Starting phenix.real_space_refine on Sat Sep 12 03:11:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cww_27030/09_2026/8cww_27030.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cww_27030/09_2026/8cww_27030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cww_27030/09_2026/8cww_27030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cww_27030/09_2026/8cww_27030.map" model { file = "/net/cci-nas-00/data/ceres_data/8cww_27030/09_2026/8cww_27030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cww_27030/09_2026/8cww_27030.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8cww_27030/09_2026/8cww_27030.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cww_27030/09_2026/8cww_27030.cif" } resolution = 2.74 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= 0.034 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 292 5.49 5 S 22 5.16 5 C 7671 2.51 5 N 2525 2.21 5 O 3113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13625 Number of models: 1 Model: "" Number of chains: 12 Chain: "P" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1620 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 713 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3009 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2977 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 125 SG CYS P 348 53.559 63.905 122.241 1.00123.63 S ATOM 146 SG CYS P 351 51.277 63.098 125.053 1.00138.42 S ATOM 306 SG CYS P 371 53.184 66.344 125.198 1.00128.32 S ATOM 330 SG CYS P 374 55.036 63.224 125.861 1.00142.86 S ATOM 12 SG CYS P 332 48.320 73.493 123.550 1.00136.18 S ATOM 27 SG CYS P 334 46.229 76.477 124.626 1.00119.33 S ATOM 209 SG CYS P 359 49.031 76.970 122.001 1.00123.04 S Time building chain proxies: 2.59, per 1000 atoms: 0.19 Number of scatterers: 13625 At special positions: 0 Unit cell: (79.2, 128.7, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 22 16.00 P 292 15.00 O 3113 8.00 N 2525 7.00 C 7671 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 372.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 601 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 351 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 371 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 374 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 348 " pdb=" ZN P 602 " pdb="ZN ZN P 602 " - pdb=" ND1 HIS P 356 " pdb="ZN ZN P 602 " - pdb=" SG CYS P 332 " pdb="ZN ZN P 602 " - pdb=" SG CYS P 334 " pdb="ZN ZN P 602 " - pdb=" SG CYS P 359 " Number of angles added : 9 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 13 sheets defined 66.2% alpha, 4.8% beta 130 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'P' and resid 358 through 361 removed outlier: 3.698A pdb=" N GLY P 361 " --> pdb=" O ILE P 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 358 through 361' Processing helix chain 'P' and resid 371 through 377 Processing helix chain 'P' and resid 384 through 404 removed outlier: 3.592A pdb=" N LYS P 404 " --> pdb=" O LEU P 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 410 through 419 Processing helix chain 'P' and resid 425 through 442 Processing helix chain 'P' and resid 498 through 502 removed outlier: 3.756A pdb=" N TYR P 501 " --> pdb=" O GLU P 498 " (cutoff:3.500A) Processing helix chain 'P' and resid 508 through 531 removed outlier: 3.513A pdb=" N VAL P 512 " --> pdb=" O SER P 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.506A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.557A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.586A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.719A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.504A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.884A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.782A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.500A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 21' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.764A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.562A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.610A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.528A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.514A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.514A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.810A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.507A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.558A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.586A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.718A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.504A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.884A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.781A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.501A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.765A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.562A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.612A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.528A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.515A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.514A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.810A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 354 through 356 removed outlier: 8.916A pdb=" N ILE P 368 " --> pdb=" O LEU P 345 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR P 347 " --> pdb=" O ILE P 368 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 445 through 447 removed outlier: 3.815A pdb=" N HIS P 484 " --> pdb=" O VAL P 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 472 through 473 removed outlier: 3.896A pdb=" N LYS P 478 " --> pdb=" O ILE P 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.062A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.450A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.776A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.009A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.522A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.425A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 77 through 78 420 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 339 hydrogen bonds 678 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 1.46 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: 3369 1.34 - 1.46: 4230 1.46 - 1.58: 6251 1.58 - 1.70: 582 1.70 - 1.82: 34 Bond restraints: 14466 Sorted by residual: bond pdb=" C3' DC I 30 " pdb=" C2' DC I 30 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DC I 70 " pdb=" C2' DC I 70 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DG J 20 " pdb=" C2' DG J 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.87e+00 bond pdb=" C3' DC J 51 " pdb=" C2' DC J 51 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.64e+00 bond pdb=" C3' DT I -61 " pdb=" C2' DT I -61 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.80e+00 ... (remaining 14461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 18246 0.94 - 1.88: 1837 1.88 - 2.83: 674 2.83 - 3.77: 30 3.77 - 4.71: 6 Bond angle restraints: 20793 Sorted by residual: angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT I -32 " pdb=" C4 DT I -32 " pdb=" O4 DT I -32 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 20788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.56: 6604 33.56 - 67.12: 1343 67.12 - 100.68: 5 100.68 - 134.24: 0 134.24 - 167.79: 1 Dihedral angle restraints: 7953 sinusoidal: 5153 harmonic: 2800 Sorted by residual: dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 52.21 167.79 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" N LYS P 395 " pdb=" CA LYS P 395 " pdb=" CB LYS P 395 " pdb=" CG LYS P 395 " ideal model delta sinusoidal sigma weight residual -180.00 -132.38 -47.62 3 1.50e+01 4.44e-03 8.52e+00 dihedral pdb=" CB MET P 391 " pdb=" CG MET P 391 " pdb=" SD MET P 391 " pdb=" CE MET P 391 " ideal model delta sinusoidal sigma weight residual 60.00 103.49 -43.49 3 1.50e+01 4.44e-03 7.82e+00 ... (remaining 7950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1376 0.031 - 0.062: 692 0.062 - 0.093: 219 0.093 - 0.124: 82 0.124 - 0.155: 2 Chirality restraints: 2371 Sorted by residual: chirality pdb=" C3' DT I 31 " pdb=" C4' DT I 31 " pdb=" O3' DT I 31 " pdb=" C2' DT I 31 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" C3' DC I 52 " pdb=" C4' DC I 52 " pdb=" O3' DC I 52 " pdb=" C2' DC I 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" P DC I 53 " pdb=" OP1 DC I 53 " pdb=" OP2 DC I 53 " pdb=" O5' DC I 53 " both_signs ideal model delta sigma weight residual True 2.34 -2.46 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 2368 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 28 " -0.022 2.00e-02 2.50e+03 9.87e-03 2.68e+00 pdb=" N9 DA I 28 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 28 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 28 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 28 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 28 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 28 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 28 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 28 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 28 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.021 2.00e-02 2.50e+03 9.00e-03 2.23e+00 pdb=" N9 DA I 47 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 33 " 0.019 2.00e-02 2.50e+03 9.79e-03 2.15e+00 pdb=" N1 DC J 33 " -0.021 2.00e-02 2.50e+03 pdb=" C2 DC J 33 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DC J 33 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DC J 33 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC J 33 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC J 33 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DC J 33 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DC J 33 " -0.004 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 4015 2.87 - 3.38: 10524 3.38 - 3.89: 22949 3.89 - 4.39: 28134 4.39 - 4.90: 39808 Nonbonded interactions: 105430 Sorted by model distance: nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.368 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.369 3.120 nonbonded pdb=" NZ LYS P 340 " pdb=" OP1 DC I 52 " model vdw 2.392 3.120 nonbonded pdb=" OE1 GLN P 388 " pdb=" NH2 ARG P 431 " model vdw 2.415 3.120 nonbonded pdb=" OG1 THR C 10 " pdb=" N ARG C 11 " model vdw 2.423 3.120 ... (remaining 105425 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 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = (chain 'D' and ((resid 30 and (name N or name CA or name C or name O or name CB \ )) or resid 31 through 121)) selection = chain 'H' } 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 individual isotropic 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.340 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 : 0.005 0.029 14474 Z= 0.476 Angle : 0.661 6.812 20802 Z= 0.602 Chirality : 0.041 0.155 2371 Planarity : 0.004 0.033 1616 Dihedral : 24.378 167.794 6141 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.25 % Allowed : 0.86 % Favored : 98.90 % 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 are not related in a simple way. whole: 0.45 (0.25), residues: 944 helix: 0.89 (0.20), residues: 597 sheet: 3.86 (1.17), residues: 19 loop : -0.95 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 67 TYR 0.008 0.001 TYR P 501 PHE 0.011 0.001 PHE P 500 TRP 0.002 0.000 TRP P 384 HIS 0.002 0.000 HIS P 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.48 (14466) covalent geometry : angle 0.65747 / 0.60 (20793) hydrogen bonds : bond 0.25127 / 16.51 ( 759) hydrogen bonds : angle 4.41700 / 3.13 ( 1914) metal coordination : bond 0.00383 / 0.23 ( 8) metal coordination : angle 3.35719 / 1.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 0.240 Fit side-chains REVERT: P 521 ASN cc_start: 0.8661 (m-40) cc_final: 0.8396 (m110) REVERT: A 79 LYS cc_start: 0.8495 (tttt) cc_final: 0.8210 (tttm) REVERT: B 24 ASP cc_start: 0.8301 (t0) cc_final: 0.7749 (t0) REVERT: C 36 LYS cc_start: 0.9017 (mttt) cc_final: 0.8750 (mmtp) REVERT: D 31 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8613 (mtpp) REVERT: D 82 LYS cc_start: 0.8917 (mttt) cc_final: 0.8713 (mttm) REVERT: G 61 GLU cc_start: 0.8805 (tp30) cc_final: 0.8557 (tp30) REVERT: G 72 ASP cc_start: 0.8577 (m-30) cc_final: 0.8370 (m-30) REVERT: H 96 ARG cc_start: 0.8599 (mtp180) cc_final: 0.8303 (mtm-85) REVERT: H 110 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8856 (mm-30) outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 0.8891 time to fit residues: 169.1456 Evaluate side-chains 123 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN A 68 GLN B 27 GLN C 112 GLN E 68 GLN F 27 GLN G 112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.064219 restraints weight = 26125.685| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.49 r_work: 0.2927 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14474 Z= 0.246 Angle : 0.680 8.385 20802 Z= 0.400 Chirality : 0.049 0.250 2371 Planarity : 0.005 0.042 1616 Dihedral : 28.738 170.596 4252 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.33 % Allowed : 9.20 % Favored : 88.47 % 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 are not related in a simple way. whole: 1.25 (0.26), residues: 944 helix: 1.68 (0.20), residues: 612 sheet: 3.53 (1.10), residues: 19 loop : -1.08 (0.30), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 23 TYR 0.016 0.002 TYR H 34 PHE 0.018 0.002 PHE D 67 TRP 0.007 0.001 TRP P 488 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.25 (14466) covalent geometry : angle 0.67582 / 0.40 (20793) hydrogen bonds : bond 0.09908 / 6.47 ( 759) hydrogen bonds : angle 3.40869 / 2.37 ( 1914) metal coordination : bond 0.01041 / 0.72 ( 8) metal coordination : angle 3.66722 / 1.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.305 Fit side-chains REVERT: P 442 ASP cc_start: 0.8340 (m-30) cc_final: 0.7683 (t0) REVERT: B 23 ARG cc_start: 0.7452 (pmt-80) cc_final: 0.7127 (pmt-80) REVERT: E 42 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8109 (mtm-85) REVERT: F 53 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: H 73 GLU cc_start: 0.9113 (tp30) cc_final: 0.8910 (mm-30) outliers start: 19 outliers final: 5 residues processed: 134 average time/residue: 0.8556 time to fit residues: 121.5297 Evaluate side-chains 122 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN A 68 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.089496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065696 restraints weight = 26296.987| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.49 r_work: 0.2961 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14474 Z= 0.171 Angle : 0.602 7.315 20802 Z= 0.360 Chirality : 0.045 0.262 2371 Planarity : 0.004 0.032 1616 Dihedral : 28.766 172.185 4252 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.84 % Allowed : 11.29 % Favored : 86.87 % 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 are not related in a simple way. whole: 1.67 (0.27), residues: 944 helix: 2.06 (0.21), residues: 612 sheet: 3.12 (1.10), residues: 19 loop : -1.01 (0.31), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.009 0.001 TYR H 34 PHE 0.011 0.001 PHE H 62 TRP 0.013 0.001 TRP P 488 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.17 (14466) covalent geometry : angle 0.59862 / 0.36 (20793) hydrogen bonds : bond 0.08320 / 5.43 ( 759) hydrogen bonds : angle 3.22650 / 2.25 ( 1914) metal coordination : bond 0.00671 / 0.47 ( 8) metal coordination : angle 3.23108 / 1.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.381 Fit side-chains REVERT: P 442 ASP cc_start: 0.8266 (m-30) cc_final: 0.7804 (t0) REVERT: P 486 TYR cc_start: 0.7652 (m-80) cc_final: 0.7369 (m-80) REVERT: B 23 ARG cc_start: 0.7445 (pmt-80) cc_final: 0.7115 (pmt-80) REVERT: B 24 ASP cc_start: 0.7726 (t0) cc_final: 0.7331 (t0) REVERT: D 102 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7908 (mt-10) outliers start: 15 outliers final: 7 residues processed: 130 average time/residue: 0.8790 time to fit residues: 121.2147 Evaluate side-chains 125 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 10.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN A 68 GLN C 73 ASN F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.090138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.066489 restraints weight = 26323.495| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.50 r_work: 0.2980 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14474 Z= 0.165 Angle : 0.573 6.813 20802 Z= 0.342 Chirality : 0.044 0.265 2371 Planarity : 0.004 0.034 1616 Dihedral : 28.904 172.090 4252 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.09 % Allowed : 11.66 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.27), residues: 944 helix: 2.27 (0.21), residues: 614 sheet: 3.21 (1.11), residues: 19 loop : -1.06 (0.30), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 352 TYR 0.009 0.001 TYR P 501 PHE 0.012 0.001 PHE P 418 TRP 0.002 0.001 TRP P 488 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (14466) covalent geometry : angle 0.56962 / 0.34 (20793) hydrogen bonds : bond 0.07337 / 4.79 ( 759) hydrogen bonds : angle 2.95800 / 2.05 ( 1914) metal coordination : bond 0.00512 / 0.33 ( 8) metal coordination : angle 3.09807 / 1.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.382 Fit side-chains REVERT: P 431 ARG cc_start: 0.8538 (mtt-85) cc_final: 0.8248 (mtp85) REVERT: P 442 ASP cc_start: 0.8137 (m-30) cc_final: 0.7747 (t0) REVERT: P 486 TYR cc_start: 0.7600 (m-80) cc_final: 0.7290 (m-80) REVERT: P 517 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 23 ARG cc_start: 0.7440 (pmt-80) cc_final: 0.7134 (pmt-80) REVERT: B 24 ASP cc_start: 0.7789 (t0) cc_final: 0.7525 (t0) outliers start: 17 outliers final: 7 residues processed: 131 average time/residue: 0.8515 time to fit residues: 118.3378 Evaluate side-chains 119 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 522 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN C 73 ASN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.088099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064197 restraints weight = 26423.453| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.51 r_work: 0.2924 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14474 Z= 0.214 Angle : 0.629 7.238 20802 Z= 0.367 Chirality : 0.048 0.260 2371 Planarity : 0.004 0.034 1616 Dihedral : 28.948 173.198 4252 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.09 % Allowed : 11.90 % Favored : 86.01 % 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 are not related in a simple way. whole: 1.68 (0.27), residues: 944 helix: 2.24 (0.21), residues: 606 sheet: 0.55 (1.00), residues: 31 loop : -1.22 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 45 TYR 0.010 0.001 TYR H 34 PHE 0.017 0.002 PHE H 62 TRP 0.002 0.001 TRP P 488 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (14466) covalent geometry : angle 0.62557 / 0.37 (20793) hydrogen bonds : bond 0.08636 / 5.65 ( 759) hydrogen bonds : angle 3.09962 / 2.15 ( 1914) metal coordination : bond 0.00811 / 0.55 ( 8) metal coordination : angle 3.42930 / 1.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.366 Fit side-chains REVERT: P 442 ASP cc_start: 0.8208 (m-30) cc_final: 0.7776 (t0) REVERT: P 486 TYR cc_start: 0.7680 (m-80) cc_final: 0.7445 (m-80) REVERT: B 23 ARG cc_start: 0.7495 (pmt-80) cc_final: 0.7235 (pmt-80) REVERT: E 42 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8041 (mtm-85) REVERT: F 53 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8084 (tt0) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 0.8279 time to fit residues: 110.8784 Evaluate side-chains 124 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 472 VAL Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 522 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 75 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 0.0070 chunk 107 optimal weight: 20.0000 chunk 74 optimal weight: 0.1980 chunk 9 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN A 68 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.089648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.065949 restraints weight = 26045.952| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.50 r_work: 0.2966 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14474 Z= 0.157 Angle : 0.593 6.765 20802 Z= 0.351 Chirality : 0.045 0.256 2371 Planarity : 0.004 0.033 1616 Dihedral : 28.920 173.056 4252 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.60 % Allowed : 13.74 % Favored : 84.66 % 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 are not related in a simple way. whole: 1.92 (0.27), residues: 944 helix: 2.43 (0.21), residues: 606 sheet: 0.54 (0.99), residues: 31 loop : -1.11 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 431 TYR 0.009 0.001 TYR P 501 PHE 0.010 0.001 PHE P 418 TRP 0.003 0.001 TRP P 488 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.16 (14466) covalent geometry : angle 0.58917 / 0.35 (20793) hydrogen bonds : bond 0.07255 / 4.74 ( 759) hydrogen bonds : angle 3.13033 / 2.17 ( 1914) metal coordination : bond 0.00372 / 0.23 ( 8) metal coordination : angle 3.16893 / 1.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.313 Fit side-chains REVERT: P 442 ASP cc_start: 0.8124 (m-30) cc_final: 0.7715 (t0) REVERT: P 486 TYR cc_start: 0.7663 (m-80) cc_final: 0.7404 (m-80) REVERT: A 79 LYS cc_start: 0.9035 (tttt) cc_final: 0.8744 (tttp) REVERT: B 23 ARG cc_start: 0.7337 (pmt-80) cc_final: 0.6968 (pmt-80) REVERT: B 24 ASP cc_start: 0.7341 (t0) cc_final: 0.6863 (OUTLIER) REVERT: G 99 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8827 (mtp85) outliers start: 13 outliers final: 10 residues processed: 124 average time/residue: 0.8647 time to fit residues: 113.7054 Evaluate side-chains 121 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 472 VAL Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN P 484 HIS A 68 GLN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.086984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.063028 restraints weight = 26145.136| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.50 r_work: 0.2839 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14474 Z= 0.274 Angle : 0.683 7.209 20802 Z= 0.392 Chirality : 0.052 0.262 2371 Planarity : 0.005 0.036 1616 Dihedral : 28.980 173.755 4252 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.21 % Allowed : 13.01 % Favored : 84.79 % 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 are not related in a simple way. whole: 1.53 (0.27), residues: 944 helix: 2.19 (0.21), residues: 606 sheet: 0.47 (1.00), residues: 31 loop : -1.43 (0.30), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 45 TYR 0.011 0.002 TYR H 34 PHE 0.020 0.002 PHE H 62 TRP 0.005 0.001 TRP P 515 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.27 (14466) covalent geometry : angle 0.67921 / 0.39 (20793) hydrogen bonds : bond 0.09525 / 6.24 ( 759) hydrogen bonds : angle 3.19959 / 2.22 ( 1914) metal coordination : bond 0.01209 / 0.86 ( 8) metal coordination : angle 3.53149 / 1.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.404 Fit side-chains REVERT: P 442 ASP cc_start: 0.8253 (m-30) cc_final: 0.7808 (t0) REVERT: B 23 ARG cc_start: 0.7389 (pmt-80) cc_final: 0.7054 (pmt-80) REVERT: B 24 ASP cc_start: 0.7845 (t0) cc_final: 0.7378 (OUTLIER) REVERT: E 42 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8026 (mtm-85) REVERT: F 53 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: G 99 ARG cc_start: 0.9102 (mmm-85) cc_final: 0.8810 (mtp85) outliers start: 18 outliers final: 12 residues processed: 126 average time/residue: 0.8975 time to fit residues: 119.7090 Evaluate side-chains 123 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 472 VAL Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN C 73 ASN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.064756 restraints weight = 26153.012| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.51 r_work: 0.2884 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14474 Z= 0.158 Angle : 0.615 8.876 20802 Z= 0.362 Chirality : 0.047 0.259 2371 Planarity : 0.004 0.060 1616 Dihedral : 28.938 173.766 4252 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.60 % Allowed : 14.23 % Favored : 84.17 % 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 are not related in a simple way. whole: 1.74 (0.27), residues: 944 helix: 2.35 (0.21), residues: 606 sheet: 0.51 (0.99), residues: 31 loop : -1.32 (0.30), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 30 TYR 0.022 0.001 TYR P 486 PHE 0.011 0.001 PHE D 67 TRP 0.003 0.001 TRP P 515 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.16 (14466) covalent geometry : angle 0.61092 / 0.36 (20793) hydrogen bonds : bond 0.07833 / 5.12 ( 759) hydrogen bonds : angle 3.11281 / 2.18 ( 1914) metal coordination : bond 0.00384 / 0.22 ( 8) metal coordination : angle 3.27569 / 1.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.283 Fit side-chains REVERT: P 442 ASP cc_start: 0.8157 (m-30) cc_final: 0.7727 (t0) REVERT: A 79 LYS cc_start: 0.9106 (tttt) cc_final: 0.8822 (tttp) REVERT: B 23 ARG cc_start: 0.7413 (pmt-80) cc_final: 0.7101 (pmt-80) REVERT: B 24 ASP cc_start: 0.7694 (t0) cc_final: 0.7188 (OUTLIER) REVERT: G 99 ARG cc_start: 0.9079 (mmm-85) cc_final: 0.8855 (mtp85) outliers start: 13 outliers final: 10 residues processed: 118 average time/residue: 0.8597 time to fit residues: 107.5438 Evaluate side-chains 117 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 472 VAL Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.089065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.065358 restraints weight = 26256.172| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.50 r_work: 0.2954 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14474 Z= 0.164 Angle : 0.599 7.517 20802 Z= 0.352 Chirality : 0.046 0.267 2371 Planarity : 0.004 0.036 1616 Dihedral : 28.962 174.402 4252 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.47 % Allowed : 14.36 % Favored : 84.17 % 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 are not related in a simple way. whole: 1.90 (0.27), residues: 944 helix: 2.47 (0.21), residues: 606 sheet: 0.56 (0.98), residues: 31 loop : -1.26 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 30 TYR 0.010 0.001 TYR P 486 PHE 0.010 0.001 PHE H 62 TRP 0.003 0.001 TRP P 384 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (14466) covalent geometry : angle 0.59547 / 0.35 (20793) hydrogen bonds : bond 0.07559 / 4.95 ( 759) hydrogen bonds : angle 2.97101 / 2.07 ( 1914) metal coordination : bond 0.00579 / 0.39 ( 8) metal coordination : angle 3.15344 / 1.67 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.311 Fit side-chains REVERT: P 442 ASP cc_start: 0.8126 (m-30) cc_final: 0.7731 (t0) REVERT: B 23 ARG cc_start: 0.7419 (pmt-80) cc_final: 0.7104 (pmt-80) REVERT: B 24 ASP cc_start: 0.7680 (t0) cc_final: 0.7163 (OUTLIER) REVERT: G 99 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8846 (mtp85) outliers start: 12 outliers final: 10 residues processed: 119 average time/residue: 0.8495 time to fit residues: 107.2748 Evaluate side-chains 117 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 472 VAL Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN A 68 GLN C 73 ASN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.089997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066422 restraints weight = 26134.767| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.51 r_work: 0.2977 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14474 Z= 0.146 Angle : 0.576 7.886 20802 Z= 0.343 Chirality : 0.044 0.267 2371 Planarity : 0.004 0.043 1616 Dihedral : 28.952 173.953 4252 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.98 % Allowed : 14.72 % Favored : 84.29 % 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 are not related in a simple way. whole: 2.00 (0.27), residues: 944 helix: 2.54 (0.21), residues: 606 sheet: 0.57 (0.97), residues: 31 loop : -1.18 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 30 TYR 0.010 0.001 TYR P 501 PHE 0.010 0.001 PHE P 418 TRP 0.004 0.001 TRP P 384 HIS 0.002 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.15 (14466) covalent geometry : angle 0.57305 / 0.34 (20793) hydrogen bonds : bond 0.06932 / 4.53 ( 759) hydrogen bonds : angle 2.92401 / 2.04 ( 1914) metal coordination : bond 0.00356 / 0.21 ( 8) metal coordination : angle 3.01208 / 1.60 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.383 Fit side-chains REVERT: P 442 ASP cc_start: 0.8104 (m-30) cc_final: 0.7739 (t0) REVERT: A 79 LYS cc_start: 0.9079 (tttt) cc_final: 0.8799 (tttp) REVERT: B 23 ARG cc_start: 0.7485 (pmt-80) cc_final: 0.7145 (pmt-80) REVERT: B 24 ASP cc_start: 0.7641 (t0) cc_final: 0.7167 (t0) REVERT: G 99 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8851 (mtp85) outliers start: 8 outliers final: 8 residues processed: 117 average time/residue: 0.8560 time to fit residues: 106.3045 Evaluate side-chains 117 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 472 VAL Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN A 68 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.065619 restraints weight = 26335.671| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.51 r_work: 0.2960 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14474 Z= 0.174 Angle : 0.593 7.335 20802 Z= 0.349 Chirality : 0.045 0.266 2371 Planarity : 0.004 0.033 1616 Dihedral : 28.990 173.632 4252 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.23 % Allowed : 14.72 % Favored : 84.05 % 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 are not related in a simple way. whole: 2.10 (0.27), residues: 944 helix: 2.64 (0.21), residues: 594 sheet: 0.53 (0.96), residues: 31 loop : -1.04 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 30 TYR 0.010 0.001 TYR P 501 PHE 0.012 0.001 PHE H 62 TRP 0.004 0.001 TRP P 384 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (14466) covalent geometry : angle 0.58994 / 0.35 (20793) hydrogen bonds : bond 0.07374 / 4.82 ( 759) hydrogen bonds : angle 2.90244 / 2.02 ( 1914) metal coordination : bond 0.00578 / 0.39 ( 8) metal coordination : angle 3.13565 / 1.68 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4273.03 seconds wall clock time: 73 minutes 7.11 seconds (4387.11 seconds total)