Starting phenix.real_space_refine on Sat Dec 28 05:21:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afm_15402/12_2024/8afm_15402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afm_15402/12_2024/8afm_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_15402/12_2024/8afm_15402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afm_15402/12_2024/8afm_15402.map" model { file = "/net/cci-nas-00/data/ceres_data/8afm_15402/12_2024/8afm_15402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afm_15402/12_2024/8afm_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-5532/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: 5.25, per 1000 atoms: 0.67 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: 1.87 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.87 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: 2.07 Time building geometry restraints manager: 2.19 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: 0.00 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.230 Find NCS groups from input model: 0.310 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.900 ------------------------------------------------------------------------------- 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 7894 Z= 0.263 Angle : 0.743 8.610 10606 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 *********************** 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 : 0.955 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: 0.3257 time to fit residues: 100.0929 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 : 0.893 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 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 7894 Z= 0.251 Angle : 0.733 9.169 10606 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 *********************** 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 : 0.919 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: 0.7433 (mm-30) cc_final: 0.6518 (mm-30) REVERT: A 393 ASP cc_start: 0.6475 (m-30) cc_final: 0.6149 (m-30) REVERT: D 802 ASP cc_start: 0.3800 (t0) cc_final: 0.3385 (t0) REVERT: D 812 GLN cc_start: 0.5446 (mp10) cc_final: 0.4144 (mp10) REVERT: D 850 THR cc_start: 0.6371 (m) cc_final: 0.5963 (t) REVERT: D 873 ARG cc_start: 0.5937 (mpp-170) cc_final: 0.5604 (mpp-170) REVERT: D 877 TYR cc_start: 0.5811 (m-80) cc_final: 0.5348 (m-80) REVERT: C 806 ILE cc_start: 0.7603 (tp) cc_final: 0.7274 (tp) REVERT: C 825 THR cc_start: 0.6733 (OUTLIER) cc_final: 0.6026 (m) REVERT: F 108 GLU cc_start: 0.7216 (tp30) cc_final: 0.6512 (tp30) REVERT: F 115 LEU cc_start: 0.8247 (mm) cc_final: 0.7968 (mm) REVERT: F 133 ASP cc_start: 0.7929 (m-30) cc_final: 0.7542 (m-30) REVERT: F 142 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6575 (tp30) REVERT: F 144 ASP cc_start: 0.6523 (m-30) cc_final: 0.6082 (m-30) REVERT: H 370 SER cc_start: 0.6926 (t) cc_final: 0.6685 (m) REVERT: J 801 ILE cc_start: 0.8251 (mm) cc_final: 0.8009 (mm) REVERT: J 808 ARG cc_start: 0.6377 (ptt-90) cc_final: 0.5970 (ptt90) REVERT: J 820 MET cc_start: 0.5783 (mpp) cc_final: 0.5048 (mpp) REVERT: I 802 ASP cc_start: 0.4894 (t70) cc_final: 0.4548 (t0) REVERT: I 807 MET cc_start: 0.6214 (ppp) cc_final: 0.5847 (ppp) REVERT: I 823 VAL cc_start: 0.7470 (p) cc_final: 0.7251 (p) REVERT: I 857 ASN cc_start: 0.7909 (t0) cc_final: 0.7629 (t0) REVERT: I 884 VAL cc_start: 0.7561 (t) cc_final: 0.5906 (t) REVERT: K 148 ASN cc_start: 0.7640 (t0) cc_final: 0.7392 (t0) REVERT: L 107 GLU cc_start: 0.8303 (tp30) cc_final: 0.8041 (mm-30) REVERT: L 115 LEU cc_start: 0.8658 (mm) cc_final: 0.8167 (mm) REVERT: L 132 GLN cc_start: 0.8542 (mp-120) cc_final: 0.7963 (pp30) REVERT: L 142 GLU cc_start: 0.5934 (tm-30) cc_final: 0.5211 (tm-30) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.3203 time to fit residues: 89.7094 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 : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 58 optimal weight: 0.0020 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5430 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7894 Z= 0.245 Angle : 0.688 7.339 10606 Z= 0.363 Chirality : 0.043 0.151 1192 Planarity : 0.005 0.061 1416 Dihedral : 5.603 24.300 1126 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.53 % 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: -1.72 (0.26), residues: 978 helix: -0.54 (0.23), residues: 504 sheet: -3.27 (0.42), residues: 110 loop : -1.04 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP J 878 HIS 0.010 0.005 HIS H 406 PHE 0.007 0.002 PHE J 840 TYR 0.026 0.002 TYR C 866 ARG 0.014 0.001 ARG B 435 *********************** 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 226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.962 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: symmetry clash REVERT: A 389 ARG cc_start: 0.5030 (ptp-170) cc_final: 0.4754 (ptp-170) REVERT: B 375 GLU cc_start: 0.7203 (tp30) cc_final: 0.6805 (tm-30) REVERT: D 812 GLN cc_start: 0.5979 (mp10) cc_final: 0.5107 (mt0) REVERT: D 850 THR cc_start: 0.6244 (m) cc_final: 0.5638 (t) REVERT: D 865 VAL cc_start: 0.6577 (t) cc_final: 0.4588 (p) REVERT: C 3 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8086 (mm110) REVERT: E 152 GLN cc_start: 0.5864 (mm-40) cc_final: 0.5654 (mm-40) REVERT: F 104 ILE cc_start: 0.7177 (tt) cc_final: 0.6648 (tt) REVERT: F 107 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6756 (mm-30) REVERT: F 108 GLU cc_start: 0.7181 (tp30) cc_final: 0.6528 (tp30) REVERT: F 115 LEU cc_start: 0.8379 (mm) cc_final: 0.7952 (mm) REVERT: F 142 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6910 (tp30) REVERT: F 144 ASP cc_start: 0.6563 (m-30) cc_final: 0.6254 (m-30) REVERT: G 375 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6084 (mt-10) REVERT: G 389 ARG cc_start: 0.5976 (ptm160) cc_final: 0.5709 (ptm-80) REVERT: J 801 ILE cc_start: 0.8143 (mm) cc_final: 0.7901 (mm) REVERT: J 807 MET cc_start: 0.3736 (ppp) cc_final: 0.2434 (ppp) REVERT: J 808 ARG cc_start: 0.5539 (ptt-90) cc_final: 0.4425 (ptt180) REVERT: I 802 ASP cc_start: 0.5622 (t70) cc_final: 0.5143 (t0) REVERT: I 807 MET cc_start: 0.6469 (ppp) cc_final: 0.5983 (ppp) REVERT: I 823 VAL cc_start: 0.7534 (p) cc_final: 0.7223 (p) REVERT: I 884 VAL cc_start: 0.7801 (t) cc_final: 0.6528 (t) REVERT: I 886 VAL cc_start: 0.6857 (p) cc_final: 0.6527 (t) REVERT: K 126 ASP cc_start: 0.7562 (m-30) cc_final: 0.6720 (p0) REVERT: K 156 LYS cc_start: 0.7793 (mppt) cc_final: 0.7193 (mppt) REVERT: L 107 GLU cc_start: 0.8696 (tp30) cc_final: 0.8010 (mm-30) REVERT: L 115 LEU cc_start: 0.8737 (mm) cc_final: 0.8242 (mm) REVERT: L 132 GLN cc_start: 0.8520 (mp-120) cc_final: 0.8006 (pp30) REVERT: L 142 GLU cc_start: 0.6268 (tm-30) cc_final: 0.5874 (tm-30) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.3230 time to fit residues: 88.7609 Evaluate side-chains 196 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 0.0070 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 75 optimal weight: 0.4980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5389 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7894 Z= 0.182 Angle : 0.609 7.197 10606 Z= 0.319 Chirality : 0.041 0.148 1192 Planarity : 0.004 0.054 1416 Dihedral : 5.097 21.755 1126 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.27), residues: 978 helix: -0.22 (0.23), residues: 510 sheet: -2.54 (0.38), residues: 160 loop : -0.74 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 827 HIS 0.005 0.003 HIS G 406 PHE 0.005 0.001 PHE I 840 TYR 0.015 0.001 TYR C 866 ARG 0.005 0.001 ARG B 380 *********************** 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 221 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.970 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: symmetry clash REVERT: A 369 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8105 (tmtt) REVERT: A 389 ARG cc_start: 0.4738 (ptp-170) cc_final: 0.4362 (ptp-170) REVERT: B 375 GLU cc_start: 0.7183 (tp30) cc_final: 0.6637 (tm-30) REVERT: B 387 GLN cc_start: 0.7891 (pt0) cc_final: 0.7493 (pp30) REVERT: D 812 GLN cc_start: 0.5840 (mp10) cc_final: 0.4817 (mt0) REVERT: D 850 THR cc_start: 0.5805 (m) cc_final: 0.5014 (t) REVERT: D 865 VAL cc_start: 0.6491 (t) cc_final: 0.4074 (p) REVERT: D 873 ARG cc_start: 0.6173 (mpp-170) cc_final: 0.5953 (mpp80) REVERT: C 841 ILE cc_start: 0.7194 (mp) cc_final: 0.6936 (mp) REVERT: E 145 ARG cc_start: 0.6973 (mtt180) cc_final: 0.6684 (mtt180) REVERT: E 156 LYS cc_start: 0.2908 (mptt) cc_final: 0.2422 (tttt) REVERT: F 107 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7088 (mm-30) REVERT: F 108 GLU cc_start: 0.7167 (tp30) cc_final: 0.6530 (tp30) REVERT: F 115 LEU cc_start: 0.8332 (mm) cc_final: 0.8016 (mm) REVERT: F 133 ASP cc_start: 0.7539 (m-30) cc_final: 0.7280 (m-30) REVERT: F 144 ASP cc_start: 0.6681 (m-30) cc_final: 0.6370 (m-30) REVERT: G 389 ARG cc_start: 0.5838 (ptm160) cc_final: 0.5573 (ptm-80) REVERT: G 422 SER cc_start: 0.4143 (p) cc_final: 0.3887 (p) REVERT: H 380 ARG cc_start: 0.7457 (ptt-90) cc_final: 0.7164 (mtm-85) REVERT: H 401 GLN cc_start: 0.6416 (tp-100) cc_final: 0.5233 (pm20) REVERT: H 443 MET cc_start: 0.1862 (ptt) cc_final: 0.1440 (ptt) REVERT: J 801 ILE cc_start: 0.8230 (mm) cc_final: 0.7998 (mm) REVERT: J 807 MET cc_start: 0.3936 (ppp) cc_final: 0.2462 (ppp) REVERT: J 808 ARG cc_start: 0.6049 (ptt-90) cc_final: 0.5054 (ptt180) REVERT: I 802 ASP cc_start: 0.4972 (t70) cc_final: 0.3874 (t0) REVERT: I 807 MET cc_start: 0.6543 (ppp) cc_final: 0.6284 (ppp) REVERT: I 823 VAL cc_start: 0.7547 (p) cc_final: 0.7240 (p) REVERT: I 884 VAL cc_start: 0.7771 (t) cc_final: 0.6286 (t) REVERT: K 126 ASP cc_start: 0.7585 (m-30) cc_final: 0.6874 (p0) REVERT: K 129 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7821 (ttp80) REVERT: K 156 LYS cc_start: 0.7764 (mppt) cc_final: 0.7471 (mppt) REVERT: L 107 GLU cc_start: 0.8737 (tp30) cc_final: 0.7729 (mm-30) REVERT: L 115 LEU cc_start: 0.8753 (mm) cc_final: 0.8306 (mm) REVERT: L 119 GLU cc_start: 0.8585 (pp20) cc_final: 0.8108 (pp20) REVERT: L 132 GLN cc_start: 0.8689 (mp-120) cc_final: 0.7950 (pp30) REVERT: L 133 ASP cc_start: 0.8076 (m-30) cc_final: 0.7620 (m-30) REVERT: L 142 GLU cc_start: 0.6504 (tm-30) cc_final: 0.6076 (tm-30) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3057 time to fit residues: 82.2018 Evaluate side-chains 199 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 0 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 30 optimal weight: 0.9990 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 HIS C 3 GLN L 100 GLN L 130 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5345 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7894 Z= 0.159 Angle : 0.605 8.224 10606 Z= 0.317 Chirality : 0.040 0.158 1192 Planarity : 0.003 0.028 1416 Dihedral : 4.837 20.586 1126 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.27), residues: 978 helix: -0.05 (0.23), residues: 506 sheet: -2.24 (0.38), residues: 172 loop : -0.62 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 827 HIS 0.004 0.002 HIS H 406 PHE 0.004 0.001 PHE I 840 TYR 0.028 0.001 TYR C 866 ARG 0.008 0.001 ARG C 811 *********************** 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 217 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.938 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: A 375 GLU cc_start: 0.6713 (tp30) cc_final: 0.6116 (mm-30) REVERT: A 389 ARG cc_start: 0.4679 (ptp-170) cc_final: 0.4450 (ptp-170) REVERT: B 375 GLU cc_start: 0.7173 (tp30) cc_final: 0.6756 (tm-30) REVERT: B 387 GLN cc_start: 0.8071 (pt0) cc_final: 0.7705 (pp30) REVERT: D 812 GLN cc_start: 0.6070 (mp10) cc_final: 0.4315 (mt0) REVERT: D 850 THR cc_start: 0.5976 (m) cc_final: 0.5278 (t) REVERT: D 865 VAL cc_start: 0.6376 (t) cc_final: 0.3722 (p) REVERT: C 3 GLN cc_start: 0.8398 (mm110) cc_final: 0.8045 (mm110) REVERT: C 825 THR cc_start: 0.7565 (t) cc_final: 0.7229 (t) REVERT: C 827 TRP cc_start: 0.5749 (m-90) cc_final: 0.3500 (m-90) REVERT: C 856 ASN cc_start: 0.7526 (t0) cc_final: 0.7308 (t0) REVERT: E 114 ARG cc_start: 0.7824 (ptp90) cc_final: 0.7510 (ptt90) REVERT: E 128 ARG cc_start: 0.7851 (mtt180) cc_final: 0.7581 (mmm160) REVERT: E 145 ARG cc_start: 0.6411 (mtt180) cc_final: 0.6170 (mtt180) REVERT: E 156 LYS cc_start: 0.2807 (mptt) cc_final: 0.2364 (tttt) REVERT: F 107 GLU cc_start: 0.7632 (mm-30) cc_final: 0.6618 (mm-30) REVERT: F 108 GLU cc_start: 0.7167 (tp30) cc_final: 0.6707 (tp30) REVERT: F 144 ASP cc_start: 0.6665 (m-30) cc_final: 0.6275 (m-30) REVERT: G 422 SER cc_start: 0.3946 (p) cc_final: 0.3508 (p) REVERT: H 401 GLN cc_start: 0.6662 (tp-100) cc_final: 0.5370 (pm20) REVERT: H 443 MET cc_start: 0.1491 (ptt) cc_final: 0.1061 (ptt) REVERT: J 801 ILE cc_start: 0.7791 (mm) cc_final: 0.7565 (mm) REVERT: J 807 MET cc_start: 0.3554 (ppp) cc_final: 0.2033 (ppp) REVERT: J 808 ARG cc_start: 0.5972 (ptt-90) cc_final: 0.4141 (mtm180) REVERT: I 802 ASP cc_start: 0.4417 (t70) cc_final: 0.3811 (t70) REVERT: I 823 VAL cc_start: 0.7481 (p) cc_final: 0.7248 (p) REVERT: I 884 VAL cc_start: 0.7797 (t) cc_final: 0.7548 (t) REVERT: K 150 LEU cc_start: 0.7931 (tp) cc_final: 0.7678 (tp) REVERT: K 156 LYS cc_start: 0.7807 (mppt) cc_final: 0.7152 (mppt) REVERT: L 105 GLN cc_start: 0.6762 (tm-30) cc_final: 0.6141 (tm-30) REVERT: L 107 GLU cc_start: 0.8208 (tp30) cc_final: 0.7987 (mm-30) REVERT: L 115 LEU cc_start: 0.8726 (mm) cc_final: 0.8349 (mm) REVERT: L 132 GLN cc_start: 0.8475 (mp-120) cc_final: 0.7940 (pp30) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.3306 time to fit residues: 86.8767 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 : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5448 moved from start: 0.7115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7894 Z= 0.210 Angle : 0.647 7.249 10606 Z= 0.338 Chirality : 0.042 0.141 1192 Planarity : 0.004 0.047 1416 Dihedral : 5.087 20.760 1126 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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: -0.97 (0.27), residues: 978 helix: 0.11 (0.23), residues: 496 sheet: -2.31 (0.40), residues: 146 loop : -0.74 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 827 HIS 0.008 0.003 HIS H 406 PHE 0.006 0.001 PHE I 840 TYR 0.024 0.002 TYR C 866 ARG 0.009 0.001 ARG B 419 *********************** 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 210 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.905 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ARG cc_start: 0.4780 (ptp-170) cc_final: 0.4493 (ptp-170) REVERT: B 369 LYS cc_start: 0.7353 (mttt) cc_final: 0.7124 (mtmm) REVERT: B 375 GLU cc_start: 0.7223 (tp30) cc_final: 0.6879 (tm-30) REVERT: B 387 GLN cc_start: 0.7850 (pt0) cc_final: 0.7462 (pp30) REVERT: D 850 THR cc_start: 0.5975 (m) cc_final: 0.5210 (t) REVERT: D 865 VAL cc_start: 0.5568 (t) cc_final: 0.5003 (p) REVERT: C 825 THR cc_start: 0.7821 (t) cc_final: 0.7583 (t) REVERT: E 114 ARG cc_start: 0.7855 (ptp90) cc_final: 0.7525 (ptt90) REVERT: E 119 GLU cc_start: 0.6805 (pp20) cc_final: 0.6473 (pp20) REVERT: F 107 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6405 (mm-30) REVERT: F 108 GLU cc_start: 0.7061 (tp30) cc_final: 0.6411 (tp30) REVERT: F 132 GLN cc_start: 0.6849 (pp30) cc_final: 0.5933 (pp30) REVERT: F 133 ASP cc_start: 0.7557 (m-30) cc_final: 0.7136 (m-30) REVERT: F 144 ASP cc_start: 0.6788 (m-30) cc_final: 0.6366 (m-30) REVERT: H 443 MET cc_start: 0.1759 (ptt) cc_final: 0.1327 (ptt) REVERT: J 807 MET cc_start: 0.4502 (ppp) cc_final: 0.3331 (ppp) REVERT: J 820 MET cc_start: 0.5528 (mpp) cc_final: 0.5098 (mpp) REVERT: I 802 ASP cc_start: 0.5232 (t70) cc_final: 0.4506 (t70) REVERT: I 884 VAL cc_start: 0.7705 (t) cc_final: 0.7446 (t) REVERT: I 886 VAL cc_start: 0.6315 (p) cc_final: 0.6026 (t) REVERT: K 129 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7921 (ttp80) REVERT: K 150 LEU cc_start: 0.8011 (tp) cc_final: 0.7761 (tt) REVERT: K 156 LYS cc_start: 0.7903 (mppt) cc_final: 0.7563 (mppt) REVERT: L 105 GLN cc_start: 0.6656 (tm-30) cc_final: 0.6237 (tm-30) REVERT: L 132 GLN cc_start: 0.8499 (mp-120) cc_final: 0.7943 (pp30) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3104 time to fit residues: 79.4450 Evaluate side-chains 187 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 0.0000 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7894 Z= 0.207 Angle : 0.648 7.542 10606 Z= 0.341 Chirality : 0.042 0.162 1192 Planarity : 0.004 0.041 1416 Dihedral : 5.078 21.510 1126 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.24), residues: 500 sheet: -2.32 (0.40), residues: 146 loop : -0.71 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 827 HIS 0.006 0.003 HIS G 406 PHE 0.005 0.001 PHE I 840 TYR 0.023 0.002 TYR C 866 ARG 0.010 0.001 ARG B 419 *********************** 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 210 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.857 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 GLU cc_start: 0.7177 (tp30) cc_final: 0.6823 (tm-30) REVERT: B 387 GLN cc_start: 0.7871 (pt0) cc_final: 0.7408 (pp30) REVERT: B 400 ASP cc_start: 0.5315 (m-30) cc_final: 0.5113 (m-30) REVERT: D 11 LEU cc_start: 0.6519 (mm) cc_final: 0.6313 (mm) REVERT: D 850 THR cc_start: 0.6020 (m) cc_final: 0.5356 (t) REVERT: C 825 THR cc_start: 0.8053 (t) cc_final: 0.7755 (t) REVERT: C 840 PHE cc_start: 0.4841 (m-10) cc_final: 0.4591 (m-80) REVERT: C 856 ASN cc_start: 0.7802 (t0) cc_final: 0.7523 (t0) REVERT: E 114 ARG cc_start: 0.7749 (ptp90) cc_final: 0.7454 (ptt90) REVERT: E 119 GLU cc_start: 0.6834 (pp20) cc_final: 0.6424 (pp20) REVERT: E 128 ARG cc_start: 0.7615 (mmp80) cc_final: 0.7145 (mmm160) REVERT: F 107 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6535 (mm-30) REVERT: F 108 GLU cc_start: 0.7089 (tp30) cc_final: 0.6473 (tp30) REVERT: F 115 LEU cc_start: 0.8421 (mm) cc_final: 0.8210 (mm) REVERT: F 132 GLN cc_start: 0.7055 (pp30) cc_final: 0.6392 (pp30) REVERT: F 133 ASP cc_start: 0.7615 (m-30) cc_final: 0.7095 (m-30) REVERT: H 443 MET cc_start: 0.2032 (ptt) cc_final: 0.1611 (ptt) REVERT: J 807 MET cc_start: 0.4153 (ppp) cc_final: 0.3315 (ppp) REVERT: J 820 MET cc_start: 0.5669 (mpp) cc_final: 0.5187 (mpp) REVERT: I 884 VAL cc_start: 0.7533 (t) cc_final: 0.7307 (t) REVERT: K 156 LYS cc_start: 0.7930 (mppt) cc_final: 0.7310 (mppt) REVERT: L 129 ARG cc_start: 0.8163 (ptt90) cc_final: 0.7961 (ppt170) REVERT: L 131 THR cc_start: 0.8307 (p) cc_final: 0.7857 (p) REVERT: L 132 GLN cc_start: 0.8554 (mp10) cc_final: 0.7956 (pp30) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3194 time to fit residues: 82.0882 Evaluate side-chains 187 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 J 869 ASN K 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.7853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7894 Z= 0.216 Angle : 0.688 7.884 10606 Z= 0.359 Chirality : 0.043 0.158 1192 Planarity : 0.005 0.069 1416 Dihedral : 5.174 25.032 1126 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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 (0.27), residues: 978 helix: 0.16 (0.23), residues: 498 sheet: -2.23 (0.36), residues: 172 loop : -0.69 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP D 809 HIS 0.006 0.003 HIS H 406 PHE 0.008 0.002 PHE I 840 TYR 0.015 0.002 TYR D 810 ARG 0.009 0.001 ARG B 419 *********************** 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 209 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.895 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: A 389 ARG cc_start: 0.4874 (ptp-170) cc_final: 0.4662 (ptt-90) REVERT: B 375 GLU cc_start: 0.7177 (tp30) cc_final: 0.6879 (tm-30) REVERT: B 387 GLN cc_start: 0.7847 (pt0) cc_final: 0.7373 (pp30) REVERT: D 11 LEU cc_start: 0.6707 (mm) cc_final: 0.6461 (mm) REVERT: D 850 THR cc_start: 0.5933 (m) cc_final: 0.5351 (t) REVERT: C 6 GLU cc_start: 0.6870 (tp30) cc_final: 0.6335 (mt-10) REVERT: C 799 ARG cc_start: 0.7162 (ttt-90) cc_final: 0.6754 (tmt170) REVERT: C 825 THR cc_start: 0.8088 (t) cc_final: 0.7765 (t) REVERT: C 840 PHE cc_start: 0.4790 (m-10) cc_final: 0.4446 (m-80) REVERT: C 856 ASN cc_start: 0.7704 (t0) cc_final: 0.7390 (t0) REVERT: E 114 ARG cc_start: 0.7983 (ptp90) cc_final: 0.7598 (ptt90) REVERT: E 119 GLU cc_start: 0.6819 (pp20) cc_final: 0.6462 (pp20) REVERT: F 107 GLU cc_start: 0.6570 (mm-30) cc_final: 0.6243 (mm-30) REVERT: F 108 GLU cc_start: 0.7132 (tp30) cc_final: 0.6500 (tp30) REVERT: F 115 LEU cc_start: 0.8459 (mm) cc_final: 0.8228 (mm) REVERT: F 132 GLN cc_start: 0.6977 (pp30) cc_final: 0.6282 (pp30) REVERT: F 133 ASP cc_start: 0.7645 (m-30) cc_final: 0.7241 (m-30) REVERT: F 144 ASP cc_start: 0.6513 (m-30) cc_final: 0.6118 (m-30) REVERT: H 443 MET cc_start: 0.2072 (ptt) cc_final: 0.1733 (ptt) REVERT: J 807 MET cc_start: 0.4555 (ppp) cc_final: 0.3707 (ppp) REVERT: J 820 MET cc_start: 0.5686 (mpp) cc_final: 0.5184 (mpp) REVERT: I 886 VAL cc_start: 0.6589 (m) cc_final: 0.6368 (t) REVERT: K 126 ASP cc_start: 0.7573 (m-30) cc_final: 0.6657 (p0) REVERT: L 129 ARG cc_start: 0.8092 (ptt90) cc_final: 0.7132 (ppt170) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.3053 time to fit residues: 77.7588 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 : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 869 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.8208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7894 Z= 0.238 Angle : 0.714 8.027 10606 Z= 0.374 Chirality : 0.044 0.157 1192 Planarity : 0.005 0.056 1416 Dihedral : 5.375 26.408 1126 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.07 (0.27), residues: 978 helix: 0.09 (0.23), residues: 496 sheet: -2.09 (0.35), residues: 192 loop : -0.76 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 809 HIS 0.007 0.002 HIS G 406 PHE 0.009 0.002 PHE I 840 TYR 0.017 0.002 TYR C 866 ARG 0.010 0.001 ARG D 873 *********************** 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 210 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.913 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 GLU cc_start: 0.7171 (tp30) cc_final: 0.6651 (tm-30) REVERT: B 379 LYS cc_start: 0.6976 (mmmm) cc_final: 0.6560 (tppt) REVERT: B 400 ASP cc_start: 0.6034 (m-30) cc_final: 0.5820 (m-30) REVERT: C 6 GLU cc_start: 0.6636 (tp30) cc_final: 0.6340 (mt-10) REVERT: C 799 ARG cc_start: 0.7144 (ttt-90) cc_final: 0.6679 (tmt170) REVERT: C 820 MET cc_start: 0.6749 (tmm) cc_final: 0.6113 (tmm) REVERT: C 825 THR cc_start: 0.7951 (t) cc_final: 0.7625 (t) REVERT: C 840 PHE cc_start: 0.4898 (m-10) cc_final: 0.4571 (m-80) REVERT: C 856 ASN cc_start: 0.7862 (t0) cc_final: 0.7658 (t0) REVERT: E 114 ARG cc_start: 0.8049 (ptp90) cc_final: 0.7645 (ptt90) REVERT: E 119 GLU cc_start: 0.6793 (pp20) cc_final: 0.6484 (pp20) REVERT: F 107 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6323 (mm-30) REVERT: F 108 GLU cc_start: 0.7234 (tp30) cc_final: 0.6602 (tp30) REVERT: F 115 LEU cc_start: 0.8457 (mm) cc_final: 0.8221 (mm) REVERT: F 132 GLN cc_start: 0.7042 (pp30) cc_final: 0.6441 (pp30) REVERT: F 133 ASP cc_start: 0.7575 (m-30) cc_final: 0.6959 (m-30) REVERT: F 144 ASP cc_start: 0.6859 (m-30) cc_final: 0.6631 (m-30) REVERT: G 389 ARG cc_start: 0.6390 (ptm160) cc_final: 0.6081 (ptm-80) REVERT: G 422 SER cc_start: 0.4135 (p) cc_final: 0.3876 (p) REVERT: H 443 MET cc_start: 0.2700 (ptt) cc_final: 0.2421 (ptt) REVERT: J 801 ILE cc_start: 0.7198 (mm) cc_final: 0.6953 (mm) REVERT: J 807 MET cc_start: 0.4457 (ppp) cc_final: 0.3790 (ppp) REVERT: J 820 MET cc_start: 0.5612 (mpp) cc_final: 0.5007 (mpp) REVERT: I 886 VAL cc_start: 0.7279 (m) cc_final: 0.7008 (t) REVERT: K 126 ASP cc_start: 0.7457 (m-30) cc_final: 0.6712 (p0) REVERT: K 156 LYS cc_start: 0.7922 (mppt) cc_final: 0.7524 (mppt) REVERT: L 129 ARG cc_start: 0.7798 (ptt90) cc_final: 0.7019 (ppt170) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3196 time to fit residues: 81.4274 Evaluate side-chains 194 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.0170 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- 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 ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 869 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5471 moved from start: 0.8427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7894 Z= 0.191 Angle : 0.681 7.755 10606 Z= 0.355 Chirality : 0.042 0.170 1192 Planarity : 0.005 0.059 1416 Dihedral : 5.063 25.325 1126 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -0.89 (0.27), residues: 978 helix: 0.18 (0.24), residues: 490 sheet: -1.61 (0.37), residues: 180 loop : -0.92 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP I 827 HIS 0.004 0.002 HIS H 406 PHE 0.007 0.001 PHE I 840 TYR 0.014 0.001 TYR D 810 ARG 0.019 0.001 ARG B 435 ********************** 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 202 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.997 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 GLU cc_start: 0.7121 (tp30) cc_final: 0.6777 (tm-30) REVERT: B 379 LYS cc_start: 0.7014 (mmmm) cc_final: 0.6677 (tppt) REVERT: B 387 GLN cc_start: 0.7584 (pt0) cc_final: 0.7298 (pp30) REVERT: D 11 LEU cc_start: 0.6480 (mm) cc_final: 0.6271 (mm) REVERT: D 839 ARG cc_start: 0.4826 (ttt180) cc_final: 0.4494 (ttt180) REVERT: C 6 GLU cc_start: 0.6614 (tp30) cc_final: 0.6089 (mt-10) REVERT: C 799 ARG cc_start: 0.7088 (ttt-90) cc_final: 0.6443 (tmt170) REVERT: C 825 THR cc_start: 0.7838 (t) cc_final: 0.7585 (t) REVERT: C 840 PHE cc_start: 0.5160 (m-10) cc_final: 0.4730 (m-80) REVERT: E 114 ARG cc_start: 0.8152 (ptp90) cc_final: 0.7746 (ptt90) REVERT: E 119 GLU cc_start: 0.6819 (pp20) cc_final: 0.6512 (pp20) REVERT: F 107 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6273 (mm-30) REVERT: F 108 GLU cc_start: 0.7302 (tp30) cc_final: 0.6547 (tp30) REVERT: F 115 LEU cc_start: 0.8436 (mm) cc_final: 0.8179 (mm) REVERT: F 132 GLN cc_start: 0.7069 (pp30) cc_final: 0.6528 (pp30) REVERT: F 144 ASP cc_start: 0.6792 (m-30) cc_final: 0.6484 (m-30) REVERT: G 389 ARG cc_start: 0.6462 (ptm160) cc_final: 0.6186 (ptm-80) REVERT: G 422 SER cc_start: 0.4188 (p) cc_final: 0.3986 (p) REVERT: H 443 MET cc_start: 0.3051 (ptt) cc_final: 0.2789 (ptt) REVERT: J 807 MET cc_start: 0.4374 (ppp) cc_final: 0.3464 (ppp) REVERT: J 820 MET cc_start: 0.5627 (mpp) cc_final: 0.5130 (mpp) REVERT: I 841 ILE cc_start: 0.7022 (mp) cc_final: 0.6726 (mp) REVERT: I 886 VAL cc_start: 0.7166 (m) cc_final: 0.6777 (t) REVERT: K 126 ASP cc_start: 0.7591 (m-30) cc_final: 0.6913 (p0) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3031 time to fit residues: 74.8425 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 : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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** J 869 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.194570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 156)---------------| | r_work = 0.4441 r_free = 0.4441 target = 0.168631 restraints weight = 12631.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.167923 restraints weight = 10697.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.168282 restraints weight = 8720.960| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.8630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7894 Z= 0.210 Angle : 0.719 8.160 10606 Z= 0.374 Chirality : 0.044 0.236 1192 Planarity : 0.005 0.069 1416 Dihedral : 5.170 25.359 1126 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.05 (0.27), residues: 978 helix: 0.06 (0.23), residues: 496 sheet: -1.87 (0.35), residues: 192 loop : -0.83 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP I 827 HIS 0.006 0.003 HIS G 406 PHE 0.008 0.002 PHE I 840 TYR 0.014 0.001 TYR D 810 ARG 0.013 0.001 ARG D 873 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2266.57 seconds wall clock time: 41 minutes 47.32 seconds (2507.32 seconds total)