Starting phenix.real_space_refine on Fri Jul 3 09:16:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cww_27030/07_2026/8cww_27030.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cww_27030/07_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_27030/07_2026/8cww_27030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cww_27030/07_2026/8cww_27030.map" model { file = "/net/cci-nas-00/data/ceres_data/8cww_27030/07_2026/8cww_27030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cww_27030/07_2026/8cww_27030.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8cww_27030/07_2026/8cww_27030.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cww_27030/07_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-dev-6108/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: 2.65, 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: 0.82 Conformation dependent library (CDL) restraints added in 342.8 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: 1.84 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: 2.36 Time building geometry restraints manager: 1.18 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: 18363 0.94 - 1.88: 1720 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: 1.070 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.260 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.880 ------------------------------------------------------------------------------- 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 : 0.654 6.812 20802 Z= 0.597 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 0.65033 / 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 : 0.291 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: 0.9416 time to fit residues: 179.0458 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 : 0.372 ------------------------------------------------------------------------------- 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 F 27 GLN G 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.088133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064058 restraints weight = 26094.306| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.49 r_work: 0.2923 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.1515 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= 0.240 Angle : 0.672 8.318 20802 Z= 0.397 Chirality : 0.050 0.234 2371 Planarity : 0.005 0.048 1616 Dihedral : 28.720 171.112 4252 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.21 % Allowed : 9.33 % 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: 1.28 (0.26), residues: 944 helix: 1.71 (0.20), residues: 612 sheet: 3.56 (1.10), residues: 19 loop : -1.07 (0.30), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 45 TYR 0.016 0.002 TYR H 34 PHE 0.017 0.002 PHE D 67 TRP 0.010 0.002 TRP P 488 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.24 (14466) covalent geometry : angle 0.66823 / 0.40 (20793) hydrogen bonds : bond 0.10329 / 6.75 ( 759) hydrogen bonds : angle 3.43734 / 2.39 ( 1914) metal coordination : bond 0.01020 / 0.71 ( 8) metal coordination : angle 3.64170 / 1.87 ( 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: 18 poor density : 121 time to evaluate : 0.388 Fit side-chains REVERT: P 442 ASP cc_start: 0.8342 (m-30) cc_final: 0.7685 (t0) REVERT: B 23 ARG cc_start: 0.7468 (pmt-80) cc_final: 0.7163 (pmt-80) REVERT: F 53 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: H 73 GLU cc_start: 0.9122 (tp30) cc_final: 0.8922 (mm-30) outliers start: 18 outliers final: 6 residues processed: 134 average time/residue: 0.9203 time to fit residues: 130.5817 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 : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 54 LYS 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: 10.0000 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN A 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.088491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064607 restraints weight = 26260.463| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.50 r_work: 0.2933 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14474 Z= 0.204 Angle : 0.615 7.193 20802 Z= 0.365 Chirality : 0.047 0.242 2371 Planarity : 0.004 0.035 1616 Dihedral : 28.925 173.569 4252 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.09 % Allowed : 11.17 % Favored : 86.75 % 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: 1.54 (0.27), residues: 944 helix: 2.01 (0.21), residues: 612 sheet: 3.14 (1.10), residues: 19 loop : -1.18 (0.30), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 45 TYR 0.011 0.001 TYR H 34 PHE 0.014 0.002 PHE D 67 TRP 0.004 0.001 TRP P 488 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (14466) covalent geometry : angle 0.61149 / 0.36 (20793) hydrogen bonds : bond 0.08664 / 5.65 ( 759) hydrogen bonds : angle 3.15420 / 2.20 ( 1914) metal coordination : bond 0.00726 / 0.48 ( 8) metal coordination : angle 3.27210 / 1.71 ( 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: 17 poor density : 116 time to evaluate : 0.365 Fit side-chains REVERT: P 442 ASP cc_start: 0.8250 (m-30) cc_final: 0.7782 (t0) REVERT: P 486 TYR cc_start: 0.7704 (m-80) cc_final: 0.7467 (m-80) REVERT: B 23 ARG cc_start: 0.7483 (pmt-80) cc_final: 0.7060 (pmt-80) REVERT: B 24 ASP cc_start: 0.7794 (t0) cc_final: 0.7171 (t0) REVERT: D 102 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7860 (mt-10) outliers start: 17 outliers final: 9 residues processed: 130 average time/residue: 0.9200 time to fit residues: 126.7344 Evaluate side-chains 121 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 468 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 D residue 102 GLU Chi-restraints excluded: chain E residue 59 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: 0.5980 chunk 115 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN A 68 GLN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.089432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.065614 restraints weight = 26292.268| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.52 r_work: 0.2958 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14474 Z= 0.157 Angle : 0.582 6.918 20802 Z= 0.350 Chirality : 0.045 0.240 2371 Planarity : 0.004 0.033 1616 Dihedral : 28.917 173.584 4252 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.96 % Allowed : 11.41 % Favored : 86.63 % 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 are not related in a simple way. whole: 1.74 (0.27), residues: 944 helix: 2.19 (0.21), residues: 612 sheet: 3.13 (1.11), residues: 19 loop : -1.16 (0.30), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 431 TYR 0.009 0.001 TYR P 501 PHE 0.010 0.001 PHE P 500 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 0.00256 / 0.16 (14466) covalent geometry : angle 0.57832 / 0.35 (20793) hydrogen bonds : bond 0.07729 / 5.04 ( 759) hydrogen bonds : angle 3.18274 / 2.22 ( 1914) metal coordination : bond 0.00441 / 0.26 ( 8) metal coordination : angle 3.12452 / 1.61 ( 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 130 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.287 Fit side-chains REVERT: P 442 ASP cc_start: 0.8225 (m-30) cc_final: 0.7756 (t0) REVERT: P 486 TYR cc_start: 0.7685 (m-80) cc_final: 0.7413 (m-80) REVERT: B 23 ARG cc_start: 0.7479 (pmt-80) cc_final: 0.7189 (pmt-80) REVERT: D 102 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7804 (mt-10) outliers start: 16 outliers final: 6 residues processed: 126 average time/residue: 0.8943 time to fit residues: 119.4390 Evaluate side-chains 118 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 102 GLU 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=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: 9.9990 chunk 64 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN P 517 GLN A 68 GLN E 68 GLN F 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.088591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064770 restraints weight = 26521.523| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.50 r_work: 0.2941 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14474 Z= 0.192 Angle : 0.596 6.723 20802 Z= 0.354 Chirality : 0.046 0.241 2371 Planarity : 0.004 0.034 1616 Dihedral : 28.986 173.644 4252 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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: 1.71 (0.27), residues: 944 helix: 2.22 (0.21), residues: 612 sheet: 3.30 (1.10), residues: 19 loop : -1.30 (0.29), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 45 TYR 0.010 0.001 TYR P 501 PHE 0.014 0.001 PHE H 62 TRP 0.002 0.001 TRP P 488 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (14466) covalent geometry : angle 0.59253 / 0.35 (20793) hydrogen bonds : bond 0.08071 / 5.27 ( 759) hydrogen bonds : angle 3.05962 / 2.13 ( 1914) metal coordination : bond 0.00716 / 0.48 ( 8) metal coordination : angle 3.21266 / 1.70 ( 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 127 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.385 Fit side-chains REVERT: P 442 ASP cc_start: 0.8190 (m-30) cc_final: 0.7756 (t0) REVERT: P 486 TYR cc_start: 0.7751 (m-80) cc_final: 0.7524 (m-80) REVERT: B 23 ARG cc_start: 0.7324 (pmt-80) cc_final: 0.6983 (pmt-80) REVERT: B 24 ASP cc_start: 0.7731 (t0) cc_final: 0.7286 (t0) REVERT: F 53 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8056 (tt0) outliers start: 17 outliers final: 9 residues processed: 123 average time/residue: 0.8517 time to fit residues: 111.3253 Evaluate side-chains 120 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 A residue 109 LEU 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: 0.7980 chunk 54 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 73 optimal weight: 0.0060 chunk 99 optimal weight: 10.0000 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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 = 0.089520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.065755 restraints weight = 26106.130| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.52 r_work: 0.2904 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14474 Z= 0.151 Angle : 0.576 7.079 20802 Z= 0.344 Chirality : 0.045 0.239 2371 Planarity : 0.004 0.033 1616 Dihedral : 28.973 173.525 4252 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.47 % Allowed : 13.13 % Favored : 85.40 % 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 are not related in a simple way. whole: 1.84 (0.27), residues: 944 helix: 2.32 (0.21), residues: 612 sheet: 3.19 (1.09), residues: 19 loop : -1.23 (0.29), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 69 TYR 0.009 0.001 TYR P 501 PHE 0.009 0.001 PHE P 500 TRP 0.002 0.001 TRP P 488 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.15 (14466) covalent geometry : angle 0.57266 / 0.34 (20793) hydrogen bonds : bond 0.07341 / 4.79 ( 759) hydrogen bonds : angle 3.06997 / 2.13 ( 1914) metal coordination : bond 0.00380 / 0.21 ( 8) metal coordination : angle 3.11215 / 1.63 ( 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 126 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.387 Fit side-chains REVERT: P 442 ASP cc_start: 0.8150 (m-30) cc_final: 0.7706 (t0) REVERT: P 486 TYR cc_start: 0.7669 (m-80) cc_final: 0.7419 (m-80) REVERT: B 23 ARG cc_start: 0.7272 (pmt-80) cc_final: 0.6849 (pmt-80) REVERT: B 24 ASP cc_start: 0.7664 (t0) cc_final: 0.7199 (t0) REVERT: G 99 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8839 (mtp85) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 0.8818 time to fit residues: 113.8816 Evaluate side-chains 118 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 A residue 109 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 99 ARG 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: 5.9990 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 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: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN P 517 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 = 0.3509 r_free = 0.3509 target = 0.088193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.064343 restraints weight = 26382.488| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.53 r_work: 0.2927 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14474 Z= 0.198 Angle : 0.602 6.927 20802 Z= 0.356 Chirality : 0.047 0.241 2371 Planarity : 0.004 0.033 1616 Dihedral : 29.009 174.234 4252 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.09 % Allowed : 12.39 % Favored : 85.52 % 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: 1.76 (0.27), residues: 944 helix: 2.37 (0.21), residues: 604 sheet: 0.47 (0.99), residues: 31 loop : -1.29 (0.30), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 45 TYR 0.010 0.001 TYR P 501 PHE 0.015 0.002 PHE H 62 TRP 0.003 0.001 TRP P 384 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (14466) covalent geometry : angle 0.59881 / 0.36 (20793) hydrogen bonds : bond 0.08102 / 5.30 ( 759) hydrogen bonds : angle 3.03220 / 2.10 ( 1914) metal coordination : bond 0.00787 / 0.54 ( 8) metal coordination : angle 3.24471 / 1.73 ( 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 128 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.286 Fit side-chains REVERT: P 442 ASP cc_start: 0.8158 (m-30) cc_final: 0.7766 (t0) REVERT: B 23 ARG cc_start: 0.7442 (pmt-80) cc_final: 0.7042 (pmt-80) REVERT: B 24 ASP cc_start: 0.7808 (t0) cc_final: 0.7396 (OUTLIER) REVERT: G 99 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8865 (mtp85) outliers start: 17 outliers final: 10 residues processed: 123 average time/residue: 0.8841 time to fit residues: 115.4725 Evaluate side-chains 120 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 419 ILE 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 E residue 59 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 97 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 483 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.088340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.064578 restraints weight = 26225.173| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.51 r_work: 0.2941 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14474 Z= 0.186 Angle : 0.597 7.269 20802 Z= 0.354 Chirality : 0.046 0.241 2371 Planarity : 0.004 0.033 1616 Dihedral : 29.016 174.399 4252 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.72 % Allowed : 13.37 % Favored : 84.91 % 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: 1.76 (0.27), residues: 944 helix: 2.37 (0.21), residues: 604 sheet: 0.44 (0.98), residues: 31 loop : -1.30 (0.30), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 45 TYR 0.015 0.001 TYR P 486 PHE 0.013 0.001 PHE H 62 TRP 0.002 0.001 TRP P 384 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.19 (14466) covalent geometry : angle 0.59362 / 0.35 (20793) hydrogen bonds : bond 0.07962 / 5.20 ( 759) hydrogen bonds : angle 3.02598 / 2.09 ( 1914) metal coordination : bond 0.00688 / 0.47 ( 8) metal coordination : angle 3.25211 / 1.72 ( 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 125 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.320 Fit side-chains REVERT: P 442 ASP cc_start: 0.8149 (m-30) cc_final: 0.7750 (t0) REVERT: B 23 ARG cc_start: 0.7348 (pmt-80) cc_final: 0.7022 (pmt-80) REVERT: B 24 ASP cc_start: 0.7749 (t0) cc_final: 0.7368 (t0) REVERT: G 99 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8856 (mtp85) outliers start: 14 outliers final: 11 residues processed: 120 average time/residue: 0.8588 time to fit residues: 109.3041 Evaluate side-chains 122 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 419 ILE 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 G residue 99 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 106 optimal weight: 30.0000 chunk 74 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 24 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 483 ASN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.088741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.064931 restraints weight = 26396.115| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.54 r_work: 0.2943 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14474 Z= 0.156 Angle : 0.584 7.608 20802 Z= 0.348 Chirality : 0.045 0.239 2371 Planarity : 0.004 0.032 1616 Dihedral : 29.013 174.301 4252 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.60 % Allowed : 13.50 % Favored : 84.91 % 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: 1.96 (0.27), residues: 944 helix: 2.53 (0.21), residues: 592 sheet: 0.48 (0.98), residues: 31 loop : -1.06 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 352 TYR 0.013 0.001 TYR P 486 PHE 0.011 0.001 PHE H 62 TRP 0.003 0.001 TRP P 488 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.16 (14466) covalent geometry : angle 0.58042 / 0.35 (20793) hydrogen bonds : bond 0.07666 / 5.01 ( 759) hydrogen bonds : angle 3.03520 / 2.10 ( 1914) metal coordination : bond 0.00524 / 0.34 ( 8) metal coordination : angle 3.23160 / 1.71 ( 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 124 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.252 Fit side-chains REVERT: P 442 ASP cc_start: 0.8133 (m-30) cc_final: 0.7733 (t0) REVERT: B 23 ARG cc_start: 0.7336 (pmt-80) cc_final: 0.7003 (pmt-80) REVERT: B 24 ASP cc_start: 0.7723 (t0) cc_final: 0.7302 (t0) REVERT: D 102 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: G 99 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8864 (mtp85) outliers start: 13 outliers final: 9 residues processed: 120 average time/residue: 0.8585 time to fit residues: 109.0316 Evaluate side-chains 121 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 419 ILE 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 D residue 102 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 99 ARG 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: 0.6980 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 13 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.089242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065480 restraints weight = 26265.549| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.53 r_work: 0.2956 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14474 Z= 0.147 Angle : 0.579 9.192 20802 Z= 0.346 Chirality : 0.044 0.239 2371 Planarity : 0.004 0.032 1616 Dihedral : 29.002 174.272 4252 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.23 % Allowed : 13.99 % 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: 2.05 (0.27), residues: 944 helix: 2.59 (0.21), residues: 592 sheet: 0.52 (0.97), residues: 31 loop : -1.01 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 352 TYR 0.017 0.001 TYR P 486 PHE 0.009 0.001 PHE P 500 TRP 0.003 0.001 TRP P 488 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.15 (14466) covalent geometry : angle 0.57533 / 0.35 (20793) hydrogen bonds : bond 0.07279 / 4.76 ( 759) hydrogen bonds : angle 3.02447 / 2.09 ( 1914) metal coordination : bond 0.00395 / 0.23 ( 8) metal coordination : angle 3.16592 / 1.67 ( 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 122 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.332 Fit side-chains REVERT: P 442 ASP cc_start: 0.8100 (m-30) cc_final: 0.7709 (t0) REVERT: B 23 ARG cc_start: 0.7337 (pmt-80) cc_final: 0.6983 (pmt-80) REVERT: B 24 ASP cc_start: 0.7676 (t0) cc_final: 0.7192 (OUTLIER) REVERT: G 99 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8850 (mtp85) outliers start: 10 outliers final: 9 residues processed: 119 average time/residue: 0.8582 time to fit residues: 108.1216 Evaluate side-chains 120 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 G residue 99 ARG 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: 5.9990 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 483 ASN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.065339 restraints weight = 26523.083| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.54 r_work: 0.2951 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.2239 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= 0.172 Angle : 0.577 7.406 20802 Z= 0.343 Chirality : 0.045 0.243 2371 Planarity : 0.004 0.033 1616 Dihedral : 29.031 174.483 4252 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.10 % Allowed : 13.99 % Favored : 84.91 % 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: 2.04 (0.27), residues: 944 helix: 2.60 (0.21), residues: 592 sheet: 0.47 (0.95), residues: 31 loop : -1.04 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 352 TYR 0.010 0.001 TYR P 501 PHE 0.011 0.001 PHE H 62 TRP 0.004 0.001 TRP P 384 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (14466) covalent geometry : angle 0.57302 / 0.34 (20793) hydrogen bonds : bond 0.07378 / 4.82 ( 759) hydrogen bonds : angle 2.93630 / 2.03 ( 1914) metal coordination : bond 0.00576 / 0.38 ( 8) metal coordination : angle 3.12074 / 1.66 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4602.59 seconds wall clock time: 78 minutes 49.39 seconds (4729.39 seconds total)