Starting phenix.real_space_refine on Fri Jul 25 16:18:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afm_15402/07_2025/8afm_15402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afm_15402/07_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_15402/07_2025/8afm_15402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afm_15402/07_2025/8afm_15402.map" model { file = "/net/cci-nas-00/data/ceres_data/8afm_15402/07_2025/8afm_15402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afm_15402/07_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-5711/modules/chem_data/mon_lib" Total number of atoms: 7842 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "B" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "E" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 455 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "G" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "I" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "K" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "L" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 455 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Time building chain proxies: 5.00, per 1000 atoms: 0.64 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: 1.69 Conformation dependent library (CDL) restraints added in 996.5 milliseconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 58.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 369 through 419 removed outlier: 3.537A pdb=" N LYS A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.766A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 removed outlier: 4.228A pdb=" N LEU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.846A pdb=" N LYS B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 391 " --> pdb=" O GLN B 387 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 429 removed outlier: 3.517A pdb=" N ALA B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 410 " --> pdb=" O HIS B 406 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.606A pdb=" N ALA B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'D' and resid 833 through 837 removed outlier: 3.505A pdb=" N LYS D 837 " --> pdb=" O ASP D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 863 removed outlier: 4.111A pdb=" N THR D 863 " --> pdb=" O PRO D 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 863 removed outlier: 3.537A pdb=" N THR C 863 " --> pdb=" O PRO C 860 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 155 removed outlier: 3.911A pdb=" N GLN E 105 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 155 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 160 removed outlier: 3.631A pdb=" N SER E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'F' and resid 97 through 139 removed outlier: 3.522A pdb=" N LEU F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F 106 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU F 124 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN F 139 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 154 removed outlier: 3.894A pdb=" N ILE F 143 " --> pdb=" O ASN F 139 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN F 148 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 419 removed outlier: 3.537A pdb=" N LYS G 376 " --> pdb=" O VAL G 372 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA G 377 " --> pdb=" O ALA G 373 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 378 " --> pdb=" O GLN G 374 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU G 382 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA G 390 " --> pdb=" O GLN G 386 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG G 391 " --> pdb=" O GLN G 387 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN G 396 " --> pdb=" O LEU G 392 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU G 407 " --> pdb=" O ARG G 403 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 408 " --> pdb=" O ARG G 404 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE G 410 " --> pdb=" O HIS G 406 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G 411 " --> pdb=" O GLU G 407 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR G 416 " --> pdb=" O GLU G 412 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 434 removed outlier: 3.766A pdb=" N LEU G 426 " --> pdb=" O SER G 422 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU G 428 " --> pdb=" O ALA G 424 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA G 430 " --> pdb=" O LEU G 426 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU G 431 " --> pdb=" O ALA G 427 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA G 434 " --> pdb=" O ALA G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 443 removed outlier: 4.228A pdb=" N LEU G 441 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 401 removed outlier: 3.846A pdb=" N LYS H 379 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG H 380 " --> pdb=" O LYS H 376 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA H 381 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU H 383 " --> pdb=" O LYS H 379 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN H 386 " --> pdb=" O GLU H 382 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG H 391 " --> pdb=" O GLN H 387 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU H 392 " --> pdb=" O LEU H 388 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN H 399 " --> pdb=" O MET H 395 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP H 400 " --> pdb=" O GLN H 396 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN H 401 " --> pdb=" O GLU H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 429 removed outlier: 3.516A pdb=" N ALA H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE H 410 " --> pdb=" O HIS H 406 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 411 " --> pdb=" O GLU H 407 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR H 416 " --> pdb=" O GLU H 412 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE H 417 " --> pdb=" O LEU H 413 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU H 418 " --> pdb=" O GLN H 414 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR H 421 " --> pdb=" O ILE H 417 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H 426 " --> pdb=" O SER H 422 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY H 429 " --> pdb=" O ALA H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 434 removed outlier: 3.606A pdb=" N ALA H 434 " --> pdb=" O ALA H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 439 Processing helix chain 'H' and resid 440 through 443 Processing helix chain 'J' and resid 833 through 837 removed outlier: 3.505A pdb=" N LYS J 837 " --> pdb=" O ASP J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 859 through 863 removed outlier: 4.111A pdb=" N THR J 863 " --> pdb=" O PRO J 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 859 through 863 removed outlier: 3.536A pdb=" N THR I 863 " --> pdb=" O PRO I 860 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 155 removed outlier: 3.911A pdb=" N GLN K 105 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA K 106 " --> pdb=" O ALA K 102 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA K 116 " --> pdb=" O SER K 112 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU K 137 " --> pdb=" O ASP K 133 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG K 145 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU K 146 " --> pdb=" O GLU K 142 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU K 155 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 160 removed outlier: 3.631A pdb=" N SER K 159 " --> pdb=" O LEU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'L' and resid 97 through 139 removed outlier: 3.523A pdb=" N LEU L 103 " --> pdb=" O ARG L 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA L 106 " --> pdb=" O ALA L 102 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU L 124 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN L 139 " --> pdb=" O ALA L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 154 removed outlier: 3.893A pdb=" N ILE L 143 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN L 148 " --> pdb=" O ASP L 144 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER L 153 " --> pdb=" O ALA L 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7 removed outlier: 4.036A pdb=" N CYS D 795 " --> pdb=" O VAL D 851 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL D 851 " --> pdb=" O CYS D 795 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 841 " --> pdb=" O GLN D 854 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 818 through 824 removed outlier: 3.561A pdb=" N GLY D 819 " --> pdb=" O ARG D 811 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP D 809 " --> pdb=" O VAL D 821 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL D 823 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N MET D 807 " --> pdb=" O VAL D 823 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 869 through 872 removed outlier: 3.693A pdb=" N ALA D 870 " --> pdb=" O TYR D 877 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 790 through 795 removed outlier: 3.516A pdb=" N CYS C 795 " --> pdb=" O VAL C 851 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN C 831 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 823 " --> pdb=" O ASN C 831 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 821 " --> pdb=" O TRP C 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 870 " --> pdb=" O TYR C 877 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN C 831 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 823 " --> pdb=" O ASN C 831 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 821 " --> pdb=" O TRP C 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 5 through 7 removed outlier: 4.036A pdb=" N CYS J 795 " --> pdb=" O VAL J 851 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL J 851 " --> pdb=" O CYS J 795 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE J 841 " --> pdb=" O GLN J 854 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 818 through 824 removed outlier: 3.562A pdb=" N GLY J 819 " --> pdb=" O ARG J 811 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP J 809 " --> pdb=" O VAL J 821 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL J 823 " --> pdb=" O MET J 807 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N MET J 807 " --> pdb=" O VAL J 823 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 869 through 872 removed outlier: 3.694A pdb=" N ALA J 870 " --> pdb=" O TYR J 877 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 790 through 795 removed outlier: 3.515A pdb=" N CYS I 795 " --> pdb=" O VAL I 851 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN I 831 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL I 823 " --> pdb=" O ASN I 831 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 821 " --> pdb=" O TRP I 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA I 870 " --> pdb=" O TYR I 877 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN I 831 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL I 823 " --> pdb=" O ASN I 831 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 821 " --> pdb=" O TRP I 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2844 1.34 - 1.46: 1129 1.46 - 1.58: 3873 1.58 - 1.70: 0 1.70 - 1.81: 48 Bond restraints: 7894 Sorted by residual: bond pdb=" N LEU E 115 " pdb=" CA LEU E 115 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.78e+00 bond pdb=" N LEU K 115 " pdb=" CA LEU K 115 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.74e+00 bond pdb=" N ARG K 114 " pdb=" CA ARG K 114 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.71e+00 bond pdb=" N ARG E 114 " pdb=" CA ARG E 114 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.46e+00 bond pdb=" N ALA K 113 " pdb=" CA ALA K 113 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.69e+00 ... (remaining 7889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 10187 1.72 - 3.44: 371 3.44 - 5.17: 39 5.17 - 6.89: 5 6.89 - 8.61: 4 Bond angle restraints: 10606 Sorted by residual: angle pdb=" N GLY I 803 " pdb=" CA GLY I 803 " pdb=" C GLY I 803 " ideal model delta sigma weight residual 113.18 106.21 6.97 2.37e+00 1.78e-01 8.65e+00 angle pdb=" N GLY C 803 " pdb=" CA GLY C 803 " pdb=" C GLY C 803 " ideal model delta sigma weight residual 113.18 106.25 6.93 2.37e+00 1.78e-01 8.55e+00 angle pdb=" N ALA C 864 " pdb=" CA ALA C 864 " pdb=" C ALA C 864 " ideal model delta sigma weight residual 107.88 111.58 -3.70 1.41e+00 5.03e-01 6.88e+00 angle pdb=" CA ARG K 99 " pdb=" CB ARG K 99 " pdb=" CG ARG K 99 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.85e+00 angle pdb=" N ALA I 864 " pdb=" CA ALA I 864 " pdb=" C ALA I 864 " ideal model delta sigma weight residual 107.88 111.56 -3.68 1.41e+00 5.03e-01 6.82e+00 ... (remaining 10601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4412 17.76 - 35.52: 412 35.52 - 53.27: 88 53.27 - 71.03: 12 71.03 - 88.79: 18 Dihedral angle restraints: 4942 sinusoidal: 2012 harmonic: 2930 Sorted by residual: dihedral pdb=" CB CYS I 795 " pdb=" SG CYS I 795 " pdb=" SG CYS I 868 " pdb=" CB CYS I 868 " ideal model delta sinusoidal sigma weight residual 93.00 47.66 45.34 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS C 795 " pdb=" SG CYS C 795 " pdb=" SG CYS C 868 " pdb=" CB CYS C 868 " ideal model delta sinusoidal sigma weight residual 93.00 47.67 45.33 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CA ILE D 804 " pdb=" C ILE D 804 " pdb=" N ASN D 805 " pdb=" CA ASN D 805 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 4939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 683 0.028 - 0.057: 311 0.057 - 0.085: 126 0.085 - 0.114: 46 0.114 - 0.142: 26 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA LEU E 115 " pdb=" N LEU E 115 " pdb=" C LEU E 115 " pdb=" CB LEU E 115 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ASN J 857 " pdb=" N ASN J 857 " pdb=" C ASN J 857 " pdb=" CB ASN J 857 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA LEU K 115 " pdb=" N LEU K 115 " pdb=" C LEU K 115 " pdb=" CB LEU K 115 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1189 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 827 " -0.015 2.00e-02 2.50e+03 9.58e-03 2.29e+00 pdb=" CG TRP D 827 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP D 827 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 827 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 827 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 827 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 827 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 827 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 827 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 827 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 827 " 0.015 2.00e-02 2.50e+03 9.38e-03 2.20e+00 pdb=" CG TRP J 827 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP J 827 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP J 827 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 827 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 827 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 827 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 827 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 827 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 827 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 809 " -0.013 2.00e-02 2.50e+03 9.04e-03 2.04e+00 pdb=" CG TRP I 809 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP I 809 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP I 809 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 809 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 809 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I 809 " 0.001 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 309 2.70 - 3.25: 8455 3.25 - 3.80: 11709 3.80 - 4.35: 15177 4.35 - 4.90: 23284 Nonbonded interactions: 58934 Sorted by model distance: nonbonded pdb=" OE1 GLN J 883 " pdb=" OG1 THR J 885 " model vdw 2.153 3.040 nonbonded pdb=" OE1 GLN D 883 " pdb=" OG1 THR D 885 " model vdw 2.153 3.040 nonbonded pdb=" O LEU C 791 " pdb=" NE2 GLN C 854 " model vdw 2.157 3.120 nonbonded pdb=" O LEU I 791 " pdb=" NE2 GLN I 854 " model vdw 2.157 3.120 nonbonded pdb=" O LEU K 160 " pdb=" OG SER K 163 " model vdw 2.157 3.040 ... (remaining 58929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'E' and resid 96 through 154) selection = chain 'F' selection = (chain 'K' and resid 96 through 154) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.050 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5120 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7898 Z= 0.214 Angle : 0.744 8.610 10614 Z= 0.446 Chirality : 0.042 0.142 1192 Planarity : 0.003 0.029 1416 Dihedral : 15.273 88.790 3022 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.25 % Allowed : 0.25 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.24), residues: 978 helix: -2.28 (0.20), residues: 504 sheet: -2.15 (0.40), residues: 166 loop : -1.97 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP D 827 HIS 0.002 0.001 HIS H 406 PHE 0.010 0.003 PHE D 840 TYR 0.019 0.002 TYR C 872 ARG 0.020 0.001 ARG B 380 Details of bonding type rmsd hydrogen bonds : bond 0.30317 ( 418) hydrogen bonds : angle 11.34145 ( 1236) SS BOND : bond 0.00658 ( 4) SS BOND : angle 1.33673 ( 8) covalent geometry : bond 0.00411 ( 7894) covalent geometry : angle 0.74289 (10606) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 256 time to evaluate : 1.104 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: 0.4583 time to fit residues: 142.9721 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 : 1.241 ------------------------------------------------------------------------------- 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 = 58)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.185382 restraints weight = 12799.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.184802 restraints weight = 12797.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.183359 restraints weight = 11842.821| |-----------------------------------------------------------------------------| r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5504 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7898 Z= 0.186 Angle : 0.733 9.169 10614 Z= 0.382 Chirality : 0.045 0.153 1192 Planarity : 0.006 0.068 1416 Dihedral : 5.760 25.092 1126 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.12 % Allowed : 6.84 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.26), residues: 978 helix: -0.94 (0.22), residues: 520 sheet: -2.65 (0.42), residues: 138 loop : -1.37 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP J 827 HIS 0.007 0.004 HIS B 406 PHE 0.011 0.002 PHE J 840 TYR 0.019 0.002 TYR I 872 ARG 0.007 0.001 ARG L 145 Details of bonding type rmsd hydrogen bonds : bond 0.04962 ( 418) hydrogen bonds : angle 5.69050 ( 1236) SS BOND : bond 0.01273 ( 4) SS BOND : angle 0.90144 ( 8) covalent geometry : bond 0.00382 ( 7894) covalent geometry : angle 0.73331 (10606) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 1.723 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: 0.7066 (mm-30) cc_final: 0.6135 (mm-30) REVERT: A 393 ASP cc_start: 0.6275 (m-30) cc_final: 0.6051 (m-30) REVERT: D 802 ASP cc_start: 0.3959 (t0) cc_final: 0.3514 (t0) REVERT: D 812 GLN cc_start: 0.5206 (mp10) cc_final: 0.3738 (mp10) REVERT: D 850 THR cc_start: 0.6562 (m) cc_final: 0.6116 (t) REVERT: D 873 ARG cc_start: 0.5959 (mpp-170) cc_final: 0.5728 (mpp-170) REVERT: D 877 TYR cc_start: 0.5879 (m-80) cc_final: 0.5190 (m-80) REVERT: C 798 SER cc_start: 0.8399 (t) cc_final: 0.8198 (m) REVERT: C 806 ILE cc_start: 0.7764 (tp) cc_final: 0.7496 (tp) REVERT: C 811 ARG cc_start: 0.5384 (ptt180) cc_final: 0.5083 (ttp80) REVERT: C 825 THR cc_start: 0.6829 (OUTLIER) cc_final: 0.6162 (m) REVERT: C 856 ASN cc_start: 0.8174 (t0) cc_final: 0.7922 (t0) REVERT: C 861 GLU cc_start: 0.8103 (tt0) cc_final: 0.7901 (tp30) REVERT: F 108 GLU cc_start: 0.6953 (tp30) cc_final: 0.6297 (tp30) REVERT: F 115 LEU cc_start: 0.8290 (mm) cc_final: 0.7995 (mm) REVERT: F 133 ASP cc_start: 0.7821 (m-30) cc_final: 0.7432 (m-30) REVERT: F 142 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6326 (tp30) REVERT: F 144 ASP cc_start: 0.6275 (m-30) cc_final: 0.5833 (m-30) REVERT: H 370 SER cc_start: 0.6857 (t) cc_final: 0.6545 (m) REVERT: J 801 ILE cc_start: 0.8333 (mm) cc_final: 0.8129 (mm) REVERT: J 808 ARG cc_start: 0.6052 (ptt-90) cc_final: 0.5628 (ptt90) REVERT: J 820 MET cc_start: 0.6032 (mpp) cc_final: 0.5333 (mpp) REVERT: I 802 ASP cc_start: 0.5415 (t70) cc_final: 0.5026 (t0) REVERT: I 807 MET cc_start: 0.6537 (ppp) cc_final: 0.6014 (ppp) REVERT: I 884 VAL cc_start: 0.7776 (t) cc_final: 0.6112 (t) REVERT: K 148 ASN cc_start: 0.7618 (t0) cc_final: 0.7384 (t0) REVERT: L 115 LEU cc_start: 0.8620 (mm) cc_final: 0.8150 (mm) REVERT: L 132 GLN cc_start: 0.8286 (mp-120) cc_final: 0.7892 (pp30) REVERT: L 142 GLU cc_start: 0.5499 (tm-30) cc_final: 0.4674 (tm-30) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.3752 time to fit residues: 107.4484 Evaluate side-chains 198 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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: 0.0870 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 13 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 = 0.4703 r_free = 0.4703 target = 0.213806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.4583 r_free = 0.4583 target = 0.191940 restraints weight = 13454.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.191968 restraints weight = 15937.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.190430 restraints weight = 13312.151| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5405 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7898 Z= 0.126 Angle : 0.624 7.578 10614 Z= 0.326 Chirality : 0.041 0.218 1192 Planarity : 0.005 0.054 1416 Dihedral : 5.080 21.743 1126 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.12 % Allowed : 4.48 % Favored : 95.40 % 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: -1.46 (0.27), residues: 978 helix: -0.43 (0.22), residues: 508 sheet: -1.96 (0.41), residues: 168 loop : -0.94 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 878 HIS 0.004 0.002 HIS H 406 PHE 0.005 0.001 PHE J 840 TYR 0.009 0.001 TYR D 810 ARG 0.013 0.001 ARG L 129 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 418) hydrogen bonds : angle 4.90419 ( 1236) SS BOND : bond 0.00338 ( 4) SS BOND : angle 0.53362 ( 8) covalent geometry : bond 0.00255 ( 7894) covalent geometry : angle 0.62413 (10606) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6390 (mm-30) REVERT: A 389 ARG cc_start: 0.4719 (ptp-170) cc_final: 0.4384 (ptp-170) REVERT: D 812 GLN cc_start: 0.5174 (mp10) cc_final: 0.4729 (mt0) REVERT: D 850 THR cc_start: 0.6253 (m) cc_final: 0.5625 (t) REVERT: D 865 VAL cc_start: 0.6298 (t) cc_final: 0.4642 (p) REVERT: D 877 TYR cc_start: 0.5917 (m-80) cc_final: 0.5613 (m-80) REVERT: C 811 ARG cc_start: 0.5467 (ptt180) cc_final: 0.4969 (ttp80) REVERT: C 827 TRP cc_start: 0.6718 (m-90) cc_final: 0.4633 (m-90) REVERT: C 856 ASN cc_start: 0.8005 (t0) cc_final: 0.7797 (t0) REVERT: F 104 ILE cc_start: 0.6938 (tt) cc_final: 0.6427 (tt) REVERT: F 107 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6564 (mm-30) REVERT: F 108 GLU cc_start: 0.6685 (tp30) cc_final: 0.6052 (tp30) REVERT: F 133 ASP cc_start: 0.7567 (m-30) cc_final: 0.7270 (m-30) REVERT: G 375 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6299 (mt-10) REVERT: G 423 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6788 (tm-30) REVERT: H 370 SER cc_start: 0.6658 (t) cc_final: 0.6407 (m) REVERT: J 807 MET cc_start: 0.2981 (ppp) cc_final: 0.2047 (ppp) REVERT: J 808 ARG cc_start: 0.5096 (ptt-90) cc_final: 0.4499 (ptt180) REVERT: J 848 LYS cc_start: 0.6430 (tptp) cc_final: 0.6157 (tptp) REVERT: I 793 LEU cc_start: 0.4523 (mt) cc_final: 0.4227 (mt) REVERT: I 802 ASP cc_start: 0.4292 (t70) cc_final: 0.3319 (t0) REVERT: I 807 MET cc_start: 0.6650 (ppp) cc_final: 0.6311 (ppp) REVERT: I 823 VAL cc_start: 0.7562 (p) cc_final: 0.7287 (p) REVERT: I 853 LEU cc_start: 0.6408 (tp) cc_final: 0.5985 (tp) REVERT: I 884 VAL cc_start: 0.7739 (t) cc_final: 0.6147 (t) REVERT: K 126 ASP cc_start: 0.7343 (m-30) cc_final: 0.6397 (p0) REVERT: K 148 ASN cc_start: 0.7733 (t0) cc_final: 0.7503 (m-40) REVERT: K 156 LYS cc_start: 0.7401 (mppt) cc_final: 0.7136 (mppt) REVERT: L 107 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7261 (mm-30) REVERT: L 115 LEU cc_start: 0.8630 (mm) cc_final: 0.8219 (mm) REVERT: L 132 GLN cc_start: 0.8241 (mp-120) cc_final: 0.7865 (pp30) REVERT: L 142 GLU cc_start: 0.5381 (tm-30) cc_final: 0.4899 (tm-30) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.3449 time to fit residues: 95.5530 Evaluate side-chains 196 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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: 2.9990 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 16 optimal weight: 0.0170 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN H 387 GLN J 869 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 = 0.4677 r_free = 0.4677 target = 0.202848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.4543 r_free = 0.4543 target = 0.177494 restraints weight = 12826.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.177494 restraints weight = 15172.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.177494 restraints weight = 15172.500| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5491 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7898 Z= 0.119 Angle : 0.581 7.395 10614 Z= 0.302 Chirality : 0.040 0.138 1192 Planarity : 0.004 0.054 1416 Dihedral : 4.776 19.595 1126 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.12 % Allowed : 2.99 % 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: -0.96 (0.27), residues: 978 helix: 0.03 (0.23), residues: 494 sheet: -1.80 (0.41), residues: 168 loop : -0.72 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 878 HIS 0.004 0.002 HIS B 406 PHE 0.006 0.001 PHE J 840 TYR 0.009 0.001 TYR C 866 ARG 0.008 0.001 ARG H 435 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 418) hydrogen bonds : angle 4.49160 ( 1236) SS BOND : bond 0.00527 ( 4) SS BOND : angle 0.58633 ( 8) covalent geometry : bond 0.00240 ( 7894) covalent geometry : angle 0.58131 (10606) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 1.184 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: 0.4728 (ptp-170) cc_final: 0.4528 (ptp-170) REVERT: D 11 LEU cc_start: 0.6451 (mm) cc_final: 0.6245 (mm) REVERT: D 812 GLN cc_start: 0.5285 (mp10) cc_final: 0.4730 (mt0) REVERT: D 850 THR cc_start: 0.6153 (m) cc_final: 0.5279 (t) REVERT: D 865 VAL cc_start: 0.6030 (t) cc_final: 0.4101 (p) REVERT: D 877 TYR cc_start: 0.5843 (m-80) cc_final: 0.5302 (m-80) REVERT: C 806 ILE cc_start: 0.7637 (tp) cc_final: 0.7321 (tp) REVERT: C 811 ARG cc_start: 0.5776 (ptt180) cc_final: 0.4970 (ttp80) REVERT: C 825 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7318 (t) REVERT: C 827 TRP cc_start: 0.6698 (m-90) cc_final: 0.4401 (m-90) REVERT: E 120 THR cc_start: 0.7403 (m) cc_final: 0.6689 (m) REVERT: F 107 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7005 (mm-30) REVERT: F 108 GLU cc_start: 0.6959 (tp30) cc_final: 0.6476 (tp30) REVERT: F 115 LEU cc_start: 0.8433 (mm) cc_final: 0.8073 (mm) REVERT: F 133 ASP cc_start: 0.7660 (m-30) cc_final: 0.7242 (m-30) REVERT: F 142 GLU cc_start: 0.7057 (pp20) cc_final: 0.6527 (mp0) REVERT: F 144 ASP cc_start: 0.6533 (m-30) cc_final: 0.6094 (m-30) REVERT: G 395 MET cc_start: 0.5266 (ttm) cc_final: 0.5063 (ttm) REVERT: G 422 SER cc_start: 0.3654 (p) cc_final: 0.3334 (p) REVERT: J 807 MET cc_start: 0.3274 (ppp) cc_final: 0.1750 (ppp) REVERT: J 808 ARG cc_start: 0.5270 (ptt-90) cc_final: 0.3562 (mtm180) REVERT: I 802 ASP cc_start: 0.4256 (t70) cc_final: 0.3621 (t70) REVERT: I 823 VAL cc_start: 0.7597 (p) cc_final: 0.7319 (p) REVERT: I 884 VAL cc_start: 0.7837 (t) cc_final: 0.6655 (t) REVERT: K 126 ASP cc_start: 0.7468 (m-30) cc_final: 0.6979 (p0) REVERT: K 156 LYS cc_start: 0.7845 (mppt) cc_final: 0.7588 (mppt) REVERT: L 105 GLN cc_start: 0.6867 (tm-30) cc_final: 0.6302 (tm-30) REVERT: L 107 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7695 (mm-30) REVERT: L 115 LEU cc_start: 0.8692 (mm) cc_final: 0.8298 (mm) REVERT: L 119 GLU cc_start: 0.8287 (pp20) cc_final: 0.7886 (pp20) REVERT: L 131 THR cc_start: 0.7788 (p) cc_final: 0.7387 (p) REVERT: L 132 GLN cc_start: 0.8476 (mp-120) cc_final: 0.7985 (pp30) REVERT: L 142 GLU cc_start: 0.6030 (tm-30) cc_final: 0.5498 (tm-30) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.3242 time to fit residues: 89.9095 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 : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 66 optimal weight: 0.0170 chunk 67 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN H 387 GLN 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 = 0.4617 r_free = 0.4617 target = 0.199359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.174750 restraints weight = 12478.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 88)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.171774 restraints weight = 13956.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.168985 restraints weight = 13153.408| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7898 Z= 0.151 Angle : 0.648 7.374 10614 Z= 0.339 Chirality : 0.041 0.151 1192 Planarity : 0.005 0.060 1416 Dihedral : 5.016 22.316 1126 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.27), residues: 978 helix: 0.15 (0.23), residues: 496 sheet: -2.45 (0.45), residues: 108 loop : -1.03 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 827 HIS 0.007 0.003 HIS H 406 PHE 0.006 0.001 PHE J 840 TYR 0.012 0.001 TYR C 866 ARG 0.006 0.001 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 418) hydrogen bonds : angle 4.64400 ( 1236) SS BOND : bond 0.00527 ( 4) SS BOND : angle 0.71069 ( 8) covalent geometry : bond 0.00308 ( 7894) covalent geometry : angle 0.64757 (10606) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ARG cc_start: 0.4832 (ptp-170) cc_final: 0.4490 (ptp-170) REVERT: D 812 GLN cc_start: 0.4905 (mp10) cc_final: 0.4585 (mt0) REVERT: D 850 THR cc_start: 0.6239 (m) cc_final: 0.5497 (t) REVERT: D 865 VAL cc_start: 0.5846 (t) cc_final: 0.4245 (p) REVERT: C 806 ILE cc_start: 0.7837 (tp) cc_final: 0.7578 (tp) REVERT: C 825 THR cc_start: 0.8036 (m) cc_final: 0.7773 (t) REVERT: C 827 TRP cc_start: 0.6654 (m-90) cc_final: 0.4501 (m-90) REVERT: C 856 ASN cc_start: 0.8066 (t0) cc_final: 0.7373 (p0) REVERT: C 861 GLU cc_start: 0.8334 (tp30) cc_final: 0.7914 (tp30) REVERT: E 128 ARG cc_start: 0.8236 (mtt180) cc_final: 0.7762 (mmm160) REVERT: E 145 ARG cc_start: 0.6777 (mtt180) cc_final: 0.6545 (mtt180) REVERT: F 107 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7168 (mm-30) REVERT: F 108 GLU cc_start: 0.7541 (tp30) cc_final: 0.6962 (tp30) REVERT: F 115 LEU cc_start: 0.8428 (mm) cc_final: 0.8097 (mm) REVERT: F 124 GLU cc_start: 0.8270 (pp20) cc_final: 0.8070 (pp20) REVERT: F 129 ARG cc_start: 0.7386 (tpt-90) cc_final: 0.7058 (tpt90) REVERT: F 133 ASP cc_start: 0.7908 (m-30) cc_final: 0.7508 (m-30) REVERT: F 142 GLU cc_start: 0.7406 (pp20) cc_final: 0.6614 (mp0) REVERT: F 144 ASP cc_start: 0.7089 (m-30) cc_final: 0.6597 (m-30) REVERT: G 389 ARG cc_start: 0.6134 (ptm160) cc_final: 0.5569 (ptm-80) REVERT: G 395 MET cc_start: 0.5408 (ttm) cc_final: 0.4951 (tpp) REVERT: G 422 SER cc_start: 0.3661 (p) cc_final: 0.3455 (p) REVERT: H 389 ARG cc_start: 0.6391 (tpp-160) cc_final: 0.6009 (tpt170) REVERT: H 443 MET cc_start: 0.1452 (ptt) cc_final: 0.1127 (ptt) REVERT: J 807 MET cc_start: 0.3679 (ppp) cc_final: 0.2208 (ppp) REVERT: J 808 ARG cc_start: 0.5252 (ptt-90) cc_final: 0.4109 (ptt180) REVERT: I 802 ASP cc_start: 0.5493 (t70) cc_final: 0.4973 (t70) REVERT: I 807 MET cc_start: 0.6944 (ppp) cc_final: 0.6740 (ppp) REVERT: I 823 VAL cc_start: 0.7540 (p) cc_final: 0.7315 (p) REVERT: I 884 VAL cc_start: 0.7871 (t) cc_final: 0.6577 (t) REVERT: K 126 ASP cc_start: 0.7873 (m-30) cc_final: 0.7178 (p0) REVERT: K 156 LYS cc_start: 0.7754 (mppt) cc_final: 0.7502 (mppt) REVERT: L 105 GLN cc_start: 0.6868 (tm-30) cc_final: 0.6446 (tm-30) REVERT: L 107 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7749 (mm-30) REVERT: L 132 GLN cc_start: 0.8465 (mp-120) cc_final: 0.8143 (pp30) REVERT: L 133 ASP cc_start: 0.7904 (m-30) cc_final: 0.7385 (m-30) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.3867 time to fit residues: 101.9689 Evaluate side-chains 194 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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: 0.4980 chunk 78 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN 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 = 0.4615 r_free = 0.4615 target = 0.197536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 162)---------------| | r_work = 0.4470 r_free = 0.4470 target = 0.172216 restraints weight = 12548.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.170493 restraints weight = 10495.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.170862 restraints weight = 9108.548| |-----------------------------------------------------------------------------| r_work (final): 0.4438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5683 moved from start: 0.6838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7898 Z= 0.145 Angle : 0.637 7.924 10614 Z= 0.331 Chirality : 0.041 0.143 1192 Planarity : 0.004 0.057 1416 Dihedral : 4.946 22.058 1126 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 978 helix: 0.32 (0.23), residues: 500 sheet: -1.72 (0.46), residues: 120 loop : -1.13 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 827 HIS 0.005 0.002 HIS G 406 PHE 0.004 0.001 PHE I 840 TYR 0.013 0.002 TYR D 810 ARG 0.006 0.001 ARG C 808 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 418) hydrogen bonds : angle 4.55755 ( 1236) SS BOND : bond 0.00822 ( 4) SS BOND : angle 1.30876 ( 8) covalent geometry : bond 0.00300 ( 7894) covalent geometry : angle 0.63630 (10606) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ARG cc_start: 0.4613 (ptp-170) cc_final: 0.4397 (ptp-170) REVERT: D 812 GLN cc_start: 0.5253 (mp10) cc_final: 0.4382 (mt0) REVERT: D 850 THR cc_start: 0.6316 (m) cc_final: 0.5520 (t) REVERT: D 865 VAL cc_start: 0.6052 (t) cc_final: 0.3898 (p) REVERT: C 806 ILE cc_start: 0.7957 (tp) cc_final: 0.7631 (tp) REVERT: C 825 THR cc_start: 0.8167 (m) cc_final: 0.7896 (t) REVERT: C 856 ASN cc_start: 0.8138 (t0) cc_final: 0.7875 (t0) REVERT: C 861 GLU cc_start: 0.8360 (tp30) cc_final: 0.8145 (tp30) REVERT: E 114 ARG cc_start: 0.8112 (ptp90) cc_final: 0.7662 (ptt90) REVERT: E 128 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7744 (mmm160) REVERT: E 145 ARG cc_start: 0.7361 (mtt180) cc_final: 0.7008 (mtt180) REVERT: E 156 LYS cc_start: 0.2945 (mptt) cc_final: 0.2670 (tttt) REVERT: F 107 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7023 (mm-30) REVERT: F 108 GLU cc_start: 0.7170 (tp30) cc_final: 0.6735 (tp30) REVERT: F 115 LEU cc_start: 0.8506 (mm) cc_final: 0.8228 (mm) REVERT: F 133 ASP cc_start: 0.7939 (m-30) cc_final: 0.7643 (m-30) REVERT: F 142 GLU cc_start: 0.6840 (pp20) cc_final: 0.6412 (mp0) REVERT: F 144 ASP cc_start: 0.7026 (m-30) cc_final: 0.6578 (m-30) REVERT: G 389 ARG cc_start: 0.6000 (ptm160) cc_final: 0.5544 (ptm-80) REVERT: G 443 MET cc_start: 0.5673 (mpp) cc_final: 0.5471 (mpp) REVERT: H 443 MET cc_start: 0.1751 (ptt) cc_final: 0.1359 (ptt) REVERT: J 807 MET cc_start: 0.4005 (ppp) cc_final: 0.2713 (ppp) REVERT: J 820 MET cc_start: 0.6085 (mpp) cc_final: 0.5555 (mpp) REVERT: I 807 MET cc_start: 0.6885 (ppp) cc_final: 0.6632 (ppp) REVERT: I 886 VAL cc_start: 0.7411 (m) cc_final: 0.7163 (p) REVERT: K 126 ASP cc_start: 0.7741 (m-30) cc_final: 0.6976 (p0) REVERT: K 128 ARG cc_start: 0.7369 (tmt170) cc_final: 0.6595 (tmt170) REVERT: K 156 LYS cc_start: 0.7801 (mppt) cc_final: 0.7528 (mppt) REVERT: L 105 GLN cc_start: 0.6376 (tm-30) cc_final: 0.6110 (tm-30) REVERT: L 107 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7913 (mm-30) REVERT: L 130 GLN cc_start: 0.8487 (mm110) cc_final: 0.7999 (mm110) REVERT: L 132 GLN cc_start: 0.8435 (mp-120) cc_final: 0.8148 (pp30) outliers start: 1 outliers final: 1 residues processed: 213 average time/residue: 0.3685 time to fit residues: 96.8065 Evaluate side-chains 194 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN H 387 GLN J 869 ASN L 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.198363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.4476 r_free = 0.4476 target = 0.173767 restraints weight = 12580.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.168722 restraints weight = 13188.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.169755 restraints weight = 10606.500| |-----------------------------------------------------------------------------| r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.7211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7898 Z= 0.134 Angle : 0.641 7.681 10614 Z= 0.336 Chirality : 0.042 0.135 1192 Planarity : 0.004 0.055 1416 Dihedral : 4.874 22.222 1126 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.27), residues: 978 helix: 0.21 (0.23), residues: 506 sheet: -1.79 (0.39), residues: 172 loop : -0.90 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 827 HIS 0.005 0.003 HIS H 406 PHE 0.003 0.001 PHE I 840 TYR 0.018 0.001 TYR D 877 ARG 0.010 0.001 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 418) hydrogen bonds : angle 4.56245 ( 1236) SS BOND : bond 0.00429 ( 4) SS BOND : angle 0.97248 ( 8) covalent geometry : bond 0.00282 ( 7894) covalent geometry : angle 0.64041 (10606) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.892 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: 0.4701 (ptp-170) cc_final: 0.4436 (ptp-170) REVERT: B 391 ARG cc_start: 0.5661 (ttm170) cc_final: 0.5423 (tmm-80) REVERT: D 11 LEU cc_start: 0.6753 (mm) cc_final: 0.6513 (mm) REVERT: D 812 GLN cc_start: 0.4463 (mp10) cc_final: 0.4160 (mt0) REVERT: D 850 THR cc_start: 0.6371 (m) cc_final: 0.5693 (t) REVERT: C 811 ARG cc_start: 0.5847 (ttt180) cc_final: 0.5428 (ttt-90) REVERT: C 856 ASN cc_start: 0.8183 (t0) cc_final: 0.7939 (t0) REVERT: E 114 ARG cc_start: 0.8058 (ptp90) cc_final: 0.7562 (ptt90) REVERT: E 128 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7820 (mmm160) REVERT: E 145 ARG cc_start: 0.6784 (mtt180) cc_final: 0.6523 (mtt180) REVERT: E 156 LYS cc_start: 0.2928 (mptt) cc_final: 0.2659 (tttt) REVERT: F 107 GLU cc_start: 0.7779 (mm-30) cc_final: 0.6654 (mm-30) REVERT: F 108 GLU cc_start: 0.7462 (tp30) cc_final: 0.6814 (tp30) REVERT: F 115 LEU cc_start: 0.8506 (mm) cc_final: 0.8171 (mm) REVERT: F 133 ASP cc_start: 0.7670 (m-30) cc_final: 0.7407 (m-30) REVERT: F 142 GLU cc_start: 0.6879 (pp20) cc_final: 0.6474 (mp0) REVERT: F 144 ASP cc_start: 0.7049 (m-30) cc_final: 0.6609 (m-30) REVERT: G 389 ARG cc_start: 0.5693 (ptm160) cc_final: 0.5319 (ptm-80) REVERT: H 389 ARG cc_start: 0.6507 (tpp-160) cc_final: 0.6039 (mmt-90) REVERT: H 443 MET cc_start: 0.1960 (ptt) cc_final: 0.1584 (ptt) REVERT: J 807 MET cc_start: 0.4219 (ppp) cc_final: 0.3193 (ppp) REVERT: J 820 MET cc_start: 0.6105 (mpp) cc_final: 0.5530 (mpp) REVERT: I 807 MET cc_start: 0.6853 (ppp) cc_final: 0.6515 (ppp) REVERT: I 853 LEU cc_start: 0.6920 (tp) cc_final: 0.6712 (tp) REVERT: I 886 VAL cc_start: 0.7458 (m) cc_final: 0.7178 (p) REVERT: K 126 ASP cc_start: 0.7809 (m-30) cc_final: 0.7393 (m-30) REVERT: K 128 ARG cc_start: 0.6989 (tmt170) cc_final: 0.6422 (tmt170) REVERT: K 156 LYS cc_start: 0.7815 (mppt) cc_final: 0.7531 (mppt) REVERT: L 107 GLU cc_start: 0.8657 (mm-30) cc_final: 0.7928 (mm-30) REVERT: L 130 GLN cc_start: 0.8373 (mm110) cc_final: 0.8088 (mm110) REVERT: L 132 GLN cc_start: 0.8457 (mp10) cc_final: 0.8207 (pp30) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2856 time to fit residues: 73.6242 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 : 0.840 ------------------------------------------------------------------------------- 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: 0.0370 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN I 857 ASN L 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.198046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.174997 restraints weight = 12701.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.173226 restraints weight = 12491.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.173234 restraints weight = 10888.481| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7898 Z= 0.138 Angle : 0.650 7.665 10614 Z= 0.338 Chirality : 0.041 0.138 1192 Planarity : 0.004 0.058 1416 Dihedral : 4.790 24.031 1126 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.27), residues: 978 helix: 0.26 (0.23), residues: 506 sheet: -1.97 (0.41), residues: 154 loop : -0.96 (0.35), residues: 318 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 0.004 0.001 PHE I 840 TYR 0.019 0.002 TYR D 877 ARG 0.009 0.001 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 418) hydrogen bonds : angle 4.59640 ( 1236) SS BOND : bond 0.00605 ( 4) SS BOND : angle 1.05614 ( 8) covalent geometry : bond 0.00293 ( 7894) covalent geometry : angle 0.64919 (10606) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 379 LYS cc_start: 0.6885 (mmmm) cc_final: 0.6588 (tppt) REVERT: B 391 ARG cc_start: 0.5622 (ttm170) cc_final: 0.5318 (tmm-80) REVERT: B 400 ASP cc_start: 0.6306 (m-30) cc_final: 0.6046 (m-30) REVERT: D 11 LEU cc_start: 0.6639 (mm) cc_final: 0.6413 (mm) REVERT: D 812 GLN cc_start: 0.4795 (mp10) cc_final: 0.4501 (mt0) REVERT: C 799 ARG cc_start: 0.7066 (ttt-90) cc_final: 0.6685 (tmt170) REVERT: C 811 ARG cc_start: 0.5766 (ttt180) cc_final: 0.5518 (ttt-90) REVERT: C 825 THR cc_start: 0.8079 (t) cc_final: 0.7659 (t) REVERT: C 827 TRP cc_start: 0.6460 (m-90) cc_final: 0.4543 (m-90) REVERT: C 856 ASN cc_start: 0.8046 (t0) cc_final: 0.7788 (t0) REVERT: E 114 ARG cc_start: 0.8024 (ptp90) cc_final: 0.7532 (ptt90) REVERT: E 156 LYS cc_start: 0.2898 (mptt) cc_final: 0.2561 (tttt) REVERT: F 107 GLU cc_start: 0.6486 (mm-30) cc_final: 0.6197 (mm-30) REVERT: F 108 GLU cc_start: 0.6841 (tp30) cc_final: 0.6241 (tp30) REVERT: F 115 LEU cc_start: 0.8477 (mm) cc_final: 0.8199 (mm) REVERT: F 133 ASP cc_start: 0.7650 (m-30) cc_final: 0.7335 (m-30) REVERT: F 144 ASP cc_start: 0.6745 (m-30) cc_final: 0.6343 (m-30) REVERT: G 389 ARG cc_start: 0.5458 (ptm160) cc_final: 0.5209 (ptm-80) REVERT: H 443 MET cc_start: 0.2095 (ptt) cc_final: 0.1763 (ptt) REVERT: J 807 MET cc_start: 0.4316 (ppp) cc_final: 0.3308 (ppp) REVERT: J 820 MET cc_start: 0.6005 (mpp) cc_final: 0.5401 (mpp) REVERT: I 807 MET cc_start: 0.6902 (ppp) cc_final: 0.6476 (ppp) REVERT: I 884 VAL cc_start: 0.7901 (t) cc_final: 0.7628 (t) REVERT: K 128 ARG cc_start: 0.6761 (tmt170) cc_final: 0.6538 (tmt170) REVERT: K 156 LYS cc_start: 0.7986 (mppt) cc_final: 0.7616 (mppt) REVERT: L 107 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7779 (mm-30) REVERT: L 131 THR cc_start: 0.8074 (p) cc_final: 0.7769 (p) REVERT: L 132 GLN cc_start: 0.8406 (mp10) cc_final: 0.8182 (pp30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2800 time to fit residues: 71.2059 Evaluate side-chains 188 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN I 805 ASN K 139 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.199886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.176946 restraints weight = 12701.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 93)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.172244 restraints weight = 12635.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.172866 restraints weight = 11475.687| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5653 moved from start: 0.7827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7898 Z= 0.126 Angle : 0.653 8.339 10614 Z= 0.340 Chirality : 0.041 0.174 1192 Planarity : 0.004 0.043 1416 Dihedral : 4.704 23.224 1126 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.27), residues: 978 helix: 0.53 (0.23), residues: 500 sheet: -1.49 (0.37), residues: 180 loop : -1.13 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 809 HIS 0.003 0.001 HIS H 406 PHE 0.003 0.001 PHE I 840 TYR 0.017 0.001 TYR D 810 ARG 0.008 0.001 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 418) hydrogen bonds : angle 4.40799 ( 1236) SS BOND : bond 0.00542 ( 4) SS BOND : angle 0.77080 ( 8) covalent geometry : bond 0.00269 ( 7894) covalent geometry : angle 0.65253 (10606) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ARG cc_start: 0.4263 (ptp-170) cc_final: 0.3910 (ptt-90) REVERT: B 379 LYS cc_start: 0.6881 (mmmm) cc_final: 0.6552 (tppt) REVERT: B 391 ARG cc_start: 0.5627 (ttm170) cc_final: 0.5375 (tmm-80) REVERT: C 799 ARG cc_start: 0.7033 (ttt-90) cc_final: 0.6622 (tmt170) REVERT: C 811 ARG cc_start: 0.5789 (ttt180) cc_final: 0.5583 (ttt-90) REVERT: C 825 THR cc_start: 0.8114 (t) cc_final: 0.7631 (t) REVERT: C 827 TRP cc_start: 0.6485 (m-90) cc_final: 0.4637 (m-90) REVERT: C 856 ASN cc_start: 0.8093 (t0) cc_final: 0.7873 (t0) REVERT: E 114 ARG cc_start: 0.8284 (ptp90) cc_final: 0.7729 (ptt90) REVERT: E 145 ARG cc_start: 0.6790 (mtt180) cc_final: 0.6476 (mtt180) REVERT: F 107 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6504 (mm-30) REVERT: F 108 GLU cc_start: 0.6967 (tp30) cc_final: 0.6403 (tp30) REVERT: F 115 LEU cc_start: 0.8488 (mm) cc_final: 0.8197 (mm) REVERT: F 144 ASP cc_start: 0.7097 (m-30) cc_final: 0.6676 (m-30) REVERT: G 389 ARG cc_start: 0.5427 (ptm160) cc_final: 0.5150 (ptm-80) REVERT: H 443 MET cc_start: 0.1984 (ptt) cc_final: 0.1681 (ptt) REVERT: J 807 MET cc_start: 0.4150 (ppp) cc_final: 0.3152 (ppp) REVERT: J 820 MET cc_start: 0.6007 (mpp) cc_final: 0.5382 (mpp) REVERT: I 807 MET cc_start: 0.6974 (ppp) cc_final: 0.6538 (ppp) REVERT: I 853 LEU cc_start: 0.7002 (tp) cc_final: 0.6763 (tp) REVERT: I 884 VAL cc_start: 0.7900 (t) cc_final: 0.7409 (t) REVERT: K 114 ARG cc_start: 0.7389 (ptt-90) cc_final: 0.7089 (ptt-90) REVERT: K 128 ARG cc_start: 0.7012 (tmt170) cc_final: 0.6602 (tmt170) REVERT: K 156 LYS cc_start: 0.7925 (mppt) cc_final: 0.7612 (mppt) REVERT: L 107 GLU cc_start: 0.8636 (mm-30) cc_final: 0.7872 (mm-30) REVERT: L 131 THR cc_start: 0.8173 (p) cc_final: 0.7962 (p) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2885 time to fit residues: 72.4706 Evaluate side-chains 183 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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: 0.9990 chunk 79 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 HIS ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.196745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.173368 restraints weight = 12501.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 107)---------------| | r_work = 0.4432 r_free = 0.4432 target = 0.168002 restraints weight = 13984.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.168916 restraints weight = 11888.762| |-----------------------------------------------------------------------------| r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 moved from start: 0.8108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7898 Z= 0.144 Angle : 0.674 7.519 10614 Z= 0.351 Chirality : 0.042 0.150 1192 Planarity : 0.004 0.051 1416 Dihedral : 4.926 24.523 1126 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % 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: -0.77 (0.27), residues: 978 helix: 0.33 (0.23), residues: 512 sheet: -1.52 (0.37), residues: 180 loop : -1.09 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 809 HIS 0.006 0.003 HIS B 406 PHE 0.005 0.001 PHE I 840 TYR 0.014 0.002 TYR D 810 ARG 0.008 0.001 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 418) hydrogen bonds : angle 4.54969 ( 1236) SS BOND : bond 0.00591 ( 4) SS BOND : angle 0.73393 ( 8) covalent geometry : bond 0.00308 ( 7894) covalent geometry : angle 0.67403 (10606) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.839 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 369 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7386 (mmmt) REVERT: B 379 LYS cc_start: 0.6877 (mmmm) cc_final: 0.6660 (tppt) REVERT: D 11 LEU cc_start: 0.6974 (mm) cc_final: 0.6747 (mm) REVERT: D 850 THR cc_start: 0.6072 (m) cc_final: 0.5463 (t) REVERT: C 799 ARG cc_start: 0.7030 (ttt-90) cc_final: 0.6531 (tmt170) REVERT: C 811 ARG cc_start: 0.5545 (ttt180) cc_final: 0.5070 (ttt-90) REVERT: C 825 THR cc_start: 0.8001 (t) cc_final: 0.7718 (t) REVERT: C 837 LYS cc_start: 0.7480 (mmtm) cc_final: 0.7157 (mmtm) REVERT: C 856 ASN cc_start: 0.8136 (t0) cc_final: 0.7917 (t0) REVERT: E 114 ARG cc_start: 0.8247 (ptp90) cc_final: 0.7697 (ptt90) REVERT: F 107 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6243 (mm-30) REVERT: F 108 GLU cc_start: 0.7307 (tp30) cc_final: 0.6655 (tp30) REVERT: F 115 LEU cc_start: 0.8512 (mm) cc_final: 0.8180 (mm) REVERT: F 144 ASP cc_start: 0.6882 (m-30) cc_final: 0.6568 (m-30) REVERT: H 443 MET cc_start: 0.2706 (ptt) cc_final: 0.2446 (ptt) REVERT: J 807 MET cc_start: 0.4353 (ppp) cc_final: 0.3468 (ppp) REVERT: J 820 MET cc_start: 0.6091 (mpp) cc_final: 0.5525 (mpp) REVERT: I 807 MET cc_start: 0.7100 (ppp) cc_final: 0.6588 (ppp) REVERT: I 853 LEU cc_start: 0.7040 (tp) cc_final: 0.6813 (tp) REVERT: I 863 THR cc_start: 0.5812 (m) cc_final: 0.5468 (m) REVERT: I 884 VAL cc_start: 0.7868 (t) cc_final: 0.7267 (t) REVERT: I 886 VAL cc_start: 0.7457 (m) cc_final: 0.6819 (t) REVERT: K 100 GLN cc_start: 0.8393 (mp10) cc_final: 0.8038 (mp10) REVERT: K 114 ARG cc_start: 0.7406 (ptt-90) cc_final: 0.7083 (ptt-90) REVERT: K 128 ARG cc_start: 0.7013 (tmt170) cc_final: 0.6676 (tmt170) REVERT: K 156 LYS cc_start: 0.7901 (mppt) cc_final: 0.7288 (mppt) REVERT: L 107 GLU cc_start: 0.8679 (mm-30) cc_final: 0.7923 (mm-30) REVERT: L 133 ASP cc_start: 0.7886 (m-30) cc_final: 0.7036 (m-30) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2949 time to fit residues: 73.5038 Evaluate side-chains 184 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 0.0770 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN I 805 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.198276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 157)---------------| | r_work = 0.4455 r_free = 0.4455 target = 0.172663 restraints weight = 12507.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.172403 restraints weight = 9609.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.172824 restraints weight = 8669.913| |-----------------------------------------------------------------------------| r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 moved from start: 0.8307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7898 Z= 0.135 Angle : 0.669 7.751 10614 Z= 0.348 Chirality : 0.041 0.149 1192 Planarity : 0.004 0.057 1416 Dihedral : 4.807 24.388 1126 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.27), residues: 978 helix: 0.32 (0.23), residues: 512 sheet: -1.38 (0.38), residues: 180 loop : -1.19 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 809 HIS 0.005 0.002 HIS H 406 PHE 0.004 0.001 PHE I 840 TYR 0.015 0.001 TYR D 810 ARG 0.012 0.001 ARG D 873 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 418) hydrogen bonds : angle 4.52627 ( 1236) SS BOND : bond 0.00555 ( 4) SS BOND : angle 0.75778 ( 8) covalent geometry : bond 0.00293 ( 7894) covalent geometry : angle 0.66880 (10606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3532.24 seconds wall clock time: 64 minutes 1.82 seconds (3841.82 seconds total)