Starting phenix.real_space_refine on Mon Apr 28 18:02:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbz_27318/04_2025/8dbz_27318.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbz_27318/04_2025/8dbz_27318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbz_27318/04_2025/8dbz_27318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbz_27318/04_2025/8dbz_27318.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbz_27318/04_2025/8dbz_27318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbz_27318/04_2025/8dbz_27318.cif" } resolution = 4.1 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4956 2.51 5 N 1409 2.21 5 O 1563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7960 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2241 Classifications: {'peptide': 291} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 273} Chain breaks: 3 Chain: "D" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "B" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 986 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "C" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 857 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "F" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 507 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 93} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 531 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 173 Chain: "H" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 507 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 93} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "I" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 531 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 173 Time building chain proxies: 4.85, per 1000 atoms: 0.61 Number of scatterers: 7960 At special positions: 0 Unit cell: (100.74, 129.94, 135.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1563 8.00 N 1409 7.00 C 4956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 93 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 29 sheets defined 9.0% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 69 through 74 removed outlier: 4.362A pdb=" N MET A 73 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.719A pdb=" N TYR A 120 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS A 124 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.813A pdb=" N MET A 156 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.863A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 removed outlier: 3.825A pdb=" N ASN B 30 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'F' and resid 41 through 45 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'G' and resid 14 through 19 Processing helix chain 'G' and resid 76 through 82 removed outlier: 3.867A pdb=" N HIS G 82 " --> pdb=" O ASP G 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 4.356A pdb=" N GLY H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 73 through 77' Processing helix chain 'I' and resid 14 through 19 Processing helix chain 'I' and resid 76 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.438A pdb=" N TYR A 24 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE A 173 " --> pdb=" O TYR A 24 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 26 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 165 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.535A pdb=" N VAL A 146 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR A 45 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 105 removed outlier: 3.852A pdb=" N LYS A 105 " --> pdb=" O GLN A 80 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN A 80 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.044A pdb=" N LEU A 259 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 250 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 297 through 301 removed outlier: 6.460A pdb=" N ALA A 318 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 316 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.959A pdb=" N THR D 122 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.347A pdb=" N LEU E 11 " --> pdb=" O GLU E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 21 through 22 removed outlier: 4.695A pdb=" N LEU E 21 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 74 " --> pdb=" O LEU E 21 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AB4, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.045A pdb=" N THR B 121 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 37 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.659A pdb=" N ILE C 21 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 68 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 50 through 53 removed outlier: 3.663A pdb=" N LEU C 52 " --> pdb=" O TRP C 40 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TRP C 40 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 7 through 11 removed outlier: 3.883A pdb=" N SER F 7 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE F 9 " --> pdb=" O LEU F 28 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 7 through 11 removed outlier: 3.883A pdb=" N SER F 7 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE F 9 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS F 27 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER F 67 " --> pdb=" O CYS F 27 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.398A pdb=" N THR F 38 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 86 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL F 85 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 94 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR F 92 " --> pdb=" O HIS F 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 56 through 57 removed outlier: 3.536A pdb=" N VAL F 56 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 9 through 11 removed outlier: 3.647A pdb=" N PHE G 9 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU G 28 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N SER G 70 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN G 30 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU G 68 " --> pdb=" O ASN G 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER G 55 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 22 through 24 removed outlier: 3.534A pdb=" N LEU G 74 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.597A pdb=" N CYS G 87 " --> pdb=" O LYS G 100 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS G 100 " --> pdb=" O CYS G 87 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL G 89 " --> pdb=" O VAL G 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 7 through 11 removed outlier: 3.653A pdb=" N LEU H 25 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL H 69 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS H 27 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER H 67 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TYR H 63 " --> pdb=" O ASP H 31 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS H 51 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 18 through 19 removed outlier: 3.653A pdb=" N LEU H 25 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL H 69 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS H 27 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER H 67 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TYR H 63 " --> pdb=" O ASP H 31 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 37 through 41 Processing sheet with id=AD1, first strand: chain 'I' and resid 7 through 11 removed outlier: 3.825A pdb=" N SER I 7 " --> pdb=" O ASN I 30 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN I 30 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE I 9 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL I 26 " --> pdb=" O PHE I 11 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER I 70 " --> pdb=" O CYS I 27 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU I 68 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN I 31 " --> pdb=" O TYR I 66 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TYR I 66 " --> pdb=" O ASN I 31 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER I 55 " --> pdb=" O SER I 69 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 38 through 43 removed outlier: 3.533A pdb=" N LYS I 38 " --> pdb=" O THR I 90 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL I 89 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL I 98 " --> pdb=" O VAL I 89 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2721 1.35 - 1.47: 1887 1.47 - 1.59: 3435 1.59 - 1.71: 0 1.71 - 1.83: 44 Bond restraints: 8087 Sorted by residual: bond pdb=" CA GLU E 17 " pdb=" CB GLU E 17 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.68e+00 bond pdb=" CA ASP E 83 " pdb=" CB ASP E 83 " ideal model delta sigma weight residual 1.524 1.543 -0.020 1.62e-02 3.81e+03 1.48e+00 bond pdb=" N PHE F 9 " pdb=" CA PHE F 9 " ideal model delta sigma weight residual 1.463 1.448 0.015 1.22e-02 6.72e+03 1.41e+00 bond pdb=" CG1 ILE D 52 " pdb=" CD1 ILE D 52 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.27e+00 bond pdb=" CB TRP B 36 " pdb=" CG TRP B 36 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.24e+00 ... (remaining 8082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 10647 1.69 - 3.38: 340 3.38 - 5.06: 43 5.06 - 6.75: 15 6.75 - 8.44: 5 Bond angle restraints: 11050 Sorted by residual: angle pdb=" N LEU C 52 " pdb=" CA LEU C 52 " pdb=" C LEU C 52 " ideal model delta sigma weight residual 114.39 108.42 5.97 1.45e+00 4.76e-01 1.69e+01 angle pdb=" C GLU E 69 " pdb=" CA GLU E 69 " pdb=" CB GLU E 69 " ideal model delta sigma weight residual 115.89 110.59 5.30 1.32e+00 5.74e-01 1.61e+01 angle pdb=" CA GLU E 17 " pdb=" CB GLU E 17 " pdb=" CG GLU E 17 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA GLY E 103 " pdb=" C GLY E 103 " pdb=" O GLY E 103 " ideal model delta sigma weight residual 122.23 120.00 2.23 6.90e-01 2.10e+00 1.04e+01 angle pdb=" CA ARG A 268 " pdb=" CB ARG A 268 " pdb=" CG ARG A 268 " ideal model delta sigma weight residual 114.10 120.34 -6.24 2.00e+00 2.50e-01 9.75e+00 ... (remaining 11045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 4390 16.38 - 32.75: 338 32.75 - 49.13: 59 49.13 - 65.50: 15 65.50 - 81.88: 8 Dihedral angle restraints: 4810 sinusoidal: 1411 harmonic: 3399 Sorted by residual: dihedral pdb=" CB CYS A 239 " pdb=" SG CYS A 239 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -139.98 53.98 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 132 " pdb=" CB CYS A 132 " ideal model delta sinusoidal sigma weight residual -86.00 -34.15 -51.85 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CA TYR E 92 " pdb=" C TYR E 92 " pdb=" N GLY E 93 " pdb=" CA GLY E 93 " ideal model delta harmonic sigma weight residual -180.00 -151.51 -28.49 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 4807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 904 0.039 - 0.077: 268 0.077 - 0.116: 124 0.116 - 0.155: 21 0.155 - 0.193: 5 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA PRO B 53 " pdb=" N PRO B 53 " pdb=" C PRO B 53 " pdb=" CB PRO B 53 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CA ILE B 52 " pdb=" N ILE B 52 " pdb=" C ILE B 52 " pdb=" CB ILE B 52 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CA ILE C 80 " pdb=" N ILE C 80 " pdb=" C ILE C 80 " pdb=" CB ILE C 80 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 1319 not shown) Planarity restraints: 1455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 72 " 0.010 2.00e-02 2.50e+03 1.86e-02 6.08e+00 pdb=" CG PHE E 72 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE E 72 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE E 72 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 72 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 72 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE E 72 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 261 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO A 262 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 80 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO E 81 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " -0.030 5.00e-02 4.00e+02 ... (remaining 1452 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 183 2.66 - 3.22: 7606 3.22 - 3.78: 11858 3.78 - 4.34: 15349 4.34 - 4.90: 24485 Nonbonded interactions: 59481 Sorted by model distance: nonbonded pdb=" OG SER E 22 " pdb=" OG1 THR E 73 " model vdw 2.101 3.040 nonbonded pdb=" ND2 ASN A 334 " pdb=" OE2 GLU A 338 " model vdw 2.108 3.120 nonbonded pdb=" O ARG A 333 " pdb=" NH1 ARG A 333 " model vdw 2.128 3.120 nonbonded pdb=" O SER A 263 " pdb=" NH2 ARG B 102 " model vdw 2.183 3.120 nonbonded pdb=" OH TYR A 248 " pdb=" O PRO A 360 " model vdw 2.216 3.040 ... (remaining 59476 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 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.020 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 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 0.044 8097 Z= 0.165 Angle : 0.737 8.438 11070 Z= 0.410 Chirality : 0.046 0.193 1322 Planarity : 0.005 0.060 1455 Dihedral : 12.606 81.876 2590 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % 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: -1.42 (0.25), residues: 1160 helix: -0.47 (0.69), residues: 55 sheet: -0.64 (0.26), residues: 421 loop : -1.17 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 117 HIS 0.003 0.001 HIS A 351 PHE 0.037 0.002 PHE E 72 TYR 0.036 0.002 TYR E 92 ARG 0.007 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.31179 ( 243) hydrogen bonds : angle 11.86299 ( 627) SS BOND : bond 0.00362 ( 10) SS BOND : angle 2.12005 ( 20) covalent geometry : bond 0.00338 ( 8087) covalent geometry : angle 0.73229 (11050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8133 (tpp) cc_final: 0.7327 (tpp) REVERT: A 363 TRP cc_start: 0.4346 (t60) cc_final: 0.3742 (t60) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2189 time to fit residues: 37.4916 Evaluate side-chains 97 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 30.0000 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 0.0670 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 overall best weight: 1.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 HIS D 65 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.195340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.166442 restraints weight = 13795.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.166131 restraints weight = 11548.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.167355 restraints weight = 10774.920| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8097 Z= 0.179 Angle : 0.675 8.752 11070 Z= 0.363 Chirality : 0.047 0.203 1322 Planarity : 0.005 0.072 1455 Dihedral : 5.899 68.048 1248 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 0.30 % Allowed : 6.84 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % 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: -1.36 (0.25), residues: 1160 helix: -0.33 (0.68), residues: 57 sheet: -0.59 (0.25), residues: 456 loop : -1.16 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 36 HIS 0.005 0.001 HIS A 351 PHE 0.023 0.002 PHE E 72 TYR 0.030 0.002 TYR C 41 ARG 0.010 0.001 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.04891 ( 243) hydrogen bonds : angle 7.67256 ( 627) SS BOND : bond 0.00278 ( 10) SS BOND : angle 1.34447 ( 20) covalent geometry : bond 0.00404 ( 8087) covalent geometry : angle 0.67359 (11050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 THR cc_start: 0.6579 (p) cc_final: 0.5944 (p) REVERT: A 231 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6109 (tt0) REVERT: A 276 MET cc_start: 0.7539 (tpp) cc_final: 0.7063 (tpp) REVERT: A 308 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7243 (m) REVERT: A 356 LYS cc_start: 0.7516 (mttm) cc_final: 0.7082 (ttmm) REVERT: D 46 GLU cc_start: 0.5052 (pt0) cc_final: 0.4215 (mm-30) REVERT: D 106 TYR cc_start: 0.5110 (t80) cc_final: 0.2773 (t80) REVERT: B 29 TYR cc_start: 0.2548 (m-80) cc_final: 0.1992 (m-80) REVERT: B 80 TYR cc_start: 0.7996 (m-80) cc_final: 0.7730 (m-80) REVERT: B 98 ARG cc_start: 0.7378 (ptm-80) cc_final: 0.7142 (ptm160) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.1888 time to fit residues: 33.9524 Evaluate side-chains 99 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 98 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 40.0000 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.197909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.167876 restraints weight = 14212.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.169674 restraints weight = 11475.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.170205 restraints weight = 9765.524| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8097 Z= 0.132 Angle : 0.624 8.302 11070 Z= 0.331 Chirality : 0.046 0.183 1322 Planarity : 0.005 0.057 1455 Dihedral : 5.548 62.659 1248 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % 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: -1.27 (0.26), residues: 1160 helix: -0.03 (0.69), residues: 57 sheet: -0.52 (0.25), residues: 452 loop : -1.13 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 36 HIS 0.003 0.001 HIS B 104 PHE 0.014 0.002 PHE E 72 TYR 0.025 0.002 TYR C 41 ARG 0.006 0.001 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 243) hydrogen bonds : angle 6.73118 ( 627) SS BOND : bond 0.00254 ( 10) SS BOND : angle 1.78692 ( 20) covalent geometry : bond 0.00296 ( 8087) covalent geometry : angle 0.61987 (11050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.7818 (tmm) cc_final: 0.7561 (tpp) REVERT: A 231 GLU cc_start: 0.6742 (tm-30) cc_final: 0.5893 (tp30) REVERT: A 276 MET cc_start: 0.7331 (tpp) cc_final: 0.6811 (tpp) REVERT: A 356 LYS cc_start: 0.7381 (mttm) cc_final: 0.7133 (ttmm) REVERT: D 106 TYR cc_start: 0.4911 (t80) cc_final: 0.2376 (t80) REVERT: B 51 ILE cc_start: 0.7842 (tp) cc_final: 0.7615 (tp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1999 time to fit residues: 36.6640 Evaluate side-chains 96 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS D 102 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.192444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.159806 restraints weight = 14740.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.161587 restraints weight = 11785.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.162815 restraints weight = 9976.733| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8097 Z= 0.211 Angle : 0.702 8.665 11070 Z= 0.372 Chirality : 0.048 0.215 1322 Planarity : 0.005 0.070 1455 Dihedral : 5.961 65.238 1248 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.33 % Favored : 92.59 % Rotamer: Outliers : 0.30 % Allowed : 6.99 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.65 (0.25), residues: 1160 helix: -0.06 (0.69), residues: 59 sheet: -0.84 (0.25), residues: 458 loop : -1.37 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP E 36 HIS 0.003 0.001 HIS A 351 PHE 0.021 0.003 PHE E 72 TYR 0.033 0.003 TYR E 92 ARG 0.005 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 243) hydrogen bonds : angle 6.71321 ( 627) SS BOND : bond 0.00344 ( 10) SS BOND : angle 1.65664 ( 20) covalent geometry : bond 0.00486 ( 8087) covalent geometry : angle 0.69902 (11050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.7751 (m) cc_final: 0.7326 (p) REVERT: A 145 THR cc_start: 0.6831 (p) cc_final: 0.6617 (p) REVERT: A 231 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6072 (tp30) REVERT: A 266 ASP cc_start: 0.6563 (t0) cc_final: 0.6146 (t0) REVERT: A 276 MET cc_start: 0.7789 (tpp) cc_final: 0.7496 (tpp) REVERT: A 308 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7284 (m) REVERT: D 106 TYR cc_start: 0.5256 (t80) cc_final: 0.2988 (t80) REVERT: B 105 TYR cc_start: 0.7148 (t80) cc_final: 0.5934 (t80) REVERT: B 106 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5634 (m-10) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.1746 time to fit residues: 30.8249 Evaluate side-chains 103 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5336 > 50: distance: 13 - 16: 7.562 distance: 17 - 18: 4.047 distance: 17 - 20: 8.571 distance: 18 - 19: 21.498 distance: 18 - 21: 5.636 distance: 21 - 22: 8.570 distance: 21 - 89: 12.695 distance: 22 - 23: 22.373 distance: 22 - 25: 23.982 distance: 23 - 24: 17.738 distance: 23 - 26: 6.690 distance: 26 - 27: 11.183 distance: 27 - 28: 8.020 distance: 27 - 30: 9.240 distance: 28 - 29: 4.544 distance: 28 - 31: 6.742 distance: 31 - 32: 4.078 distance: 32 - 33: 8.491 distance: 32 - 35: 7.030 distance: 33 - 34: 18.817 distance: 33 - 36: 18.087 distance: 36 - 37: 3.852 distance: 37 - 38: 10.570 distance: 37 - 40: 13.707 distance: 38 - 39: 17.079 distance: 38 - 41: 5.997 distance: 39 - 56: 16.150 distance: 41 - 42: 9.798 distance: 42 - 43: 4.646 distance: 42 - 45: 6.279 distance: 43 - 44: 7.718 distance: 43 - 46: 6.304 distance: 44 - 61: 16.776 distance: 46 - 47: 4.326 distance: 47 - 48: 3.893 distance: 48 - 49: 9.775 distance: 48 - 51: 4.055 distance: 53 - 54: 6.587 distance: 53 - 56: 3.317 distance: 56 - 57: 4.673 distance: 57 - 58: 4.171 distance: 57 - 60: 5.954 distance: 58 - 59: 7.060 distance: 58 - 61: 5.651 distance: 61 - 62: 4.743 distance: 62 - 63: 5.170 distance: 62 - 65: 10.041 distance: 63 - 66: 4.561