Starting phenix.real_space_refine on Thu Jul 31 09:37:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cww_27030/07_2025/8cww_27030.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cww_27030/07_2025/8cww_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_2025/8cww_27030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cww_27030/07_2025/8cww_27030.map" model { file = "/net/cci-nas-00/data/ceres_data/8cww_27030/07_2025/8cww_27030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cww_27030/07_2025/8cww_27030.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.034 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.22, per 1000 atoms: 0.68 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: 3.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 6.10 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: 7.72 Time building geometry restraints manager: 4.13 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 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" C3' DC I 30 " pdb=" C2' DC I 30 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 9.97e-01 bond pdb=" C4' DC I 30 " pdb=" O4' DC I 30 " ideal model delta sigma weight residual 1.450 1.434 0.016 2.00e-02 2.50e+03 6.76e-01 bond pdb=" C3' DC I 70 " pdb=" C2' DC I 70 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.00e-02 2.50e+03 6.68e-01 bond pdb=" O4' DG I 63 " pdb=" C1' DG I 63 " ideal model delta sigma weight residual 1.414 1.398 0.016 2.00e-02 2.50e+03 6.62e-01 ... (remaining 14461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 19614 0.94 - 1.88: 931 1.88 - 2.83: 225 2.83 - 3.77: 17 3.77 - 4.71: 6 Bond angle restraints: 20793 Sorted by residual: angle pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sigma weight residual 120.20 123.45 -3.25 1.50e+00 4.44e-01 4.71e+00 angle pdb=" N LEU P 530 " pdb=" CA LEU P 530 " pdb=" C LEU P 530 " ideal model delta sigma weight residual 111.36 113.57 -2.21 1.09e+00 8.42e-01 4.11e+00 angle pdb=" C3' DC J -62 " pdb=" C2' DC J -62 " pdb=" C1' DC J -62 " ideal model delta sigma weight residual 101.60 104.44 -2.84 1.50e+00 4.44e-01 3.60e+00 angle pdb=" C3' DC I -40 " pdb=" C2' DC I -40 " pdb=" C1' DC I -40 " ideal model delta sigma weight residual 101.60 104.36 -2.76 1.50e+00 4.44e-01 3.39e+00 angle pdb=" C3' DC I 70 " pdb=" C2' DC I 70 " pdb=" C1' DC I 70 " ideal model delta sigma weight residual 101.60 104.23 -2.63 1.50e+00 4.44e-01 3.07e+00 ... (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 - 0.024: 1507 0.024 - 0.049: 584 0.049 - 0.073: 200 0.073 - 0.098: 35 0.098 - 0.122: 45 Chirality restraints: 2371 Sorted by residual: chirality pdb=" CA ILE P 473 " pdb=" N ILE P 473 " pdb=" C ILE P 473 " pdb=" CB ILE P 473 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-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: 48.910 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: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.120 Set scattering table: 0.210 Process input model: 42.390 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.100 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: 0.020 Load rotamer database and sin/cos tables:36.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.003 0.041 14474 Z= 0.139 Angle : 0.485 6.812 20802 Z= 0.299 Chirality : 0.032 0.122 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (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 TRP 0.002 0.000 TRP P 384 HIS 0.002 0.000 HIS P 356 PHE 0.011 0.001 PHE P 500 TYR 0.008 0.001 TYR P 501 ARG 0.002 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.25127 ( 759) hydrogen bonds : angle 4.41700 ( 1914) metal coordination : bond 0.00383 ( 8) metal coordination : angle 3.35719 ( 9) covalent geometry : bond 0.00297 (14466) covalent geometry : angle 0.47990 (20793) *********************** 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 : 1.216 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: 2.0415 time to fit residues: 389.6748 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 : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3526 r_free = 0.3526 target = 0.089135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065352 restraints weight = 26068.292| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.51 r_work: 0.2894 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14474 Z= 0.214 Angle : 0.566 7.334 20802 Z= 0.342 Chirality : 0.036 0.123 2371 Planarity : 0.004 0.038 1616 Dihedral : 28.431 170.516 4252 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.96 % Allowed : 9.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.27), residues: 944 helix: 2.08 (0.21), residues: 612 sheet: 3.72 (1.13), residues: 19 loop : -1.00 (0.30), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 488 HIS 0.003 0.001 HIS E 39 PHE 0.012 0.001 PHE H 62 TYR 0.010 0.001 TYR P 501 ARG 0.003 0.000 ARG P 509 Details of bonding type rmsd hydrogen bonds : bond 0.07795 ( 759) hydrogen bonds : angle 3.05616 ( 1914) metal coordination : bond 0.00606 ( 8) metal coordination : angle 3.27211 ( 9) covalent geometry : bond 0.00472 (14466) covalent geometry : angle 0.56153 (20793) *********************** 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 142 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.369 Fit side-chains REVERT: P 486 TYR cc_start: 0.7817 (m-80) cc_final: 0.7275 (m-80) REVERT: A 79 LYS cc_start: 0.8917 (tttt) cc_final: 0.8698 (tttm) REVERT: B 23 ARG cc_start: 0.7519 (pmt-80) cc_final: 0.7315 (pmt-80) outliers start: 16 outliers final: 6 residues processed: 139 average time/residue: 2.0998 time to fit residues: 310.9075 Evaluate side-chains 124 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 G residue 113 SER 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 5 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 73 optimal weight: 0.0770 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3517 r_free = 0.3517 target = 0.088716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.064912 restraints weight = 26265.847| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.51 r_work: 0.2941 rms_B_bonded: 2.49 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: 0.8900 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14474 Z= 0.210 Angle : 0.551 7.307 20802 Z= 0.334 Chirality : 0.036 0.128 2371 Planarity : 0.004 0.033 1616 Dihedral : 28.449 171.998 4252 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.96 % Allowed : 11.04 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.27), residues: 944 helix: 2.28 (0.21), residues: 604 sheet: 0.72 (1.02), residues: 31 loop : -1.08 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 384 HIS 0.003 0.001 HIS E 39 PHE 0.012 0.001 PHE H 62 TYR 0.010 0.001 TYR P 501 ARG 0.003 0.000 ARG P 509 Details of bonding type rmsd hydrogen bonds : bond 0.07565 ( 759) hydrogen bonds : angle 2.97180 ( 1914) metal coordination : bond 0.00593 ( 8) metal coordination : angle 3.38765 ( 9) covalent geometry : bond 0.00465 (14466) covalent geometry : angle 0.54666 (20793) *********************** 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 136 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: P 431 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.8396 (mtp85) REVERT: P 442 ASP cc_start: 0.8106 (m-30) cc_final: 0.7581 (t0) REVERT: P 486 TYR cc_start: 0.7662 (m-80) cc_final: 0.7230 (m-80) REVERT: B 23 ARG cc_start: 0.7522 (pmt-80) cc_final: 0.7273 (pmt-80) REVERT: B 24 ASP cc_start: 0.8220 (t0) cc_final: 0.7865 (t0) REVERT: H 68 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8359 (tm-30) outliers start: 16 outliers final: 8 residues processed: 132 average time/residue: 2.1142 time to fit residues: 295.9705 Evaluate side-chains 122 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3525 r_free = 0.3525 target = 0.089147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.065411 restraints weight = 25993.028| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.51 r_work: 0.2954 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14474 Z= 0.191 Angle : 0.535 6.993 20802 Z= 0.326 Chirality : 0.035 0.123 2371 Planarity : 0.004 0.033 1616 Dihedral : 28.430 172.208 4252 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.27), residues: 944 helix: 2.36 (0.21), residues: 606 sheet: 0.60 (0.99), residues: 31 loop : -1.05 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 488 HIS 0.003 0.001 HIS E 39 PHE 0.011 0.001 PHE D 67 TYR 0.009 0.001 TYR P 501 ARG 0.003 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.07120 ( 759) hydrogen bonds : angle 2.91225 ( 1914) metal coordination : bond 0.00558 ( 8) metal coordination : angle 3.26890 ( 9) covalent geometry : bond 0.00414 (14466) covalent geometry : angle 0.53068 (20793) *********************** 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 129 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: P 431 ARG cc_start: 0.8669 (mtt-85) cc_final: 0.8428 (mtp85) REVERT: P 442 ASP cc_start: 0.8080 (m-30) cc_final: 0.7749 (t0) REVERT: P 521 ASN cc_start: 0.8737 (m-40) cc_final: 0.8522 (m-40) REVERT: B 23 ARG cc_start: 0.7551 (pmt-80) cc_final: 0.7314 (pmt-80) REVERT: B 24 ASP cc_start: 0.8166 (t0) cc_final: 0.7878 (t0) REVERT: G 99 ARG cc_start: 0.9064 (mmm-85) cc_final: 0.8840 (mtp85) REVERT: H 68 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8338 (tm-30) outliers start: 16 outliers final: 9 residues processed: 126 average time/residue: 2.0953 time to fit residues: 280.2878 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 : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 120 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.089400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065694 restraints weight = 26212.703| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.51 r_work: 0.2959 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: 0.8887 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14474 Z= 0.181 Angle : 0.526 6.788 20802 Z= 0.321 Chirality : 0.034 0.123 2371 Planarity : 0.004 0.032 1616 Dihedral : 28.424 172.217 4252 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.96 % Allowed : 12.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.27), residues: 944 helix: 2.43 (0.21), residues: 606 sheet: 0.55 (0.98), residues: 31 loop : -1.04 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 488 HIS 0.003 0.001 HIS E 39 PHE 0.010 0.001 PHE D 67 TYR 0.015 0.001 TYR P 486 ARG 0.002 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.06902 ( 759) hydrogen bonds : angle 2.88752 ( 1914) metal coordination : bond 0.00521 ( 8) metal coordination : angle 3.15182 ( 9) covalent geometry : bond 0.00388 (14466) covalent geometry : angle 0.52216 (20793) *********************** 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 128 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: P 431 ARG cc_start: 0.8671 (mtt-85) cc_final: 0.8451 (mtp85) REVERT: P 442 ASP cc_start: 0.8029 (m-30) cc_final: 0.7701 (t0) REVERT: B 24 ASP cc_start: 0.8145 (t0) cc_final: 0.7879 (t0) REVERT: E 59 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: G 99 ARG cc_start: 0.9061 (mmm-85) cc_final: 0.8848 (mtp85) REVERT: H 68 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8339 (tm-30) outliers start: 16 outliers final: 10 residues processed: 125 average time/residue: 1.8294 time to fit residues: 243.1750 Evaluate side-chains 122 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 419 ILE 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 D residue 120 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 0.0060 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3537 r_free = 0.3537 target = 0.089664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.065981 restraints weight = 26708.962| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.53 r_work: 0.2968 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 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 : 0.003 0.040 14474 Z= 0.161 Angle : 0.519 6.574 20802 Z= 0.318 Chirality : 0.034 0.123 2371 Planarity : 0.004 0.047 1616 Dihedral : 28.419 172.279 4252 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.60 % Allowed : 12.76 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.27), residues: 944 helix: 2.48 (0.21), residues: 606 sheet: 0.56 (0.98), residues: 31 loop : -1.00 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP P 488 HIS 0.002 0.001 HIS H 79 PHE 0.009 0.001 PHE D 67 TYR 0.009 0.001 TYR P 501 ARG 0.003 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.06534 ( 759) hydrogen bonds : angle 2.85828 ( 1914) metal coordination : bond 0.00407 ( 8) metal coordination : angle 3.07046 ( 9) covalent geometry : bond 0.00330 (14466) covalent geometry : angle 0.51540 (20793) *********************** 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 123 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.008 Fit side-chains REVERT: P 431 ARG cc_start: 0.8674 (mtt-85) cc_final: 0.8465 (mtp85) REVERT: P 442 ASP cc_start: 0.7999 (m-30) cc_final: 0.7710 (t0) REVERT: E 59 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: G 99 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8854 (mtp85) outliers start: 13 outliers final: 7 residues processed: 121 average time/residue: 1.8319 time to fit residues: 235.9511 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 : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 419 ILE 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 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 3 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 483 ASN ** P 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.085435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.061240 restraints weight = 26159.252| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.56 r_work: 0.2784 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 14474 Z= 0.352 Angle : 0.656 7.583 20802 Z= 0.392 Chirality : 0.043 0.149 2371 Planarity : 0.005 0.035 1616 Dihedral : 28.559 173.339 4252 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.45 % Allowed : 13.01 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.27), residues: 944 helix: 2.20 (0.21), residues: 594 sheet: 0.40 (0.98), residues: 31 loop : -1.24 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP P 384 HIS 0.007 0.001 HIS E 39 PHE 0.018 0.002 PHE H 62 TYR 0.014 0.002 TYR H 34 ARG 0.006 0.001 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.09877 ( 759) hydrogen bonds : angle 3.22381 ( 1914) metal coordination : bond 0.01392 ( 8) metal coordination : angle 3.82793 ( 9) covalent geometry : bond 0.00817 (14466) covalent geometry : angle 0.65094 (20793) *********************** 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: 20 poor density : 110 time to evaluate : 1.111 Fit side-chains REVERT: P 442 ASP cc_start: 0.8251 (m-30) cc_final: 0.7850 (t0) REVERT: B 23 ARG cc_start: 0.7347 (pmt-80) cc_final: 0.7110 (pmt-80) REVERT: B 24 ASP cc_start: 0.8077 (t0) cc_final: 0.7819 (t0) REVERT: G 99 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8894 (mtp85) REVERT: H 65 ASP cc_start: 0.9302 (t0) cc_final: 0.8946 (t0) outliers start: 20 outliers final: 14 residues processed: 126 average time/residue: 1.9762 time to fit residues: 264.8535 Evaluate side-chains 124 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 380 LEU Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 472 VAL Chi-restraints excluded: chain P residue 478 LYS Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 523 ARG Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 99 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 483 ASN P 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065430 restraints weight = 26594.472| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.55 r_work: 0.2952 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14474 Z= 0.173 Angle : 0.556 6.737 20802 Z= 0.338 Chirality : 0.036 0.152 2371 Planarity : 0.004 0.032 1616 Dihedral : 28.400 174.801 4252 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.35 % Allowed : 13.62 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.27), residues: 944 helix: 2.53 (0.21), residues: 594 sheet: 0.50 (0.99), residues: 31 loop : -1.02 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 384 HIS 0.003 0.001 HIS H 79 PHE 0.010 0.001 PHE P 500 TYR 0.018 0.001 TYR P 486 ARG 0.004 0.000 ARG P 352 Details of bonding type rmsd hydrogen bonds : bond 0.06817 ( 759) hydrogen bonds : angle 2.86501 ( 1914) metal coordination : bond 0.00513 ( 8) metal coordination : angle 3.11943 ( 9) covalent geometry : bond 0.00352 (14466) covalent geometry : angle 0.55266 (20793) *********************** 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 120 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.940 Fit side-chains REVERT: P 442 ASP cc_start: 0.8066 (m-30) cc_final: 0.7718 (t0) REVERT: A 79 LYS cc_start: 0.9078 (tttm) cc_final: 0.8877 (tttp) REVERT: B 23 ARG cc_start: 0.7323 (pmt-80) cc_final: 0.7122 (pmt-80) REVERT: B 24 ASP cc_start: 0.8061 (t0) cc_final: 0.7802 (t0) outliers start: 11 outliers final: 5 residues processed: 118 average time/residue: 2.5386 time to fit residues: 317.0182 Evaluate side-chains 113 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 472 VAL Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 523 ARG Chi-restraints excluded: chain A residue 94 GLU 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 11 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3468 r_free = 0.3468 target = 0.086186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.062272 restraints weight = 26106.221| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.51 r_work: 0.2880 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 14474 Z= 0.333 Angle : 0.641 7.723 20802 Z= 0.383 Chirality : 0.042 0.148 2371 Planarity : 0.005 0.033 1616 Dihedral : 28.552 173.404 4252 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.23 % Allowed : 14.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.27), residues: 944 helix: 2.30 (0.21), residues: 594 sheet: 0.38 (0.99), residues: 31 loop : -1.29 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 384 HIS 0.006 0.001 HIS E 39 PHE 0.033 0.002 PHE P 418 TYR 0.014 0.002 TYR H 34 ARG 0.005 0.001 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.09330 ( 759) hydrogen bonds : angle 3.12369 ( 1914) metal coordination : bond 0.01255 ( 8) metal coordination : angle 3.72860 ( 9) covalent geometry : bond 0.00770 (14466) covalent geometry : angle 0.63681 (20793) *********************** 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 117 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.163 Fit side-chains REVERT: P 442 ASP cc_start: 0.8179 (m-30) cc_final: 0.7848 (t0) REVERT: B 23 ARG cc_start: 0.7403 (pmt-80) cc_final: 0.7178 (pmt-80) REVERT: B 24 ASP cc_start: 0.8105 (t0) cc_final: 0.7858 (t0) REVERT: H 65 ASP cc_start: 0.9298 (t0) cc_final: 0.8968 (t0) outliers start: 10 outliers final: 7 residues processed: 116 average time/residue: 2.1976 time to fit residues: 271.1612 Evaluate side-chains 113 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 472 VAL Chi-restraints excluded: chain P residue 478 LYS Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 523 ARG Chi-restraints excluded: chain A residue 94 GLU 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 67 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.087926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064216 restraints weight = 26271.089| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.52 r_work: 0.2931 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14474 Z= 0.175 Angle : 0.580 7.375 20802 Z= 0.352 Chirality : 0.037 0.143 2371 Planarity : 0.004 0.034 1616 Dihedral : 28.513 173.890 4252 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.74 % Allowed : 14.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.27), residues: 944 helix: 2.47 (0.21), residues: 594 sheet: 0.41 (0.98), residues: 31 loop : -1.19 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 384 HIS 0.003 0.001 HIS D 46 PHE 0.031 0.001 PHE P 418 TYR 0.024 0.001 TYR P 486 ARG 0.004 0.001 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.07290 ( 759) hydrogen bonds : angle 3.07542 ( 1914) metal coordination : bond 0.00395 ( 8) metal coordination : angle 3.41264 ( 9) covalent geometry : bond 0.00349 (14466) covalent geometry : angle 0.57554 (20793) ********************** 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: 6 poor density : 111 time to evaluate : 1.151 Fit side-chains REVERT: P 442 ASP cc_start: 0.8097 (m-30) cc_final: 0.7745 (t0) REVERT: B 24 ASP cc_start: 0.7983 (t0) cc_final: 0.7716 (t0) outliers start: 6 outliers final: 6 residues processed: 117 average time/residue: 1.9887 time to fit residues: 246.5589 Evaluate side-chains 115 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 472 VAL Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 523 ARG Chi-restraints excluded: chain A residue 94 GLU 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 19 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 517 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.088119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.064392 restraints weight = 26556.246| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.54 r_work: 0.2930 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14474 Z= 0.180 Angle : 0.564 7.629 20802 Z= 0.342 Chirality : 0.035 0.143 2371 Planarity : 0.004 0.032 1616 Dihedral : 28.476 174.252 4252 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.10 % Allowed : 14.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.27), residues: 944 helix: 2.56 (0.21), residues: 594 sheet: 0.40 (0.98), residues: 31 loop : -1.13 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 384 HIS 0.003 0.001 HIS E 39 PHE 0.029 0.001 PHE P 418 TYR 0.010 0.001 TYR P 501 ARG 0.008 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.07221 ( 759) hydrogen bonds : angle 2.93484 ( 1914) metal coordination : bond 0.00611 ( 8) metal coordination : angle 3.31731 ( 9) covalent geometry : bond 0.00381 (14466) covalent geometry : angle 0.56028 (20793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10583.63 seconds wall clock time: 186 minutes 40.68 seconds (11200.68 seconds total)