Starting phenix.real_space_refine on Fri Aug 22 20:44:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afm_15402/08_2025/8afm_15402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afm_15402/08_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_15402/08_2025/8afm_15402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afm_15402/08_2025/8afm_15402.map" model { file = "/net/cci-nas-00/data/ceres_data/8afm_15402/08_2025/8afm_15402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afm_15402/08_2025/8afm_15402.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.80, per 1000 atoms: 0.23 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: 0.60 Conformation dependent library (CDL) restraints added in 410.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.18 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: 0.93 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2844 1.34 - 1.46: 1129 1.46 - 1.58: 3873 1.58 - 1.70: 0 1.70 - 1.81: 48 Bond restraints: 7894 Sorted by residual: bond pdb=" N LEU E 115 " pdb=" CA LEU E 115 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.78e+00 bond pdb=" N LEU K 115 " pdb=" CA LEU K 115 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.74e+00 bond pdb=" N ARG K 114 " pdb=" CA ARG K 114 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.71e+00 bond pdb=" N ARG E 114 " pdb=" CA ARG E 114 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.46e+00 bond pdb=" N ALA K 113 " pdb=" CA ALA K 113 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.69e+00 ... (remaining 7889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 10187 1.72 - 3.44: 371 3.44 - 5.17: 39 5.17 - 6.89: 5 6.89 - 8.61: 4 Bond angle restraints: 10606 Sorted by residual: angle pdb=" N GLY I 803 " pdb=" CA GLY I 803 " pdb=" C GLY I 803 " ideal model delta sigma weight residual 113.18 106.21 6.97 2.37e+00 1.78e-01 8.65e+00 angle pdb=" N GLY C 803 " pdb=" CA GLY C 803 " pdb=" C GLY C 803 " ideal model delta sigma weight residual 113.18 106.25 6.93 2.37e+00 1.78e-01 8.55e+00 angle pdb=" N ALA C 864 " pdb=" CA ALA C 864 " pdb=" C ALA C 864 " ideal model delta sigma weight residual 107.88 111.58 -3.70 1.41e+00 5.03e-01 6.88e+00 angle pdb=" CA ARG K 99 " pdb=" CB ARG K 99 " pdb=" CG ARG K 99 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.85e+00 angle pdb=" N ALA I 864 " pdb=" CA ALA I 864 " pdb=" C ALA I 864 " ideal model delta sigma weight residual 107.88 111.56 -3.68 1.41e+00 5.03e-01 6.82e+00 ... (remaining 10601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4412 17.76 - 35.52: 412 35.52 - 53.27: 88 53.27 - 71.03: 12 71.03 - 88.79: 18 Dihedral angle restraints: 4942 sinusoidal: 2012 harmonic: 2930 Sorted by residual: dihedral pdb=" CB CYS I 795 " pdb=" SG CYS I 795 " pdb=" SG CYS I 868 " pdb=" CB CYS I 868 " ideal model delta sinusoidal sigma weight residual 93.00 47.66 45.34 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS C 795 " pdb=" SG CYS C 795 " pdb=" SG CYS C 868 " pdb=" CB CYS C 868 " ideal model delta sinusoidal sigma weight residual 93.00 47.67 45.33 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CA ILE D 804 " pdb=" C ILE D 804 " pdb=" N ASN D 805 " pdb=" CA ASN D 805 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 4939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 683 0.028 - 0.057: 311 0.057 - 0.085: 126 0.085 - 0.114: 46 0.114 - 0.142: 26 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA LEU E 115 " pdb=" N LEU E 115 " pdb=" C LEU E 115 " pdb=" CB LEU E 115 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ASN J 857 " pdb=" N ASN J 857 " pdb=" C ASN J 857 " pdb=" CB ASN J 857 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA LEU K 115 " pdb=" N LEU K 115 " pdb=" C LEU K 115 " pdb=" CB LEU K 115 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1189 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 827 " -0.015 2.00e-02 2.50e+03 9.58e-03 2.29e+00 pdb=" CG TRP D 827 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP D 827 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 827 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 827 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 827 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 827 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 827 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 827 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 827 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 827 " 0.015 2.00e-02 2.50e+03 9.38e-03 2.20e+00 pdb=" CG TRP J 827 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP J 827 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP J 827 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 827 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 827 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 827 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 827 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 827 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 827 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 809 " -0.013 2.00e-02 2.50e+03 9.04e-03 2.04e+00 pdb=" CG TRP I 809 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP I 809 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP I 809 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 809 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 809 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I 809 " 0.001 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 309 2.70 - 3.25: 8455 3.25 - 3.80: 11709 3.80 - 4.35: 15177 4.35 - 4.90: 23284 Nonbonded interactions: 58934 Sorted by model distance: nonbonded pdb=" OE1 GLN J 883 " pdb=" OG1 THR J 885 " model vdw 2.153 3.040 nonbonded pdb=" OE1 GLN D 883 " pdb=" OG1 THR D 885 " model vdw 2.153 3.040 nonbonded pdb=" O LEU C 791 " pdb=" NE2 GLN C 854 " model vdw 2.157 3.120 nonbonded pdb=" O LEU I 791 " pdb=" NE2 GLN I 854 " model vdw 2.157 3.120 nonbonded pdb=" O LEU K 160 " pdb=" OG SER K 163 " model vdw 2.157 3.040 ... (remaining 58929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'E' and resid 96 through 154) selection = chain 'F' selection = (chain 'K' and resid 96 through 154) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.800 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.850 ------------------------------------------------------------------------------- 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 : 18.36 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.020 0.001 ARG B 380 TYR 0.019 0.002 TYR C 872 PHE 0.010 0.003 PHE D 840 TRP 0.025 0.004 TRP D 827 HIS 0.002 0.001 HIS H 406 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 7894) covalent geometry : angle 0.74289 (10606) SS BOND : bond 0.00658 ( 4) SS BOND : angle 1.33673 ( 8) hydrogen bonds : bond 0.30317 ( 418) hydrogen bonds : angle 11.34145 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 256 time to evaluate : 0.289 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: 0.1370 time to fit residues: 42.3856 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 : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 74 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 374 GLN C 805 ASN F 96 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 854 GLN I 805 ASN L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.210756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.4564 r_free = 0.4564 target = 0.187294 restraints weight = 12926.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.186214 restraints weight = 14701.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.184484 restraints weight = 13104.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.184484 restraints weight = 14474.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.184484 restraints weight = 14474.403| |-----------------------------------------------------------------------------| r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5461 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7898 Z= 0.160 Angle : 0.696 9.419 10614 Z= 0.363 Chirality : 0.044 0.187 1192 Planarity : 0.006 0.079 1416 Dihedral : 5.556 23.611 1126 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.12 % Allowed : 6.47 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.26), residues: 978 helix: -0.96 (0.22), residues: 518 sheet: -1.93 (0.48), residues: 116 loop : -1.58 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 145 TYR 0.016 0.002 TYR I 872 PHE 0.010 0.002 PHE J 840 TRP 0.019 0.002 TRP J 827 HIS 0.004 0.002 HIS H 406 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7894) covalent geometry : angle 0.69589 (10606) SS BOND : bond 0.00442 ( 4) SS BOND : angle 0.80195 ( 8) hydrogen bonds : bond 0.05139 ( 418) hydrogen bonds : angle 5.80828 ( 1236) *********************** 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 228 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.209 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: 0.6756 (mm-30) cc_final: 0.5846 (mm-30) REVERT: D 802 ASP cc_start: 0.3975 (t0) cc_final: 0.3598 (t0) REVERT: D 865 VAL cc_start: 0.6031 (t) cc_final: 0.5196 (p) REVERT: D 877 TYR cc_start: 0.6023 (m-80) cc_final: 0.5463 (m-80) REVERT: C 798 SER cc_start: 0.8332 (t) cc_final: 0.8079 (m) REVERT: C 806 ILE cc_start: 0.7680 (tp) cc_final: 0.7404 (tp) REVERT: C 811 ARG cc_start: 0.5258 (ptt180) cc_final: 0.4990 (ttp80) REVERT: C 856 ASN cc_start: 0.8189 (t0) cc_final: 0.7950 (t0) REVERT: E 148 ASN cc_start: 0.7407 (m-40) cc_final: 0.6742 (p0) REVERT: F 108 GLU cc_start: 0.6938 (tp30) cc_final: 0.6304 (tp30) REVERT: F 133 ASP cc_start: 0.7827 (m-30) cc_final: 0.7600 (m-30) REVERT: F 142 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6368 (tp30) REVERT: F 144 ASP cc_start: 0.6303 (m-30) cc_final: 0.5810 (m-30) REVERT: G 438 ARG cc_start: 0.5369 (ptt-90) cc_final: 0.3292 (mmp-170) REVERT: H 370 SER cc_start: 0.6846 (t) cc_final: 0.6519 (m) REVERT: J 807 MET cc_start: 0.3623 (ppp) cc_final: 0.2613 (ppp) REVERT: J 808 ARG cc_start: 0.5703 (ptt-90) cc_final: 0.4676 (ptt90) REVERT: J 820 MET cc_start: 0.5944 (mpp) cc_final: 0.5249 (mpp) REVERT: J 878 TRP cc_start: 0.5115 (m100) cc_final: 0.4790 (m100) REVERT: I 807 MET cc_start: 0.6657 (ppp) cc_final: 0.6006 (ppp) REVERT: I 884 VAL cc_start: 0.7775 (t) cc_final: 0.5981 (t) REVERT: L 115 LEU cc_start: 0.8563 (mm) cc_final: 0.8094 (mm) REVERT: L 132 GLN cc_start: 0.8315 (mp-120) cc_final: 0.7841 (pp30) REVERT: L 142 GLU cc_start: 0.5482 (tm-30) cc_final: 0.4632 (tm-30) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1294 time to fit residues: 35.8162 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 : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 90 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** D 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 GLN ** H 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.204887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.181485 restraints weight = 12756.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.180647 restraints weight = 13341.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.179851 restraints weight = 12929.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.179825 restraints weight = 11793.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.179824 restraints weight = 11921.687| |-----------------------------------------------------------------------------| r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7898 Z= 0.176 Angle : 0.685 7.567 10614 Z= 0.359 Chirality : 0.043 0.158 1192 Planarity : 0.005 0.059 1416 Dihedral : 5.528 26.931 1126 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.12 % Allowed : 4.23 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.27), residues: 978 helix: -0.58 (0.22), residues: 510 sheet: -2.44 (0.44), residues: 130 loop : -1.12 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 435 TYR 0.015 0.001 TYR D 810 PHE 0.007 0.002 PHE J 840 TRP 0.028 0.003 TRP J 827 HIS 0.008 0.004 HIS H 406 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7894) covalent geometry : angle 0.68460 (10606) SS BOND : bond 0.00547 ( 4) SS BOND : angle 0.62006 ( 8) hydrogen bonds : bond 0.04570 ( 418) hydrogen bonds : angle 5.25661 ( 1236) *********************** 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 225 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.180 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: 0.4786 (ptp-170) cc_final: 0.4503 (ptp-170) REVERT: B 375 GLU cc_start: 0.6876 (tp30) cc_final: 0.6645 (tm-30) REVERT: D 802 ASP cc_start: 0.4264 (t0) cc_final: 0.3713 (t0) REVERT: D 818 ARG cc_start: 0.5484 (mtp180) cc_final: 0.4893 (mtm110) REVERT: D 850 THR cc_start: 0.6474 (m) cc_final: 0.5914 (t) REVERT: D 877 TYR cc_start: 0.5905 (m-80) cc_final: 0.5616 (m-80) REVERT: C 798 SER cc_start: 0.8358 (t) cc_final: 0.8110 (m) REVERT: C 811 ARG cc_start: 0.5678 (ptt180) cc_final: 0.5046 (ttp80) REVERT: F 107 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6646 (mm-30) REVERT: F 108 GLU cc_start: 0.6972 (tp30) cc_final: 0.6330 (tp30) REVERT: F 133 ASP cc_start: 0.7813 (m-30) cc_final: 0.7525 (m-30) REVERT: F 142 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6727 (tp30) REVERT: F 144 ASP cc_start: 0.6300 (m-30) cc_final: 0.6033 (m-30) REVERT: G 422 SER cc_start: 0.5344 (t) cc_final: 0.4651 (p) REVERT: H 370 SER cc_start: 0.6783 (t) cc_final: 0.6558 (m) REVERT: I 807 MET cc_start: 0.6744 (ppp) cc_final: 0.6052 (ppp) REVERT: I 823 VAL cc_start: 0.7569 (p) cc_final: 0.7348 (p) REVERT: I 846 SER cc_start: 0.5683 (t) cc_final: 0.5408 (t) REVERT: I 884 VAL cc_start: 0.7896 (t) cc_final: 0.6701 (t) REVERT: L 115 LEU cc_start: 0.8596 (mm) cc_final: 0.8128 (mm) REVERT: L 132 GLN cc_start: 0.8433 (mp-120) cc_final: 0.7986 (pp30) REVERT: L 142 GLU cc_start: 0.5922 (tm-30) cc_final: 0.5542 (tm-30) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1179 time to fit residues: 32.6665 Evaluate side-chains 197 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN L 100 GLN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4626 r_free = 0.4626 target = 0.197890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 146)---------------| | r_work = 0.4489 r_free = 0.4489 target = 0.173283 restraints weight = 12739.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.168440 restraints weight = 13100.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.169252 restraints weight = 11051.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.169936 restraints weight = 9401.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.170129 restraints weight = 8497.959| |-----------------------------------------------------------------------------| r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5684 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7898 Z= 0.153 Angle : 0.644 7.231 10614 Z= 0.340 Chirality : 0.042 0.151 1192 Planarity : 0.004 0.060 1416 Dihedral : 5.263 22.384 1126 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.12 % Allowed : 5.47 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.27), residues: 978 helix: -0.25 (0.23), residues: 494 sheet: -1.97 (0.40), residues: 168 loop : -0.75 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 380 TYR 0.013 0.001 TYR D 810 PHE 0.006 0.002 PHE J 840 TRP 0.023 0.003 TRP J 878 HIS 0.005 0.003 HIS H 406 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7894) covalent geometry : angle 0.64428 (10606) SS BOND : bond 0.00586 ( 4) SS BOND : angle 0.64559 ( 8) hydrogen bonds : bond 0.04114 ( 418) hydrogen bonds : angle 4.90998 ( 1236) *********************** 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 217 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 GLU cc_start: 0.6695 (tp30) cc_final: 0.6485 (tm-30) REVERT: D 850 THR cc_start: 0.6273 (m) cc_final: 0.5716 (t) REVERT: D 873 ARG cc_start: 0.6238 (mpp-170) cc_final: 0.5980 (mpp80) REVERT: C 798 SER cc_start: 0.8419 (t) cc_final: 0.8104 (m) REVERT: C 811 ARG cc_start: 0.5818 (ptt180) cc_final: 0.5002 (ttp80) REVERT: C 827 TRP cc_start: 0.6077 (m-90) cc_final: 0.4485 (m-90) REVERT: E 145 ARG cc_start: 0.7457 (mtt180) cc_final: 0.7144 (mtt180) REVERT: F 107 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7113 (mm-30) REVERT: F 108 GLU cc_start: 0.7283 (tp30) cc_final: 0.6824 (tp30) REVERT: F 115 LEU cc_start: 0.8529 (mm) cc_final: 0.8194 (mm) REVERT: F 144 ASP cc_start: 0.7005 (m-30) cc_final: 0.6660 (m-30) REVERT: G 422 SER cc_start: 0.5285 (t) cc_final: 0.4844 (p) REVERT: G 443 MET cc_start: 0.5413 (mpp) cc_final: 0.5193 (mpp) REVERT: H 443 MET cc_start: 0.2082 (ptt) cc_final: 0.1695 (ptt) REVERT: J 807 MET cc_start: 0.3971 (ppp) cc_final: 0.2682 (ppp) REVERT: J 808 ARG cc_start: 0.5029 (ptt-90) cc_final: 0.3904 (ptt180) REVERT: J 848 LYS cc_start: 0.7441 (tmtt) cc_final: 0.7221 (tptp) REVERT: I 807 MET cc_start: 0.6955 (ppp) cc_final: 0.6386 (ppp) REVERT: I 823 VAL cc_start: 0.7560 (p) cc_final: 0.7310 (p) REVERT: I 884 VAL cc_start: 0.7912 (t) cc_final: 0.6736 (t) REVERT: I 886 VAL cc_start: 0.7053 (p) cc_final: 0.6667 (t) REVERT: L 115 LEU cc_start: 0.8693 (mm) cc_final: 0.8220 (mm) REVERT: L 132 GLN cc_start: 0.8522 (mp-120) cc_final: 0.8117 (pp30) REVERT: L 142 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6717 (tm-30) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.1124 time to fit residues: 30.0167 Evaluate side-chains 195 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 54 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 44 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.199384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.172188 restraints weight = 12632.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.171482 restraints weight = 13270.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.173290 restraints weight = 10198.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.173808 restraints weight = 7935.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.173771 restraints weight = 6208.605| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5611 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7898 Z= 0.128 Angle : 0.614 8.039 10614 Z= 0.324 Chirality : 0.041 0.144 1192 Planarity : 0.004 0.038 1416 Dihedral : 4.993 20.676 1126 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.12 % Allowed : 2.24 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.28), residues: 978 helix: -0.03 (0.23), residues: 500 sheet: -1.74 (0.40), residues: 180 loop : -0.82 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 404 TYR 0.010 0.001 TYR D 877 PHE 0.005 0.001 PHE J 840 TRP 0.015 0.002 TRP D 827 HIS 0.004 0.002 HIS H 406 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7894) covalent geometry : angle 0.61360 (10606) SS BOND : bond 0.00520 ( 4) SS BOND : angle 0.72959 ( 8) hydrogen bonds : bond 0.03911 ( 418) hydrogen bonds : angle 4.70846 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.295 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: 0.4355 (ptp-170) cc_final: 0.3965 (ptt-90) REVERT: B 375 GLU cc_start: 0.6767 (tp30) cc_final: 0.6557 (tm-30) REVERT: D 850 THR cc_start: 0.6107 (m) cc_final: 0.5372 (t) REVERT: C 811 ARG cc_start: 0.5846 (ptt180) cc_final: 0.5224 (ttp80) REVERT: C 827 TRP cc_start: 0.5734 (m-90) cc_final: 0.4658 (m-90) REVERT: C 861 GLU cc_start: 0.8081 (tp30) cc_final: 0.7844 (tp30) REVERT: E 114 ARG cc_start: 0.7864 (ptp90) cc_final: 0.7649 (ptt90) REVERT: E 128 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7705 (mmm160) REVERT: E 156 LYS cc_start: 0.3013 (mptt) cc_final: 0.2669 (tttt) REVERT: F 107 GLU cc_start: 0.7761 (mm-30) cc_final: 0.6641 (mm-30) REVERT: F 108 GLU cc_start: 0.7382 (tp30) cc_final: 0.6777 (tp30) REVERT: F 115 LEU cc_start: 0.8446 (mm) cc_final: 0.8193 (mm) REVERT: F 133 ASP cc_start: 0.7575 (m-30) cc_final: 0.7364 (m-30) REVERT: F 142 GLU cc_start: 0.6748 (pp20) cc_final: 0.6505 (mp0) REVERT: F 144 ASP cc_start: 0.6862 (m-30) cc_final: 0.6458 (m-30) REVERT: G 389 ARG cc_start: 0.6196 (ptm160) cc_final: 0.5814 (ptm-80) REVERT: G 422 SER cc_start: 0.5023 (t) cc_final: 0.4441 (p) REVERT: H 389 ARG cc_start: 0.6767 (tpp-160) cc_final: 0.6022 (mmt180) REVERT: H 443 MET cc_start: 0.1408 (ptt) cc_final: 0.1081 (ptt) REVERT: J 807 MET cc_start: 0.4192 (ppp) cc_final: 0.2839 (ppp) REVERT: J 808 ARG cc_start: 0.5729 (ptt-90) cc_final: 0.4452 (ptt180) REVERT: I 802 ASP cc_start: 0.5709 (t0) cc_final: 0.5160 (t0) REVERT: I 807 MET cc_start: 0.7012 (ppp) cc_final: 0.6380 (ppp) REVERT: I 823 VAL cc_start: 0.7523 (p) cc_final: 0.7215 (p) REVERT: K 150 LEU cc_start: 0.7962 (tp) cc_final: 0.7737 (tp) REVERT: K 156 LYS cc_start: 0.7810 (mppt) cc_final: 0.7493 (mtmm) REVERT: L 107 GLU cc_start: 0.7924 (mp0) cc_final: 0.6865 (mp0) REVERT: L 115 LEU cc_start: 0.8685 (mm) cc_final: 0.8133 (mm) REVERT: L 119 GLU cc_start: 0.8532 (pp20) cc_final: 0.8022 (pp20) REVERT: L 132 GLN cc_start: 0.8460 (mp-120) cc_final: 0.8009 (pp30) REVERT: L 142 GLU cc_start: 0.6480 (tm-30) cc_final: 0.6238 (tm-30) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1126 time to fit residues: 30.2157 Evaluate side-chains 193 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN L 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.193540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.170084 restraints weight = 12880.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.164395 restraints weight = 14562.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.165615 restraints weight = 11279.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.165743 restraints weight = 9628.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.165743 restraints weight = 9000.950| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7898 Z= 0.178 Angle : 0.689 8.123 10614 Z= 0.364 Chirality : 0.043 0.149 1192 Planarity : 0.005 0.056 1416 Dihedral : 5.354 22.120 1126 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.27), residues: 978 helix: -0.28 (0.23), residues: 508 sheet: -2.02 (0.40), residues: 158 loop : -1.01 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 404 TYR 0.017 0.002 TYR D 877 PHE 0.007 0.001 PHE I 840 TRP 0.024 0.003 TRP D 827 HIS 0.008 0.005 HIS H 406 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7894) covalent geometry : angle 0.68894 (10606) SS BOND : bond 0.00704 ( 4) SS BOND : angle 0.79238 ( 8) hydrogen bonds : bond 0.04219 ( 418) hydrogen bonds : angle 5.04387 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.204 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: 0.8215 (mmmt) cc_final: 0.7549 (mmmt) REVERT: B 379 LYS cc_start: 0.6746 (mmmm) cc_final: 0.6216 (tppt) REVERT: D 818 ARG cc_start: 0.6139 (mtp180) cc_final: 0.5408 (mtm110) REVERT: D 839 ARG cc_start: 0.5549 (ttt90) cc_final: 0.5262 (mtp180) REVERT: D 850 THR cc_start: 0.6603 (m) cc_final: 0.5924 (t) REVERT: C 811 ARG cc_start: 0.5828 (ptt180) cc_final: 0.5190 (ttp80) REVERT: C 825 THR cc_start: 0.7923 (t) cc_final: 0.7703 (t) REVERT: E 114 ARG cc_start: 0.7960 (ptp90) cc_final: 0.7588 (ptt90) REVERT: E 119 GLU cc_start: 0.7083 (pp20) cc_final: 0.6668 (pp20) REVERT: E 128 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7701 (mmm160) REVERT: E 145 ARG cc_start: 0.6784 (mtt180) cc_final: 0.6543 (mtt180) REVERT: E 156 LYS cc_start: 0.3131 (mptt) cc_final: 0.2729 (tttt) REVERT: F 107 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6651 (mm-30) REVERT: F 108 GLU cc_start: 0.6988 (tp30) cc_final: 0.6485 (tp30) REVERT: F 115 LEU cc_start: 0.8621 (mm) cc_final: 0.8335 (mm) REVERT: F 129 ARG cc_start: 0.7423 (tpt-90) cc_final: 0.7152 (tpt90) REVERT: F 133 ASP cc_start: 0.7595 (m-30) cc_final: 0.7378 (m-30) REVERT: F 144 ASP cc_start: 0.7060 (m-30) cc_final: 0.6688 (m-30) REVERT: G 389 ARG cc_start: 0.5814 (ptm160) cc_final: 0.5374 (ptm-80) REVERT: H 443 MET cc_start: 0.2143 (ptt) cc_final: 0.1764 (ptt) REVERT: J 807 MET cc_start: 0.4386 (ppp) cc_final: 0.3299 (ppp) REVERT: I 807 MET cc_start: 0.7132 (ppp) cc_final: 0.6610 (ppp) REVERT: I 855 MET cc_start: 0.6468 (mmp) cc_final: 0.6199 (mpp) REVERT: I 884 VAL cc_start: 0.7937 (t) cc_final: 0.7577 (t) REVERT: I 886 VAL cc_start: 0.7636 (m) cc_final: 0.7268 (t) REVERT: K 129 ARG cc_start: 0.8515 (ptt90) cc_final: 0.8255 (ttp80) REVERT: L 107 GLU cc_start: 0.8157 (mp0) cc_final: 0.7686 (mm-30) REVERT: L 119 GLU cc_start: 0.8677 (pp20) cc_final: 0.8332 (pp20) REVERT: L 132 GLN cc_start: 0.8398 (mp-120) cc_final: 0.8159 (pp30) outliers start: 1 outliers final: 1 residues processed: 212 average time/residue: 0.1243 time to fit residues: 32.4034 Evaluate side-chains 192 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 HIS C 3 GLN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN K 139 ASN ** 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 = 0.4590 r_free = 0.4590 target = 0.194165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.170030 restraints weight = 12975.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.168995 restraints weight = 15851.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.169831 restraints weight = 14583.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.170131 restraints weight = 11474.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.170624 restraints weight = 10057.490| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7898 Z= 0.172 Angle : 0.689 8.786 10614 Z= 0.364 Chirality : 0.043 0.148 1192 Planarity : 0.004 0.052 1416 Dihedral : 5.371 25.234 1126 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.27), residues: 978 helix: -0.19 (0.23), residues: 510 sheet: -2.02 (0.38), residues: 184 loop : -1.18 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 404 TYR 0.023 0.002 TYR D 877 PHE 0.007 0.001 PHE I 840 TRP 0.031 0.003 TRP I 878 HIS 0.007 0.004 HIS G 406 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7894) covalent geometry : angle 0.68796 (10606) SS BOND : bond 0.00567 ( 4) SS BOND : angle 1.54107 ( 8) hydrogen bonds : bond 0.04176 ( 418) hydrogen bonds : angle 5.05428 ( 1236) *********************** 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 207 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8375 (mmmt) cc_final: 0.7574 (mmmt) REVERT: B 379 LYS cc_start: 0.6964 (mmmm) cc_final: 0.6336 (tppt) REVERT: D 839 ARG cc_start: 0.5517 (ttt90) cc_final: 0.5173 (mtp180) REVERT: D 850 THR cc_start: 0.6400 (m) cc_final: 0.5744 (t) REVERT: D 873 ARG cc_start: 0.5996 (mpp-170) cc_final: 0.5754 (mpp80) REVERT: C 811 ARG cc_start: 0.5941 (ptt180) cc_final: 0.5394 (ttp80) REVERT: C 825 THR cc_start: 0.8271 (t) cc_final: 0.7973 (t) REVERT: E 114 ARG cc_start: 0.7990 (ptp90) cc_final: 0.7728 (ptt90) REVERT: E 119 GLU cc_start: 0.6754 (pp20) cc_final: 0.6415 (pp20) REVERT: E 128 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7503 (mmm160) REVERT: E 156 LYS cc_start: 0.3257 (mptt) cc_final: 0.2528 (tttt) REVERT: F 107 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6528 (mm-30) REVERT: F 108 GLU cc_start: 0.6967 (tp30) cc_final: 0.6364 (tp30) REVERT: F 115 LEU cc_start: 0.8530 (mm) cc_final: 0.8287 (mm) REVERT: F 133 ASP cc_start: 0.7531 (m-30) cc_final: 0.7180 (m-30) REVERT: F 142 GLU cc_start: 0.6455 (pp20) cc_final: 0.6204 (mp0) REVERT: F 144 ASP cc_start: 0.6809 (m-30) cc_final: 0.6406 (m-30) REVERT: H 443 MET cc_start: 0.2392 (ptt) cc_final: 0.2041 (ptt) REVERT: J 807 MET cc_start: 0.4765 (ppp) cc_final: 0.3903 (ppp) REVERT: J 820 MET cc_start: 0.5908 (mpp) cc_final: 0.5151 (mpp) REVERT: I 802 ASP cc_start: 0.6516 (t70) cc_final: 0.6259 (t70) REVERT: I 807 MET cc_start: 0.7173 (ppp) cc_final: 0.6238 (ppp) REVERT: I 808 ARG cc_start: 0.6927 (ptt180) cc_final: 0.6725 (ptt90) REVERT: I 884 VAL cc_start: 0.7739 (t) cc_final: 0.7382 (t) REVERT: I 886 VAL cc_start: 0.7399 (m) cc_final: 0.6955 (t) REVERT: K 100 GLN cc_start: 0.8392 (mp10) cc_final: 0.8037 (mp10) REVERT: L 119 GLU cc_start: 0.8530 (pp20) cc_final: 0.8167 (pp20) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1254 time to fit residues: 31.8720 Evaluate side-chains 190 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 91 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 812 GLN F 132 GLN H 387 GLN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 869 ASN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4613 r_free = 0.4613 target = 0.195022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.171666 restraints weight = 12754.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.168178 restraints weight = 12119.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.169340 restraints weight = 9354.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.169803 restraints weight = 7935.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.171080 restraints weight = 7229.854| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 0.7686 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= 0.147 Angle : 0.678 8.904 10614 Z= 0.360 Chirality : 0.043 0.204 1192 Planarity : 0.004 0.039 1416 Dihedral : 5.157 24.423 1126 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.27), residues: 978 helix: -0.16 (0.23), residues: 510 sheet: -1.98 (0.38), residues: 180 loop : -1.07 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 404 TYR 0.019 0.002 TYR D 810 PHE 0.008 0.001 PHE I 840 TRP 0.042 0.003 TRP D 809 HIS 0.005 0.002 HIS H 406 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7894) covalent geometry : angle 0.67801 (10606) SS BOND : bond 0.00462 ( 4) SS BOND : angle 1.02804 ( 8) hydrogen bonds : bond 0.03995 ( 418) hydrogen bonds : angle 4.94145 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7514 (mmmt) REVERT: A 389 ARG cc_start: 0.4662 (ptp-170) cc_final: 0.4332 (ptt-90) REVERT: B 379 LYS cc_start: 0.6872 (mmmm) cc_final: 0.6186 (tppt) REVERT: D 11 LEU cc_start: 0.6840 (mm) cc_final: 0.6639 (mm) REVERT: D 850 THR cc_start: 0.6299 (m) cc_final: 0.5694 (t) REVERT: C 811 ARG cc_start: 0.5944 (ptt180) cc_final: 0.5339 (ttp80) REVERT: C 825 THR cc_start: 0.8042 (t) cc_final: 0.7781 (t) REVERT: C 840 PHE cc_start: 0.5894 (m-10) cc_final: 0.5467 (m-80) REVERT: C 861 GLU cc_start: 0.7648 (tp30) cc_final: 0.7413 (tp30) REVERT: E 114 ARG cc_start: 0.8346 (ptp90) cc_final: 0.7801 (ptt90) REVERT: E 119 GLU cc_start: 0.6975 (pp20) cc_final: 0.6629 (pp20) REVERT: E 128 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7826 (mmm160) REVERT: E 145 ARG cc_start: 0.6833 (mtt180) cc_final: 0.6558 (mtt180) REVERT: F 107 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6664 (mm-30) REVERT: F 108 GLU cc_start: 0.6966 (tp30) cc_final: 0.6447 (tp30) REVERT: F 115 LEU cc_start: 0.8570 (mm) cc_final: 0.8265 (mm) REVERT: F 133 ASP cc_start: 0.7697 (m-30) cc_final: 0.7480 (m-30) REVERT: F 142 GLU cc_start: 0.6601 (pp20) cc_final: 0.6298 (mp0) REVERT: F 144 ASP cc_start: 0.7267 (m-30) cc_final: 0.6910 (m-30) REVERT: H 443 MET cc_start: 0.2492 (ptt) cc_final: 0.2134 (ptt) REVERT: J 807 MET cc_start: 0.4835 (ppp) cc_final: 0.4236 (ppp) REVERT: J 820 MET cc_start: 0.5937 (mpp) cc_final: 0.5371 (mpp) REVERT: I 802 ASP cc_start: 0.5950 (t70) cc_final: 0.5743 (t70) REVERT: I 807 MET cc_start: 0.6986 (ppp) cc_final: 0.6452 (ppp) REVERT: I 863 THR cc_start: 0.5943 (m) cc_final: 0.5552 (m) REVERT: I 884 VAL cc_start: 0.8003 (t) cc_final: 0.7092 (t) REVERT: I 886 VAL cc_start: 0.7461 (m) cc_final: 0.6950 (t) outliers start: 1 outliers final: 1 residues processed: 208 average time/residue: 0.1308 time to fit residues: 33.0619 Evaluate side-chains 184 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 73 optimal weight: 0.0770 chunk 41 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN H 387 GLN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 805 ASN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.192372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.165008 restraints weight = 12181.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.165133 restraints weight = 10471.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.166765 restraints weight = 8066.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.167333 restraints weight = 5947.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.167460 restraints weight = 5794.967| |-----------------------------------------------------------------------------| r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 moved from start: 0.7888 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= 0.132 Angle : 0.655 8.536 10614 Z= 0.346 Chirality : 0.043 0.230 1192 Planarity : 0.005 0.075 1416 Dihedral : 4.952 23.980 1126 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.27), residues: 978 helix: -0.05 (0.23), residues: 512 sheet: -1.83 (0.36), residues: 180 loop : -1.21 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 129 TYR 0.014 0.001 TYR D 810 PHE 0.006 0.001 PHE I 840 TRP 0.029 0.003 TRP D 809 HIS 0.004 0.002 HIS G 406 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7894) covalent geometry : angle 0.65520 (10606) SS BOND : bond 0.00424 ( 4) SS BOND : angle 0.77785 ( 8) hydrogen bonds : bond 0.03757 ( 418) hydrogen bonds : angle 4.73433 ( 1236) *********************** 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 207 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.212 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: 0.8022 (mmmt) cc_final: 0.7498 (mmmt) REVERT: A 389 ARG cc_start: 0.4481 (ptp-170) cc_final: 0.4280 (ptt-90) REVERT: B 379 LYS cc_start: 0.6891 (mmmm) cc_final: 0.6549 (tppt) REVERT: D 11 LEU cc_start: 0.6758 (mm) cc_final: 0.6552 (mm) REVERT: D 839 ARG cc_start: 0.5678 (ttt-90) cc_final: 0.5267 (mtp180) REVERT: D 850 THR cc_start: 0.6000 (m) cc_final: 0.5421 (t) REVERT: C 811 ARG cc_start: 0.5844 (ptt180) cc_final: 0.5390 (ttp80) REVERT: C 825 THR cc_start: 0.7999 (t) cc_final: 0.7739 (t) REVERT: C 837 LYS cc_start: 0.7211 (mttp) cc_final: 0.7004 (mmtm) REVERT: C 840 PHE cc_start: 0.5789 (m-10) cc_final: 0.5421 (m-80) REVERT: E 114 ARG cc_start: 0.8275 (ptp90) cc_final: 0.7778 (ptt90) REVERT: E 119 GLU cc_start: 0.6814 (pp20) cc_final: 0.6465 (pp20) REVERT: F 107 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6634 (mm-30) REVERT: F 108 GLU cc_start: 0.6948 (tp30) cc_final: 0.6401 (tp30) REVERT: F 115 LEU cc_start: 0.8517 (mm) cc_final: 0.8247 (mm) REVERT: F 133 ASP cc_start: 0.8020 (m-30) cc_final: 0.7746 (m-30) REVERT: F 142 GLU cc_start: 0.6850 (pp20) cc_final: 0.6505 (mp0) REVERT: F 144 ASP cc_start: 0.7110 (m-30) cc_final: 0.6733 (m-30) REVERT: H 389 ARG cc_start: 0.6608 (tpp-160) cc_final: 0.6001 (mmt-90) REVERT: H 443 MET cc_start: 0.2699 (ptt) cc_final: 0.2440 (ptt) REVERT: J 807 MET cc_start: 0.4587 (ppp) cc_final: 0.4015 (ppp) REVERT: J 820 MET cc_start: 0.5645 (mpp) cc_final: 0.5024 (mpp) REVERT: I 807 MET cc_start: 0.6898 (ppp) cc_final: 0.6318 (ppp) REVERT: I 863 THR cc_start: 0.5986 (m) cc_final: 0.5700 (m) REVERT: I 884 VAL cc_start: 0.7935 (t) cc_final: 0.6989 (t) REVERT: I 886 VAL cc_start: 0.7272 (m) cc_final: 0.6766 (t) REVERT: K 156 LYS cc_start: 0.7728 (mppt) cc_final: 0.7389 (mtmm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1167 time to fit residues: 29.8763 Evaluate side-chains 187 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 6 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 0.0030 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 387 GLN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.195724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.165664 restraints weight = 11929.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.168120 restraints weight = 8177.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.169467 restraints weight = 6295.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.170741 restraints weight = 5368.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.171717 restraints weight = 4808.045| |-----------------------------------------------------------------------------| r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7898 Z= 0.120 Angle : 0.638 8.194 10614 Z= 0.335 Chirality : 0.042 0.202 1192 Planarity : 0.004 0.060 1416 Dihedral : 4.682 22.918 1126 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.27), residues: 978 helix: 0.07 (0.23), residues: 510 sheet: -1.48 (0.37), residues: 176 loop : -1.08 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 129 TYR 0.020 0.001 TYR I 810 PHE 0.007 0.001 PHE I 840 TRP 0.024 0.002 TRP D 809 HIS 0.003 0.001 HIS H 406 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7894) covalent geometry : angle 0.63790 (10606) SS BOND : bond 0.00399 ( 4) SS BOND : angle 0.82792 ( 8) hydrogen bonds : bond 0.03667 ( 418) hydrogen bonds : angle 4.57327 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 379 LYS cc_start: 0.6837 (mmmm) cc_final: 0.6521 (tppt) REVERT: C 825 THR cc_start: 0.7830 (t) cc_final: 0.7574 (t) REVERT: C 832 TYR cc_start: 0.7437 (m-80) cc_final: 0.7053 (m-80) REVERT: C 837 LYS cc_start: 0.7157 (mttp) cc_final: 0.6885 (mmtm) REVERT: C 840 PHE cc_start: 0.5908 (m-10) cc_final: 0.5070 (m-80) REVERT: C 861 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7557 (tp30) REVERT: E 114 ARG cc_start: 0.8440 (ptp90) cc_final: 0.7870 (ptt90) REVERT: E 119 GLU cc_start: 0.7014 (pp20) cc_final: 0.6617 (pp20) REVERT: F 107 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6759 (mm-30) REVERT: F 108 GLU cc_start: 0.7135 (tp30) cc_final: 0.6551 (tp30) REVERT: F 115 LEU cc_start: 0.8566 (mm) cc_final: 0.8273 (mm) REVERT: F 129 ARG cc_start: 0.7090 (tpt170) cc_final: 0.6716 (tpt170) REVERT: F 133 ASP cc_start: 0.8072 (m-30) cc_final: 0.7809 (m-30) REVERT: F 142 GLU cc_start: 0.6921 (pp20) cc_final: 0.6627 (mp0) REVERT: F 144 ASP cc_start: 0.7206 (m-30) cc_final: 0.6898 (m-30) REVERT: G 422 SER cc_start: 0.3790 (p) cc_final: 0.3583 (p) REVERT: H 443 MET cc_start: 0.2734 (ptt) cc_final: 0.2510 (ptt) REVERT: J 807 MET cc_start: 0.4590 (ppp) cc_final: 0.4011 (ppp) REVERT: J 820 MET cc_start: 0.5589 (mpp) cc_final: 0.4958 (mpp) REVERT: I 807 MET cc_start: 0.7009 (ppp) cc_final: 0.6375 (ppp) REVERT: I 863 THR cc_start: 0.5735 (m) cc_final: 0.5504 (m) REVERT: I 884 VAL cc_start: 0.8007 (t) cc_final: 0.6973 (t) REVERT: I 886 VAL cc_start: 0.7107 (m) cc_final: 0.6573 (t) REVERT: K 156 LYS cc_start: 0.7633 (mppt) cc_final: 0.7401 (mtmm) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1155 time to fit residues: 29.7175 Evaluate side-chains 186 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN H 387 GLN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4603 r_free = 0.4603 target = 0.195688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.4480 r_free = 0.4480 target = 0.172098 restraints weight = 12823.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 108)---------------| | r_work = 0.4465 r_free = 0.4465 target = 0.171489 restraints weight = 12284.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.169824 restraints weight = 9452.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.170402 restraints weight = 8802.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.170403 restraints weight = 7408.777| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.8277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7898 Z= 0.155 Angle : 0.702 8.717 10614 Z= 0.365 Chirality : 0.044 0.183 1192 Planarity : 0.005 0.063 1416 Dihedral : 5.029 22.941 1126 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.27), residues: 978 helix: 0.05 (0.23), residues: 500 sheet: -1.69 (0.36), residues: 184 loop : -1.20 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 873 TYR 0.015 0.002 TYR D 810 PHE 0.007 0.002 PHE I 840 TRP 0.022 0.002 TRP D 809 HIS 0.006 0.003 HIS G 406 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7894) covalent geometry : angle 0.70216 (10606) SS BOND : bond 0.00486 ( 4) SS BOND : angle 0.69191 ( 8) hydrogen bonds : bond 0.03838 ( 418) hydrogen bonds : angle 4.80017 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1426.81 seconds wall clock time: 25 minutes 9.86 seconds (1509.86 seconds total)