Starting phenix.real_space_refine on Wed Feb 12 11:30:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afm_15402/02_2025/8afm_15402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afm_15402/02_2025/8afm_15402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8afm_15402/02_2025/8afm_15402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afm_15402/02_2025/8afm_15402.map" model { file = "/net/cci-nas-00/data/ceres_data/8afm_15402/02_2025/8afm_15402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afm_15402/02_2025/8afm_15402.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4754 2.51 5 N 1492 2.21 5 O 1568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7842 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "B" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "E" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 455 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "G" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "I" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "K" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "L" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 455 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Time building chain proxies: 4.97, per 1000 atoms: 0.63 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: 1.81 Conformation dependent library (CDL) restraints added in 1.1 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: 0.83 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: 1.94 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2844 1.34 - 1.46: 1129 1.46 - 1.58: 3873 1.58 - 1.70: 0 1.70 - 1.81: 48 Bond restraints: 7894 Sorted by residual: bond pdb=" N LEU E 115 " pdb=" CA LEU E 115 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.78e+00 bond pdb=" N LEU K 115 " pdb=" CA LEU K 115 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.74e+00 bond pdb=" N ARG K 114 " pdb=" CA ARG K 114 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.71e+00 bond pdb=" N ARG E 114 " pdb=" CA ARG E 114 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.46e+00 bond pdb=" N ALA K 113 " pdb=" CA ALA K 113 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.69e+00 ... (remaining 7889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 10187 1.72 - 3.44: 371 3.44 - 5.17: 39 5.17 - 6.89: 5 6.89 - 8.61: 4 Bond angle restraints: 10606 Sorted by residual: angle pdb=" N GLY I 803 " pdb=" CA GLY I 803 " pdb=" C GLY I 803 " ideal model delta sigma weight residual 113.18 106.21 6.97 2.37e+00 1.78e-01 8.65e+00 angle pdb=" N GLY C 803 " pdb=" CA GLY C 803 " pdb=" C GLY C 803 " ideal model delta sigma weight residual 113.18 106.25 6.93 2.37e+00 1.78e-01 8.55e+00 angle pdb=" N ALA C 864 " pdb=" CA ALA C 864 " pdb=" C ALA C 864 " ideal model delta sigma weight residual 107.88 111.58 -3.70 1.41e+00 5.03e-01 6.88e+00 angle pdb=" CA ARG K 99 " pdb=" CB ARG K 99 " pdb=" CG ARG K 99 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.85e+00 angle pdb=" N ALA I 864 " pdb=" CA ALA I 864 " pdb=" C ALA I 864 " ideal model delta sigma weight residual 107.88 111.56 -3.68 1.41e+00 5.03e-01 6.82e+00 ... (remaining 10601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4412 17.76 - 35.52: 412 35.52 - 53.27: 88 53.27 - 71.03: 12 71.03 - 88.79: 18 Dihedral angle restraints: 4942 sinusoidal: 2012 harmonic: 2930 Sorted by residual: dihedral pdb=" CB CYS I 795 " pdb=" SG CYS I 795 " pdb=" SG CYS I 868 " pdb=" CB CYS I 868 " ideal model delta sinusoidal sigma weight residual 93.00 47.66 45.34 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS C 795 " pdb=" SG CYS C 795 " pdb=" SG CYS C 868 " pdb=" CB CYS C 868 " ideal model delta sinusoidal sigma weight residual 93.00 47.67 45.33 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CA ILE D 804 " pdb=" C ILE D 804 " pdb=" N ASN D 805 " pdb=" CA ASN D 805 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 4939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 683 0.028 - 0.057: 311 0.057 - 0.085: 126 0.085 - 0.114: 46 0.114 - 0.142: 26 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA LEU E 115 " pdb=" N LEU E 115 " pdb=" C LEU E 115 " pdb=" CB LEU E 115 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ASN J 857 " pdb=" N ASN J 857 " pdb=" C ASN J 857 " pdb=" CB ASN J 857 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA LEU K 115 " pdb=" N LEU K 115 " pdb=" C LEU K 115 " pdb=" CB LEU K 115 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1189 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 827 " -0.015 2.00e-02 2.50e+03 9.58e-03 2.29e+00 pdb=" CG TRP D 827 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP D 827 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 827 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 827 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 827 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 827 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 827 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 827 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 827 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 827 " 0.015 2.00e-02 2.50e+03 9.38e-03 2.20e+00 pdb=" CG TRP J 827 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP J 827 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP J 827 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 827 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 827 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 827 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 827 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 827 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 827 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 809 " -0.013 2.00e-02 2.50e+03 9.04e-03 2.04e+00 pdb=" CG TRP I 809 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP I 809 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP I 809 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 809 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 809 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I 809 " 0.001 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 309 2.70 - 3.25: 8455 3.25 - 3.80: 11709 3.80 - 4.35: 15177 4.35 - 4.90: 23284 Nonbonded interactions: 58934 Sorted by model distance: nonbonded pdb=" OE1 GLN J 883 " pdb=" OG1 THR J 885 " model vdw 2.153 3.040 nonbonded pdb=" OE1 GLN D 883 " pdb=" OG1 THR D 885 " model vdw 2.153 3.040 nonbonded pdb=" O LEU C 791 " pdb=" NE2 GLN C 854 " model vdw 2.157 3.120 nonbonded pdb=" O LEU I 791 " pdb=" NE2 GLN I 854 " model vdw 2.157 3.120 nonbonded pdb=" O LEU K 160 " pdb=" OG SER K 163 " model vdw 2.157 3.040 ... (remaining 58929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'E' and resid 96 through 154) selection = chain 'F' selection = (chain 'K' and resid 96 through 154) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.710 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.110 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.530 ------------------------------------------------------------------------------- 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 : 0.873 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: 0.3503 time to fit residues: 107.8921 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 : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 0.0030 chunk 85 optimal weight: 5.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN C 805 ASN F 96 GLN F 130 GLN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 805 ASN L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.207801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.185239 restraints weight = 12799.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 82)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.183567 restraints weight = 14269.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.183373 restraints weight = 13976.335| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 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 : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6146 (mm-30) REVERT: A 393 ASP cc_start: 0.6291 (m-30) cc_final: 0.6038 (m-30) REVERT: D 802 ASP cc_start: 0.3934 (t0) cc_final: 0.3485 (t0) REVERT: D 812 GLN cc_start: 0.5204 (mp10) cc_final: 0.3735 (mp10) REVERT: D 850 THR cc_start: 0.6572 (m) cc_final: 0.6125 (t) REVERT: D 873 ARG cc_start: 0.5967 (mpp-170) cc_final: 0.5735 (mpp-170) REVERT: D 877 TYR cc_start: 0.5865 (m-80) cc_final: 0.5172 (m-80) REVERT: C 798 SER cc_start: 0.8415 (t) cc_final: 0.8210 (m) REVERT: C 806 ILE cc_start: 0.7758 (tp) cc_final: 0.7486 (tp) REVERT: C 811 ARG cc_start: 0.5391 (ptt180) cc_final: 0.5091 (ttp80) REVERT: C 825 THR cc_start: 0.6820 (OUTLIER) cc_final: 0.6143 (m) REVERT: C 856 ASN cc_start: 0.8175 (t0) cc_final: 0.7920 (t0) REVERT: F 108 GLU cc_start: 0.6970 (tp30) cc_final: 0.6314 (tp30) REVERT: F 115 LEU cc_start: 0.8286 (mm) cc_final: 0.7992 (mm) REVERT: F 133 ASP cc_start: 0.7812 (m-30) cc_final: 0.7429 (m-30) REVERT: F 142 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6305 (tp30) REVERT: F 144 ASP cc_start: 0.6268 (m-30) cc_final: 0.5824 (m-30) REVERT: H 370 SER cc_start: 0.6847 (t) cc_final: 0.6536 (m) REVERT: J 808 ARG cc_start: 0.6041 (ptt-90) cc_final: 0.5615 (ptt90) REVERT: J 820 MET cc_start: 0.6058 (mpp) cc_final: 0.5357 (mpp) REVERT: I 802 ASP cc_start: 0.5418 (t70) cc_final: 0.5023 (t0) REVERT: I 807 MET cc_start: 0.6537 (ppp) cc_final: 0.6017 (ppp) REVERT: I 884 VAL cc_start: 0.7786 (t) cc_final: 0.6117 (t) REVERT: K 148 ASN cc_start: 0.7609 (t0) cc_final: 0.7377 (t0) REVERT: L 115 LEU cc_start: 0.8613 (mm) cc_final: 0.8145 (mm) REVERT: L 132 GLN cc_start: 0.8281 (mp-120) cc_final: 0.7891 (pp30) REVERT: L 142 GLU cc_start: 0.5487 (tm-30) cc_final: 0.4662 (tm-30) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.3228 time to fit residues: 90.7274 Evaluate side-chains 198 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.0070 chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 GLN H 387 GLN L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.203110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 127)---------------| | r_work = 0.4522 r_free = 0.4522 target = 0.175201 restraints weight = 12792.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.172034 restraints weight = 12302.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.172619 restraints weight = 10026.919| |-----------------------------------------------------------------------------| r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 moved from start: 0.5459 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= 0.180 Angle : 0.628 7.347 10606 Z= 0.330 Chirality : 0.041 0.153 1192 Planarity : 0.005 0.052 1416 Dihedral : 5.136 21.988 1126 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.12 % Allowed : 4.60 % 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: -1.50 (0.27), residues: 978 helix: -0.45 (0.22), residues: 508 sheet: -2.00 (0.40), residues: 168 loop : -0.95 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 878 HIS 0.005 0.002 HIS H 406 PHE 0.005 0.001 PHE J 840 TYR 0.008 0.001 TYR I 832 ARG 0.011 0.001 ARG L 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.843 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: A 389 ARG cc_start: 0.5001 (ptp-170) cc_final: 0.4792 (ptp-170) REVERT: D 812 GLN cc_start: 0.5078 (mp10) cc_final: 0.4603 (mt0) REVERT: D 850 THR cc_start: 0.6302 (m) cc_final: 0.5611 (t) REVERT: D 865 VAL cc_start: 0.5807 (t) cc_final: 0.4421 (p) REVERT: D 877 TYR cc_start: 0.5990 (m-80) cc_final: 0.5463 (m-80) REVERT: C 811 ARG cc_start: 0.5727 (ptt180) cc_final: 0.4990 (ttp80) REVERT: C 827 TRP cc_start: 0.6771 (m-90) cc_final: 0.4837 (m-90) REVERT: F 107 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6789 (mm-30) REVERT: F 108 GLU cc_start: 0.7343 (tp30) cc_final: 0.6807 (tp30) REVERT: F 129 ARG cc_start: 0.7677 (tpt-90) cc_final: 0.7466 (tpt-90) REVERT: F 133 ASP cc_start: 0.7788 (m-30) cc_final: 0.7421 (m-30) REVERT: F 139 ASN cc_start: 0.7316 (p0) cc_final: 0.6959 (p0) REVERT: F 142 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7411 (tm-30) REVERT: F 144 ASP cc_start: 0.6805 (m-30) cc_final: 0.6534 (m-30) REVERT: G 375 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6270 (mt-10) REVERT: H 370 SER cc_start: 0.6650 (t) cc_final: 0.6443 (m) REVERT: J 807 MET cc_start: 0.3128 (ppp) cc_final: 0.2090 (ppp) REVERT: J 808 ARG cc_start: 0.4805 (ptt-90) cc_final: 0.4186 (ptt180) REVERT: J 848 LYS cc_start: 0.7050 (tptp) cc_final: 0.6773 (tptp) REVERT: I 793 LEU cc_start: 0.4919 (mt) cc_final: 0.4604 (mt) REVERT: I 802 ASP cc_start: 0.5566 (t70) cc_final: 0.4500 (t0) REVERT: I 807 MET cc_start: 0.6864 (ppp) cc_final: 0.6292 (ppp) REVERT: I 823 VAL cc_start: 0.7503 (p) cc_final: 0.7251 (p) REVERT: I 853 LEU cc_start: 0.6578 (tp) cc_final: 0.6135 (tp) REVERT: I 855 MET cc_start: 0.6049 (mmp) cc_final: 0.5775 (mmm) REVERT: I 884 VAL cc_start: 0.7765 (t) cc_final: 0.6283 (t) REVERT: K 126 ASP cc_start: 0.7605 (m-30) cc_final: 0.6773 (p0) REVERT: K 156 LYS cc_start: 0.7182 (mppt) cc_final: 0.6972 (mppt) REVERT: L 107 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7538 (mm-30) REVERT: L 115 LEU cc_start: 0.8745 (mm) cc_final: 0.8317 (mm) REVERT: L 132 GLN cc_start: 0.8507 (mp-120) cc_final: 0.8161 (pp30) REVERT: L 142 GLU cc_start: 0.6503 (tm-30) cc_final: 0.6279 (tm-30) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.3128 time to fit residues: 84.7678 Evaluate side-chains 200 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 6.9990 chunk 13 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.199672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.175833 restraints weight = 12683.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.175091 restraints weight = 14105.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.176090 restraints weight = 12831.653| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.6131 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= 0.195 Angle : 0.618 7.304 10606 Z= 0.324 Chirality : 0.041 0.145 1192 Planarity : 0.005 0.062 1416 Dihedral : 5.069 21.544 1126 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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: -1.06 (0.27), residues: 978 helix: -0.08 (0.23), residues: 496 sheet: -1.79 (0.41), residues: 168 loop : -0.75 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 827 HIS 0.006 0.003 HIS B 406 PHE 0.007 0.002 PHE J 840 TYR 0.012 0.001 TYR I 832 ARG 0.007 0.001 ARG G 419 *********************** 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 220 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.001 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: A 375 GLU cc_start: 0.6325 (mm-30) cc_final: 0.6029 (mm-30) REVERT: A 389 ARG cc_start: 0.4989 (ptp-170) cc_final: 0.4667 (ptp-170) REVERT: B 375 GLU cc_start: 0.6795 (tp30) cc_final: 0.6482 (tm-30) REVERT: B 387 GLN cc_start: 0.8015 (pt0) cc_final: 0.7714 (pp30) REVERT: D 812 GLN cc_start: 0.5692 (mp10) cc_final: 0.4854 (mt0) REVERT: D 839 ARG cc_start: 0.4735 (ttt-90) cc_final: 0.4129 (mtp180) REVERT: D 850 THR cc_start: 0.6189 (m) cc_final: 0.5411 (t) REVERT: D 865 VAL cc_start: 0.6140 (t) cc_final: 0.3944 (p) REVERT: D 877 TYR cc_start: 0.6041 (m-80) cc_final: 0.5622 (m-80) REVERT: C 806 ILE cc_start: 0.7704 (tp) cc_final: 0.7422 (tp) REVERT: C 811 ARG cc_start: 0.5778 (ptt180) cc_final: 0.5096 (ttp-170) REVERT: C 825 THR cc_start: 0.7798 (m) cc_final: 0.7462 (t) REVERT: C 861 GLU cc_start: 0.8090 (tp30) cc_final: 0.7779 (tp30) REVERT: E 145 ARG cc_start: 0.6885 (mtt180) cc_final: 0.6611 (mtt180) REVERT: F 107 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7122 (mm-30) REVERT: F 108 GLU cc_start: 0.7237 (tp30) cc_final: 0.6577 (tp30) REVERT: F 115 LEU cc_start: 0.8413 (mm) cc_final: 0.8069 (mm) REVERT: F 129 ARG cc_start: 0.7173 (tpt-90) cc_final: 0.6960 (tpt-90) REVERT: F 133 ASP cc_start: 0.7679 (m-30) cc_final: 0.7454 (m-30) REVERT: F 144 ASP cc_start: 0.6592 (m-30) cc_final: 0.6295 (m-30) REVERT: G 422 SER cc_start: 0.3703 (p) cc_final: 0.3297 (p) REVERT: H 443 MET cc_start: 0.1999 (ptt) cc_final: 0.1591 (ptt) REVERT: J 807 MET cc_start: 0.3626 (ppp) cc_final: 0.1987 (ppp) REVERT: J 808 ARG cc_start: 0.5413 (ptt-90) cc_final: 0.3581 (mtm180) REVERT: I 802 ASP cc_start: 0.5404 (t70) cc_final: 0.4382 (t0) REVERT: I 807 MET cc_start: 0.6668 (ppp) cc_final: 0.6325 (ppp) REVERT: I 823 VAL cc_start: 0.7582 (p) cc_final: 0.7278 (p) REVERT: I 884 VAL cc_start: 0.7854 (t) cc_final: 0.6502 (t) REVERT: I 886 VAL cc_start: 0.6886 (p) cc_final: 0.6496 (t) REVERT: K 156 LYS cc_start: 0.7874 (mppt) cc_final: 0.7621 (mppt) REVERT: L 105 GLN cc_start: 0.6872 (tm-30) cc_final: 0.6389 (tm-30) REVERT: L 107 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7834 (mm-30) REVERT: L 115 LEU cc_start: 0.8694 (mm) cc_final: 0.8283 (mm) REVERT: L 119 GLU cc_start: 0.8466 (pp20) cc_final: 0.8098 (pp20) REVERT: L 131 THR cc_start: 0.7817 (p) cc_final: 0.7504 (p) REVERT: L 132 GLN cc_start: 0.8454 (mp-120) cc_final: 0.7943 (pp30) REVERT: L 142 GLU cc_start: 0.6219 (tm-30) cc_final: 0.5790 (tm-30) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2890 time to fit residues: 78.6307 Evaluate side-chains 197 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.0000 chunk 80 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.200338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 187)---------------| | r_work = 0.4513 r_free = 0.4513 target = 0.175866 restraints weight = 12446.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.173576 restraints weight = 11319.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.173576 restraints weight = 11384.328| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.6508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7894 Z= 0.182 Angle : 0.615 7.852 10606 Z= 0.324 Chirality : 0.041 0.155 1192 Planarity : 0.004 0.047 1416 Dihedral : 4.936 20.812 1126 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.25 % Allowed : 2.86 % Favored : 96.89 % 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: -1.18 (0.28), residues: 978 helix: -0.10 (0.23), residues: 512 sheet: -1.95 (0.38), residues: 194 loop : -0.77 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 827 HIS 0.005 0.003 HIS H 406 PHE 0.005 0.001 PHE J 840 TYR 0.011 0.001 TYR C 866 ARG 0.007 0.001 ARG A 384 *********************** 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 218 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.826 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 383 GLU cc_start: 0.5388 (OUTLIER) cc_final: 0.5114 (pm20) REVERT: A 384 ARG cc_start: 0.5329 (tmm160) cc_final: 0.4578 (ttp-170) REVERT: D 812 GLN cc_start: 0.4743 (mp10) cc_final: 0.4472 (mt0) REVERT: D 839 ARG cc_start: 0.5286 (ttt-90) cc_final: 0.4771 (mtp180) REVERT: D 850 THR cc_start: 0.6172 (m) cc_final: 0.5376 (t) REVERT: D 865 VAL cc_start: 0.5905 (t) cc_final: 0.4195 (p) REVERT: C 806 ILE cc_start: 0.7788 (tp) cc_final: 0.7572 (tp) REVERT: C 827 TRP cc_start: 0.5771 (m-90) cc_final: 0.4780 (m-90) REVERT: C 861 GLU cc_start: 0.8386 (tp30) cc_final: 0.7916 (tp30) REVERT: E 119 GLU cc_start: 0.7057 (pp20) cc_final: 0.6592 (pp20) REVERT: E 128 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7902 (mmm160) REVERT: F 107 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7117 (mm-30) REVERT: F 108 GLU cc_start: 0.7164 (tp30) cc_final: 0.6711 (tp30) REVERT: F 115 LEU cc_start: 0.8524 (mm) cc_final: 0.8200 (mm) REVERT: F 129 ARG cc_start: 0.7535 (tpt-90) cc_final: 0.7190 (tpt-90) REVERT: F 132 GLN cc_start: 0.7068 (pp30) cc_final: 0.6855 (pp30) REVERT: F 133 ASP cc_start: 0.7903 (m-30) cc_final: 0.7255 (m-30) REVERT: F 144 ASP cc_start: 0.6947 (m-30) cc_final: 0.6605 (m-30) REVERT: G 389 ARG cc_start: 0.6019 (ptm160) cc_final: 0.5603 (ptm-80) REVERT: G 422 SER cc_start: 0.3661 (p) cc_final: 0.3438 (p) REVERT: H 389 ARG cc_start: 0.6404 (tpp-160) cc_final: 0.6082 (tpt170) REVERT: H 401 GLN cc_start: 0.5968 (tp-100) cc_final: 0.5237 (pm20) REVERT: H 443 MET cc_start: 0.2309 (ptt) cc_final: 0.1925 (ptt) REVERT: J 807 MET cc_start: 0.3911 (ppp) cc_final: 0.2389 (ppp) REVERT: J 808 ARG cc_start: 0.5518 (ptt-90) cc_final: 0.4574 (ptt180) REVERT: I 802 ASP cc_start: 0.5412 (t70) cc_final: 0.4582 (t70) REVERT: I 807 MET cc_start: 0.6940 (ppp) cc_final: 0.6478 (ppp) REVERT: I 823 VAL cc_start: 0.7541 (p) cc_final: 0.7276 (p) REVERT: I 884 VAL cc_start: 0.7865 (t) cc_final: 0.6527 (t) REVERT: K 156 LYS cc_start: 0.7713 (mppt) cc_final: 0.7115 (mppt) REVERT: L 105 GLN cc_start: 0.6749 (tm-30) cc_final: 0.6420 (tm-30) REVERT: L 107 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7706 (mm-30) REVERT: L 130 GLN cc_start: 0.8225 (mp10) cc_final: 0.8006 (mp10) REVERT: L 132 GLN cc_start: 0.8639 (mp-120) cc_final: 0.8154 (pp30) outliers start: 2 outliers final: 0 residues processed: 218 average time/residue: 0.3047 time to fit residues: 80.8123 Evaluate side-chains 193 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 83 optimal weight: 0.5980 chunk 78 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 23 optimal weight: 0.0170 chunk 77 optimal weight: 0.0270 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 HIS F 100 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.205062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.178449 restraints weight = 12440.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.175830 restraints weight = 10206.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.177198 restraints weight = 8001.573| |-----------------------------------------------------------------------------| r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5566 moved from start: 0.6807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7894 Z= 0.148 Angle : 0.592 7.737 10606 Z= 0.312 Chirality : 0.041 0.146 1192 Planarity : 0.003 0.033 1416 Dihedral : 4.587 19.329 1126 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.27), residues: 978 helix: 0.24 (0.23), residues: 498 sheet: -1.64 (0.39), residues: 184 loop : -0.85 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 809 HIS 0.002 0.001 HIS H 406 PHE 0.003 0.001 PHE I 840 TYR 0.010 0.001 TYR D 877 ARG 0.008 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 212 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.016 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 384 ARG cc_start: 0.5146 (tmm160) cc_final: 0.4721 (ttp-170) REVERT: A 389 ARG cc_start: 0.4646 (ptp-170) cc_final: 0.4401 (ptt-90) REVERT: D 812 GLN cc_start: 0.5468 (mp10) cc_final: 0.4049 (mt0) REVERT: D 865 VAL cc_start: 0.5610 (t) cc_final: 0.3304 (p) REVERT: C 799 ARG cc_start: 0.6773 (ttt-90) cc_final: 0.6449 (tmt170) REVERT: C 825 THR cc_start: 0.7770 (t) cc_final: 0.7419 (t) REVERT: C 827 TRP cc_start: 0.5819 (m-90) cc_final: 0.3788 (m-90) REVERT: E 114 ARG cc_start: 0.8125 (ptp90) cc_final: 0.7666 (ptt90) REVERT: E 119 GLU cc_start: 0.7258 (pp20) cc_final: 0.7013 (mm-30) REVERT: E 120 THR cc_start: 0.7386 (m) cc_final: 0.6635 (m) REVERT: E 128 ARG cc_start: 0.8353 (mtt180) cc_final: 0.8029 (mmp-170) REVERT: E 145 ARG cc_start: 0.7437 (mtt180) cc_final: 0.7056 (mtt180) REVERT: F 107 GLU cc_start: 0.7941 (mm-30) cc_final: 0.6777 (mm-30) REVERT: F 108 GLU cc_start: 0.7528 (tp30) cc_final: 0.7010 (tp30) REVERT: F 115 LEU cc_start: 0.8543 (mm) cc_final: 0.8196 (mm) REVERT: F 133 ASP cc_start: 0.7876 (m-30) cc_final: 0.7536 (m-30) REVERT: F 144 ASP cc_start: 0.7021 (m-30) cc_final: 0.6619 (m-30) REVERT: G 389 ARG cc_start: 0.5545 (ptm160) cc_final: 0.5274 (ptm-80) REVERT: H 389 ARG cc_start: 0.6493 (tpp-160) cc_final: 0.5766 (mmt180) REVERT: H 443 MET cc_start: 0.2200 (ptt) cc_final: 0.1802 (ptt) REVERT: J 807 MET cc_start: 0.3475 (ppp) cc_final: 0.3059 (mmt) REVERT: J 820 MET cc_start: 0.5911 (mpp) cc_final: 0.5565 (mpp) REVERT: I 807 MET cc_start: 0.6769 (ppp) cc_final: 0.6476 (ppp) REVERT: K 156 LYS cc_start: 0.7701 (mppt) cc_final: 0.7220 (mppt) REVERT: L 107 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8025 (mm-30) REVERT: L 132 GLN cc_start: 0.8604 (mp-120) cc_final: 0.8142 (pp30) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3283 time to fit residues: 85.1373 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 : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 857 ASN L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.203964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.4557 r_free = 0.4557 target = 0.181161 restraints weight = 12403.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.179658 restraints weight = 12712.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.177232 restraints weight = 10734.660| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7894 Z= 0.167 Angle : 0.633 8.273 10606 Z= 0.336 Chirality : 0.041 0.139 1192 Planarity : 0.004 0.058 1416 Dihedral : 4.584 19.396 1126 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.28), residues: 978 helix: 0.36 (0.24), residues: 498 sheet: -1.48 (0.37), residues: 204 loop : -0.79 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 809 HIS 0.003 0.002 HIS B 406 PHE 0.004 0.001 PHE I 840 TYR 0.013 0.001 TYR I 810 ARG 0.008 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 204 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.901 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: A 384 ARG cc_start: 0.5369 (tmm160) cc_final: 0.4575 (ttp-170) REVERT: D 865 VAL cc_start: 0.4657 (t) cc_final: 0.4454 (p) REVERT: C 799 ARG cc_start: 0.7117 (ttt-90) cc_final: 0.6704 (tmt170) REVERT: C 811 ARG cc_start: 0.5617 (ttt180) cc_final: 0.4870 (ttp-110) REVERT: C 825 THR cc_start: 0.7963 (t) cc_final: 0.7551 (t) REVERT: C 827 TRP cc_start: 0.5901 (m-90) cc_final: 0.4042 (m-90) REVERT: E 114 ARG cc_start: 0.8085 (ptp90) cc_final: 0.7623 (ptt90) REVERT: E 120 THR cc_start: 0.7491 (m) cc_final: 0.6752 (m) REVERT: E 128 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7776 (mmm160) REVERT: F 107 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6516 (mm-30) REVERT: F 108 GLU cc_start: 0.6943 (tp30) cc_final: 0.6402 (tp30) REVERT: F 115 LEU cc_start: 0.8556 (mm) cc_final: 0.8260 (mm) REVERT: F 133 ASP cc_start: 0.7971 (m-30) cc_final: 0.7700 (m-30) REVERT: F 144 ASP cc_start: 0.6982 (m-30) cc_final: 0.6610 (m-30) REVERT: G 389 ARG cc_start: 0.5421 (ptm160) cc_final: 0.5030 (ptm-80) REVERT: H 389 ARG cc_start: 0.6461 (tpp-160) cc_final: 0.6198 (tpt170) REVERT: H 443 MET cc_start: 0.2305 (ptt) cc_final: 0.1940 (ptt) REVERT: J 807 MET cc_start: 0.4038 (ppp) cc_final: 0.2870 (ppp) REVERT: J 820 MET cc_start: 0.5895 (mpp) cc_final: 0.5504 (mpp) REVERT: I 807 MET cc_start: 0.6860 (ppp) cc_final: 0.6525 (ppp) REVERT: I 855 MET cc_start: 0.6308 (mmp) cc_final: 0.6014 (mpp) REVERT: I 857 ASN cc_start: 0.8130 (t0) cc_final: 0.7927 (m-40) REVERT: I 884 VAL cc_start: 0.7800 (t) cc_final: 0.7577 (t) REVERT: K 128 ARG cc_start: 0.7092 (ptt90) cc_final: 0.6377 (ptt90) REVERT: K 156 LYS cc_start: 0.7808 (mppt) cc_final: 0.7577 (mppt) REVERT: L 107 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7880 (mm-30) REVERT: L 129 ARG cc_start: 0.7576 (ptt90) cc_final: 0.6987 (ppt170) REVERT: L 131 THR cc_start: 0.8052 (p) cc_final: 0.7684 (p) REVERT: L 132 GLN cc_start: 0.8393 (mp-120) cc_final: 0.8073 (pp30) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2999 time to fit residues: 74.8443 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 : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 869 ASN I 805 ASN K 139 ASN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.199510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.175345 restraints weight = 12634.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.170937 restraints weight = 11734.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.171847 restraints weight = 9523.887| |-----------------------------------------------------------------------------| r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7894 Z= 0.202 Angle : 0.667 8.329 10606 Z= 0.351 Chirality : 0.042 0.149 1192 Planarity : 0.004 0.040 1416 Dihedral : 4.844 22.663 1126 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.12 % Allowed : 0.87 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 978 helix: 0.19 (0.23), residues: 508 sheet: -1.49 (0.38), residues: 192 loop : -0.76 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 827 HIS 0.005 0.003 HIS G 406 PHE 0.005 0.001 PHE I 840 TYR 0.011 0.001 TYR I 866 ARG 0.008 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: 1 poor density : 208 time to evaluate : 0.859 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: A 384 ARG cc_start: 0.5443 (tmm160) cc_final: 0.4360 (ttp-170) REVERT: A 389 ARG cc_start: 0.4581 (ptp-170) cc_final: 0.4348 (ptp-170) REVERT: B 387 GLN cc_start: 0.8147 (pt0) cc_final: 0.7867 (pp30) REVERT: D 850 THR cc_start: 0.6421 (m) cc_final: 0.5684 (t) REVERT: C 799 ARG cc_start: 0.7242 (ttt-90) cc_final: 0.6575 (tmt170) REVERT: C 811 ARG cc_start: 0.5714 (ttt180) cc_final: 0.4843 (ttp80) REVERT: C 825 THR cc_start: 0.8003 (t) cc_final: 0.7636 (t) REVERT: C 827 TRP cc_start: 0.6538 (m-90) cc_final: 0.4988 (m-90) REVERT: E 114 ARG cc_start: 0.8341 (ptp90) cc_final: 0.7776 (ptt90) REVERT: E 128 ARG cc_start: 0.8212 (mtt180) cc_final: 0.7778 (mmm160) REVERT: F 107 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6613 (mm-30) REVERT: F 108 GLU cc_start: 0.7105 (tp30) cc_final: 0.6543 (tp30) REVERT: F 115 LEU cc_start: 0.8519 (mm) cc_final: 0.8299 (mm) REVERT: F 133 ASP cc_start: 0.7916 (m-30) cc_final: 0.7668 (m-30) REVERT: F 144 ASP cc_start: 0.7224 (m-30) cc_final: 0.6943 (m-30) REVERT: G 389 ARG cc_start: 0.5629 (ptm160) cc_final: 0.5234 (ptm-80) REVERT: H 443 MET cc_start: 0.2065 (ptt) cc_final: 0.1646 (ptt) REVERT: J 807 MET cc_start: 0.4228 (ppp) cc_final: 0.3212 (ppp) REVERT: J 820 MET cc_start: 0.6091 (mpp) cc_final: 0.5591 (mpp) REVERT: I 807 MET cc_start: 0.7013 (ppp) cc_final: 0.6714 (ppp) REVERT: I 855 MET cc_start: 0.6419 (mmp) cc_final: 0.6111 (mpp) REVERT: I 884 VAL cc_start: 0.7776 (t) cc_final: 0.7454 (t) REVERT: K 156 LYS cc_start: 0.7769 (mppt) cc_final: 0.7530 (mppt) REVERT: L 107 GLU cc_start: 0.8705 (mm-30) cc_final: 0.7917 (mm-30) REVERT: L 129 ARG cc_start: 0.7521 (ptt90) cc_final: 0.7269 (ppt170) REVERT: L 131 THR cc_start: 0.8139 (p) cc_final: 0.7793 (p) REVERT: L 132 GLN cc_start: 0.8275 (mp-120) cc_final: 0.8072 (pp30) REVERT: L 133 ASP cc_start: 0.7622 (m-30) cc_final: 0.7363 (m-30) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2948 time to fit residues: 75.6548 Evaluate side-chains 190 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 16 optimal weight: 0.0370 chunk 81 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 75 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 10 optimal weight: 1.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 805 ASN K 130 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.202153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 136)---------------| | r_work = 0.4525 r_free = 0.4525 target = 0.177570 restraints weight = 12702.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.175796 restraints weight = 12125.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.176295 restraints weight = 9711.016| |-----------------------------------------------------------------------------| r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5595 moved from start: 0.7730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7894 Z= 0.163 Angle : 0.641 8.607 10606 Z= 0.336 Chirality : 0.041 0.152 1192 Planarity : 0.004 0.041 1416 Dihedral : 4.583 22.663 1126 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.12 % Allowed : 1.37 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.28), residues: 978 helix: 0.31 (0.23), residues: 510 sheet: -1.35 (0.38), residues: 192 loop : -0.84 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 809 HIS 0.003 0.001 HIS H 406 PHE 0.003 0.001 PHE I 840 TYR 0.015 0.001 TYR C 810 ARG 0.009 0.001 ARG B 419 *********************** 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 206 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.810 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 384 ARG cc_start: 0.5207 (tmm160) cc_final: 0.4214 (ttp-170) REVERT: A 389 ARG cc_start: 0.4503 (ptp-170) cc_final: 0.4212 (ptt-90) REVERT: C 811 ARG cc_start: 0.5759 (ttt180) cc_final: 0.5418 (ttp-170) REVERT: C 825 THR cc_start: 0.7997 (t) cc_final: 0.7758 (t) REVERT: E 114 ARG cc_start: 0.8175 (ptp90) cc_final: 0.7663 (ptt90) REVERT: F 107 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6519 (mm-30) REVERT: F 108 GLU cc_start: 0.6886 (tp30) cc_final: 0.6376 (tp30) REVERT: F 115 LEU cc_start: 0.8506 (mm) cc_final: 0.8232 (mm) REVERT: F 129 ARG cc_start: 0.7040 (tpt90) cc_final: 0.6710 (tpt170) REVERT: F 144 ASP cc_start: 0.7012 (m-30) cc_final: 0.6794 (m-30) REVERT: H 389 ARG cc_start: 0.6509 (tpp-160) cc_final: 0.6213 (tpt170) REVERT: H 443 MET cc_start: 0.2194 (ptt) cc_final: 0.1760 (ptt) REVERT: J 807 MET cc_start: 0.3996 (ppp) cc_final: 0.3158 (ppp) REVERT: J 820 MET cc_start: 0.5875 (mpp) cc_final: 0.5512 (mpp) REVERT: I 807 MET cc_start: 0.7069 (ppp) cc_final: 0.6554 (ppp) REVERT: I 855 MET cc_start: 0.6507 (mmp) cc_final: 0.6109 (mpp) REVERT: I 884 VAL cc_start: 0.7958 (t) cc_final: 0.7175 (t) REVERT: L 107 GLU cc_start: 0.8682 (mm-30) cc_final: 0.7901 (mm-30) REVERT: L 129 ARG cc_start: 0.7351 (ptt90) cc_final: 0.6527 (ppt170) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.3059 time to fit residues: 77.2256 Evaluate side-chains 186 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN I 805 ASN L 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.195406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.171852 restraints weight = 12673.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.171268 restraints weight = 12573.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.169380 restraints weight = 10132.964| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5724 moved from start: 0.8094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7894 Z= 0.257 Angle : 0.750 9.540 10606 Z= 0.395 Chirality : 0.044 0.239 1192 Planarity : 0.005 0.059 1416 Dihedral : 5.222 26.321 1126 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.27), residues: 978 helix: 0.27 (0.23), residues: 502 sheet: -1.63 (0.37), residues: 184 loop : -1.01 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 827 HIS 0.008 0.004 HIS G 406 PHE 0.007 0.001 PHE I 840 TYR 0.020 0.002 TYR D 877 ARG 0.009 0.001 ARG B 419 ********************** 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 204 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 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: A 369 LYS cc_start: 0.8012 (tmtt) cc_final: 0.7049 (tptp) REVERT: A 384 ARG cc_start: 0.5547 (tmm160) cc_final: 0.4523 (ttp-170) REVERT: D 11 LEU cc_start: 0.6892 (mm) cc_final: 0.6677 (mm) REVERT: D 837 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8275 (mmmm) REVERT: D 850 THR cc_start: 0.6461 (m) cc_final: 0.5724 (t) REVERT: C 3 GLN cc_start: 0.7939 (mp10) cc_final: 0.6462 (tt0) REVERT: C 811 ARG cc_start: 0.5781 (ttt180) cc_final: 0.5324 (ttt-90) REVERT: C 825 THR cc_start: 0.8015 (t) cc_final: 0.7734 (t) REVERT: C 856 ASN cc_start: 0.7982 (t0) cc_final: 0.7314 (p0) REVERT: E 114 ARG cc_start: 0.8114 (ptp90) cc_final: 0.7522 (ptt90) REVERT: E 128 ARG cc_start: 0.7708 (ptt180) cc_final: 0.7258 (ptt90) REVERT: F 107 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6461 (mm-30) REVERT: F 108 GLU cc_start: 0.7187 (tp30) cc_final: 0.6536 (tp30) REVERT: F 115 LEU cc_start: 0.8468 (mm) cc_final: 0.8244 (mm) REVERT: F 133 ASP cc_start: 0.7764 (m-30) cc_final: 0.7435 (m-30) REVERT: F 144 ASP cc_start: 0.6828 (m-30) cc_final: 0.6596 (m-30) REVERT: G 375 GLU cc_start: 0.6706 (mp0) cc_final: 0.6359 (mp0) REVERT: J 820 MET cc_start: 0.6169 (mpp) cc_final: 0.5577 (mpp) REVERT: I 807 MET cc_start: 0.7110 (ppp) cc_final: 0.6525 (ppp) REVERT: I 855 MET cc_start: 0.6683 (mmp) cc_final: 0.6260 (mpp) REVERT: I 863 THR cc_start: 0.5897 (m) cc_final: 0.5566 (m) REVERT: I 884 VAL cc_start: 0.7749 (t) cc_final: 0.7546 (t) REVERT: I 886 VAL cc_start: 0.7541 (m) cc_final: 0.6958 (t) REVERT: K 100 GLN cc_start: 0.8371 (mp10) cc_final: 0.7788 (mp10) REVERT: K 128 ARG cc_start: 0.7542 (tmt170) cc_final: 0.7298 (tmt170) REVERT: K 156 LYS cc_start: 0.7933 (mppt) cc_final: 0.7611 (mppt) REVERT: L 107 GLU cc_start: 0.8714 (mm-30) cc_final: 0.7643 (mm-30) REVERT: L 129 ARG cc_start: 0.7392 (ptt90) cc_final: 0.6538 (ppt170) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3008 time to fit residues: 75.2796 Evaluate side-chains 181 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.0060 chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.201632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.178521 restraints weight = 12521.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 88)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.177562 restraints weight = 12044.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.177742 restraints weight = 10267.843| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 moved from start: 0.8243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7894 Z= 0.175 Angle : 0.678 8.079 10606 Z= 0.352 Chirality : 0.042 0.179 1192 Planarity : 0.004 0.081 1416 Dihedral : 4.691 24.783 1126 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.27), residues: 978 helix: 0.41 (0.23), residues: 502 sheet: -1.41 (0.38), residues: 176 loop : -1.05 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 809 HIS 0.003 0.001 HIS H 406 PHE 0.004 0.001 PHE C 840 TYR 0.015 0.001 TYR C 810 ARG 0.009 0.001 ARG A 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3125.37 seconds wall clock time: 56 minutes 29.78 seconds (3389.78 seconds total)