 0.8013 (tp30) REVERT: E 114 ARG cc_start: 0.8131 (ptp90) cc_final: 0.7681 (ptt90) REVERT: E 120 THR cc_start: 0.7401 (m) cc_final: 0.6621 (m) REVERT: E 128 ARG cc_start: 0.7922 (mmp80) cc_final: 0.7610 (mmm160) REVERT: E 145 ARG cc_start: 0.6771 (mtt180) cc_final: 0.6486 (mtt180) REVERT: E 156 LYS cc_start: 0.2872 (mptt) cc_final: 0.2593 (tttt) REVERT: F 107 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7062 (mm-30) REVERT: F 108 GLU cc_start: 0.7446 (tp30) cc_final: 0.6906 (tp30) REVERT: F 115 LEU cc_start: 0.8528 (mm) cc_final: 0.8259 (mm) REVERT: F 129 ARG cc_start: 0.7529 (tpt-90) cc_final: 0.7302 (tpt-90) REVERT: F 133 ASP cc_start: 0.7827 (m-30) cc_final: 0.7372 (m-30) REVERT: F 144 ASP cc_start: 0.6886 (m-30) cc_final: 0.6533 (m-30) REVERT: G 389 ARG cc_start: 0.5512 (ptm160) cc_final: 0.5247 (ptm-80) REVERT: H 389 ARG cc_start: 0.6539 (tpp-160) cc_final: 0.6154 (tpt170) REVERT: H 443 MET cc_start: 0.1745 (ptt) cc_final: 0.1341 (ptt) REVERT: J 807 MET cc_start: 0.3903 (ppp) cc_final: 0.2739 (ppp) REVERT: J 808 ARG cc_start: 0.5666 (ptt-90) cc_final: 0.4555 (ptt180) REVERT: I 807 MET cc_start: 0.6817 (ppp) cc_final: 0.6615 (ppp) REVERT: I 855 MET cc_start: 0.6215 (mmp) cc_final: 0.5669 (mmp) REVERT: I 869 ASN cc_start: 0.6158 (t0) cc_final: 0.5775 (t0) REVERT: K 126 ASP cc_start: 0.6966 (p0) cc_final: 0.6687 (p0) REVERT: K 156 LYS cc_start: 0.7753 (mppt) cc_final: 0.7232 (mppt) REVERT: L 107 GLU cc_start: 0.8666 (mm-30) cc_final: 0.7922 (mm-30) REVERT: L 131 THR cc_start: 0.8265 (p) cc_final: 0.7938 (p) REVERT: L 132 GLN cc_start: 0.8540 (mp10) cc_final: 0.8258 (pp30) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3151 time to fit residues: 81.6157 Evaluate side-chains 192 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 80 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN H 387 GLN J 869 ASN I 857 ASN L 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.197758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 147)---------------| | r_work = 0.4494 r_free = 0.4494 target = 0.173925 restraints weight = 12630.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.172365 restraints weight = 14923.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.173848 restraints weight = 12591.412| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 moved from start: 0.7168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7898 Z= 0.148 Angle : 0.652 8.095 10614 Z= 0.343 Chirality : 0.042 0.165 1192 Planarity : 0.006 0.123 1416 Dihedral : 4.948 22.208 1126 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -0.79 (0.27), residues: 978 helix: 0.30 (0.23), residues: 498 sheet: -1.61 (0.45), residues: 132 loop : -1.13 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 827 HIS 0.005 0.003 HIS G 406 PHE 0.005 0.001 PHE I 840 TYR 0.013 0.001 TYR D 810 ARG 0.009 0.001 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 418) hydrogen bonds : angle 4.56305 ( 1236) SS BOND : bond 0.00436 ( 4) SS BOND : angle 1.15476 ( 8) covalent geometry : bond 0.00310 ( 7894) covalent geometry : angle 0.65122 (10606) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ARG cc_start: 0.4573 (ptp-170) cc_final: 0.4266 (ptt-90) REVERT: D 11 LEU cc_start: 0.6610 (mm) cc_final: 0.6407 (mm) REVERT: D 812 GLN cc_start: 0.4609 (mp10) cc_final: 0.4368 (mt0) REVERT: D 850 THR cc_start: 0.6307 (m) cc_final: 0.5672 (t) REVERT: D 865 VAL cc_start: 0.5069 (t) cc_final: 0.4779 (p) REVERT: C 811 ARG cc_start: 0.5700 (ptt180) cc_final: 0.5236 (ttp80) REVERT: C 825 THR cc_start: 0.8199 (t) cc_final: 0.7786 (t) REVERT: C 827 TRP cc_start: 0.6526 (m-90) cc_final: 0.4980 (m-90) REVERT: C 861 GLU cc_start: 0.8105 (tp30) cc_final: 0.7627 (tp30) REVERT: E 114 ARG cc_start: 0.7868 (ptp90) cc_final: 0.7569 (ptt90) REVERT: E 128 ARG cc_start: 0.7505 (mmp80) cc_final: 0.7300 (mmm160) REVERT: E 145 ARG cc_start: 0.6294 (mtt180) cc_final: 0.6067 (mtt180) REVERT: E 156 LYS cc_start: 0.2955 (mptt) cc_final: 0.2592 (tttt) REVERT: F 107 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6985 (mm-30) REVERT: F 108 GLU cc_start: 0.7271 (tp30) cc_final: 0.6590 (tp30) REVERT: F 115 LEU cc_start: 0.8439 (mm) cc_final: 0.8234 (mm) REVERT: F 133 ASP cc_start: 0.7674 (m-30) cc_final: 0.7242 (m-30) REVERT: F 144 ASP cc_start: 0.6716 (m-30) cc_final: 0.6315 (m-30) REVERT: G 389 ARG cc_start: 0.5523 (ptm160) cc_final: 0.5156 (ptm-80) REVERT: H 443 MET cc_start: 0.2086 (ptt) cc_final: 0.1700 (ptt) REVERT: J 807 MET cc_start: 0.4178 (ppp) cc_final: 0.3079 (ppp) REVERT: J 820 MET cc_start: 0.5888 (mpp) cc_final: 0.5386 (mpp) REVERT: I 855 MET cc_start: 0.6255 (mmp) cc_final: 0.6041 (mpp) REVERT: K 156 LYS cc_start: 0.7951 (mppt) cc_final: 0.7588 (mppt) REVERT: L 107 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7707 (mm-30) REVERT: L 122 LEU cc_start: 0.5965 (mt) cc_final: 0.5716 (tp) REVERT: L 132 GLN cc_start: 0.8535 (mp10) cc_final: 0.8277 (pp30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3035 time to fit residues: 78.1051 Evaluate side-chains 193 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 chunk 20 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN I 805 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.199222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.174987 restraints weight = 12608.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.170380 restraints weight = 11408.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.170929 restraints weight = 9462.999| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.7493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7898 Z= 0.139 Angle : 0.680 8.209 10614 Z= 0.354 Chirality : 0.042 0.143 1192 Planarity : 0.004 0.038 1416 Dihedral : 4.881 23.849 1126 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.12 % Allowed : 1.37 % Favored : 98.51 % 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: -0.86 (0.27), residues: 978 helix: 0.17 (0.23), residues: 508 sheet: -1.85 (0.39), residues: 166 loop : -0.78 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 878 HIS 0.004 0.002 HIS H 406 PHE 0.004 0.001 PHE I 840 TYR 0.016 0.001 TYR D 810 ARG 0.009 0.001 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 418) hydrogen bonds : angle 4.65436 ( 1236) SS BOND : bond 0.00568 ( 4) SS BOND : angle 1.18610 ( 8) covalent geometry : bond 0.00297 ( 7894) covalent geometry : angle 0.67922 (10606) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 379 LYS cc_start: 0.6622 (mmmm) cc_final: 0.6260 (tppt) REVERT: D 11 LEU cc_start: 0.6773 (mm) cc_final: 0.6573 (mm) REVERT: D 865 VAL cc_start: 0.4565 (t) cc_final: 0.4207 (p) REVERT: C 799 ARG cc_start: 0.7127 (ttt-90) cc_final: 0.6769 (tmt170) REVERT: C 825 THR cc_start: 0.8156 (t) cc_final: 0.7686 (t) REVERT: C 827 TRP cc_start: 0.6550 (m-90) cc_final: 0.4128 (m-90) REVERT: C 861 GLU cc_start: 0.8353 (tp30) cc_final: 0.7935 (tp30) REVERT: E 114 ARG cc_start: 0.8272 (ptp90) cc_final: 0.7705 (ptt90) REVERT: E 128 ARG cc_start: 0.7946 (mmp80) cc_final: 0.7501 (mmm160) REVERT: E 145 ARG cc_start: 0.6750 (mtt180) cc_final: 0.6516 (mtt180) REVERT: E 156 LYS cc_start: 0.2909 (mptt) cc_final: 0.2599 (tttt) REVERT: F 107 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7155 (mm-30) REVERT: F 108 GLU cc_start: 0.7521 (tp30) cc_final: 0.6930 (tp30) REVERT: F 115 LEU cc_start: 0.8507 (mm) cc_final: 0.8205 (mm) REVERT: F 129 ARG cc_start: 0.7198 (tpt-90) cc_final: 0.6719 (tpt170) REVERT: F 133 ASP cc_start: 0.7829 (m-30) cc_final: 0.7501 (m-30) REVERT: F 144 ASP cc_start: 0.7060 (m-30) cc_final: 0.6730 (m-30) REVERT: H 443 MET cc_start: 0.2079 (ptt) cc_final: 0.1713 (ptt) REVERT: J 807 MET cc_start: 0.4327 (ppp) cc_final: 0.3278 (ppp) REVERT: J 820 MET cc_start: 0.6050 (mpp) cc_final: 0.5462 (mpp) REVERT: I 855 MET cc_start: 0.6466 (mmp) cc_final: 0.6089 (mpp) REVERT: I 884 VAL cc_start: 0.7865 (t) cc_final: 0.7540 (t) REVERT: K 156 LYS cc_start: 0.7847 (mppt) cc_final: 0.7580 (mppt) REVERT: L 107 GLU cc_start: 0.8709 (mm-30) cc_final: 0.7920 (mm-30) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.2988 time to fit residues: 77.0546 Evaluate side-chains 188 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 16 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 0.0770 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 HIS ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN I 805 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.204274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.188564 restraints weight = 10231.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.188756 restraints weight = 10912.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.187982 restraints weight = 10564.465| |-----------------------------------------------------------------------------| r_work (final): 0.4576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.7744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7898 Z= 0.125 Angle : 0.654 7.867 10614 Z= 0.344 Chirality : 0.042 0.227 1192 Planarity : 0.004 0.051 1416 Dihedral : 4.715 22.348 1126 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.25 % 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: -0.71 (0.27), residues: 978 helix: 0.29 (0.24), residues: 504 sheet: -1.43 (0.39), residues: 172 loop : -0.90 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 809 HIS 0.003 0.001 HIS H 406 PHE 0.004 0.001 PHE I 840 TYR 0.023 0.001 TYR D 877 ARG 0.009 0.001 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 418) hydrogen bonds : angle 4.50470 ( 1236) SS BOND : bond 0.00563 ( 4) SS BOND : angle 0.95805 ( 8) covalent geometry : bond 0.00263 ( 7894) covalent geometry : angle 0.65408 (10606) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ARG cc_start: 0.4842 (ptp-170) cc_final: 0.4392 (ptt-90) REVERT: B 379 LYS cc_start: 0.6777 (mmmm) cc_final: 0.6538 (tppt) REVERT: C 799 ARG cc_start: 0.7068 (ttt-90) cc_final: 0.6492 (tmt170) REVERT: C 825 THR cc_start: 0.8077 (t) cc_final: 0.7776 (t) REVERT: C 861 GLU cc_start: 0.8144 (tp30) cc_final: 0.7720 (tp30) REVERT: E 114 ARG cc_start: 0.7976 (ptp90) cc_final: 0.7660 (ptt90) REVERT: E 128 ARG cc_start: 0.7577 (mmp80) cc_final: 0.6997 (mmm160) REVERT: E 145 ARG cc_start: 0.6220 (mtt180) cc_final: 0.5931 (mtt180) REVERT: E 156 LYS cc_start: 0.2951 (mptt) cc_final: 0.2371 (tttt) REVERT: F 107 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7178 (mm-30) REVERT: F 108 GLU cc_start: 0.7409 (tp30) cc_final: 0.6576 (tp30) REVERT: F 115 LEU cc_start: 0.8395 (mm) cc_final: 0.8139 (mm) REVERT: F 124 GLU cc_start: 0.8120 (pp20) cc_final: 0.7547 (tp30) REVERT: F 129 ARG cc_start: 0.6852 (tpt-90) cc_final: 0.6479 (tpt170) REVERT: F 133 ASP cc_start: 0.7697 (m-30) cc_final: 0.7261 (m-30) REVERT: F 144 ASP cc_start: 0.6654 (m-30) cc_final: 0.6220 (m-30) REVERT: G 422 SER cc_start: 0.3749 (p) cc_final: 0.3542 (p) REVERT: H 443 MET cc_start: 0.2119 (ptt) cc_final: 0.1749 (ptt) REVERT: J 807 MET cc_start: 0.4164 (ppp) cc_final: 0.3166 (ppp) REVERT: J 808 ARG cc_start: 0.5701 (ptt-90) cc_final: 0.4453 (ptt180) REVERT: I 855 MET cc_start: 0.6158 (mmp) cc_final: 0.5903 (mpp) REVERT: I 884 VAL cc_start: 0.7752 (t) cc_final: 0.7178 (m) REVERT: K 156 LYS cc_start: 0.8033 (mppt) cc_final: 0.7614 (mppt) REVERT: L 107 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7853 (mm-30) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.2888 time to fit residues: 71.3240 Evaluate side-chains 188 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 805 ASN K 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.195648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.170810 restraints weight = 12785.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 97)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.166235 restraints weight = 13321.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.167079 restraints weight = 10697.893| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.8121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7898 Z= 0.177 Angle : 0.730 8.717 10614 Z= 0.386 Chirality : 0.044 0.230 1192 Planarity : 0.005 0.076 1416 Dihedral : 5.261 26.389 1126 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: -0.88 (0.27), residues: 978 helix: 0.17 (0.23), residues: 498 sheet: -1.52 (0.35), residues: 200 loop : -0.88 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 809 HIS 0.008 0.004 HIS G 406 PHE 0.007 0.002 PHE I 840 TYR 0.018 0.002 TYR D 810 ARG 0.007 0.001 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 418) hydrogen bonds : angle 4.88754 ( 1236) SS BOND : bond 0.00646 ( 4) SS BOND : angle 1.04497 ( 8) covalent geometry : bond 0.00378 ( 7894) covalent geometry : angle 0.72994 (10606) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 379 LYS cc_start: 0.6799 (mmmm) cc_final: 0.6503 (tppt) REVERT: B 400 ASP cc_start: 0.5898 (m-30) cc_final: 0.5563 (m-30) REVERT: C 3 GLN cc_start: 0.8345 (mm110) cc_final: 0.6020 (tp40) REVERT: C 793 LEU cc_start: 0.6496 (mt) cc_final: 0.6280 (mt) REVERT: C 811 ARG cc_start: 0.6086 (ttp-170) cc_final: 0.5722 (ttp-110) REVERT: C 825 THR cc_start: 0.8048 (t) cc_final: 0.7730 (t) REVERT: E 114 ARG cc_start: 0.8382 (ptp90) cc_final: 0.7791 (ptt90) REVERT: E 128 ARG cc_start: 0.7552 (mmp80) cc_final: 0.7180 (mmm160) REVERT: E 156 LYS cc_start: 0.3269 (mptt) cc_final: 0.2542 (tttt) REVERT: F 107 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7282 (mm-30) REVERT: F 108 GLU cc_start: 0.7642 (tp30) cc_final: 0.6932 (tp30) REVERT: F 115 LEU cc_start: 0.8509 (mm) cc_final: 0.8180 (mm) REVERT: F 124 GLU cc_start: 0.8322 (pp20) cc_final: 0.7863 (tp30) REVERT: F 129 ARG cc_start: 0.7153 (tpt-90) cc_final: 0.6703 (tpt170) REVERT: F 133 ASP cc_start: 0.7777 (m-30) cc_final: 0.7371 (m-30) REVERT: F 144 ASP cc_start: 0.7112 (m-30) cc_final: 0.6819 (m-30) REVERT: J 807 MET cc_start: 0.4514 (ppp) cc_final: 0.3567 (ppp) REVERT: J 820 MET cc_start: 0.5985 (mpp) cc_final: 0.5388 (mpp) REVERT: I 824 VAL cc_start: 0.6940 (m) cc_final: 0.6375 (m) REVERT: I 853 LEU cc_start: 0.7017 (tp) cc_final: 0.6752 (tp) REVERT: I 886 VAL cc_start: 0.7913 (m) cc_final: 0.7344 (t) REVERT: K 100 GLN cc_start: 0.8342 (mp10) cc_final: 0.7778 (mp10) REVERT: K 128 ARG cc_start: 0.7134 (ptt90) cc_final: 0.6872 (ptt90) REVERT: L 107 GLU cc_start: 0.8774 (mm-30) cc_final: 0.7660 (mm-30) REVERT: L 129 ARG cc_start: 0.8559 (pmt-80) cc_final: 0.8208 (pmt-80) REVERT: L 133 ASP cc_start: 0.8051 (m-30) cc_final: 0.7618 (m-30) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2899 time to fit residues: 73.7694 Evaluate side-chains 184 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.195360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.4454 r_free = 0.4454 target = 0.170283 restraints weight = 12794.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 115)---------------| | r_work = 0.4408 r_free = 0.4408 target = 0.166626 restraints weight = 12413.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.166626 restraints weight = 10763.764| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.8403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7898 Z= 0.158 Angle : 0.712 8.273 10614 Z= 0.376 Chirality : 0.044 0.235 1192 Planarity : 0.006 0.065 1416 Dihedral : 5.123 26.694 1126 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.98 (0.27), residues: 978 helix: 0.15 (0.24), residues: 498 sheet: -1.60 (0.34), residues: 212 loop : -0.99 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 809 HIS 0.006 0.003 HIS H 406 PHE 0.006 0.001 PHE I 840 TYR 0.018 0.002 TYR D 810 ARG 0.011 0.001 ARG G 389 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 418) hydrogen bonds : angle 4.79567 ( 1236) SS BOND : bond 0.00587 ( 4) SS BOND : angle 0.88788 ( 8) covalent geometry : bond 0.00339 ( 7894) covalent geometry : angle 0.71225 (10606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3113.95 seconds wall clock time: 55 minutes 1.73 seconds (3301.73 seconds total)