Starting phenix.real_space_refine on Tue Mar 3 18:13:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbz_27318/03_2026/8dbz_27318.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbz_27318/03_2026/8dbz_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dbz_27318/03_2026/8dbz_27318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbz_27318/03_2026/8dbz_27318.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbz_27318/03_2026/8dbz_27318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbz_27318/03_2026/8dbz_27318.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'PHE:plan': 3, 'ASP:plan': 2, 'TYR:plan': 3, 'GLU:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'GLN:plan1': 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: {'ARG:plan': 4, 'PHE:plan': 4, 'ASP:plan': 5, 'GLU:plan': 7, 'GLN:plan1': 6, 'ASN:plan1': 5, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2} 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: {'PHE:plan': 3, 'ASP:plan': 2, 'TYR:plan': 3, 'GLU:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'GLN:plan1': 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: {'ARG:plan': 4, 'PHE:plan': 4, 'ASP:plan': 5, 'GLU:plan': 7, 'GLN:plan1': 6, 'ASN:plan1': 5, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 173 Time building chain proxies: 1.80, per 1000 atoms: 0.23 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: 0.62 Conformation dependent library (CDL) restraints added in 257.2 milliseconds 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: 0.32 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: 1.18 Time building geometry restraints manager: 0.81 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.020 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (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 ARG 0.007 0.001 ARG B 98 TYR 0.036 0.002 TYR E 92 PHE 0.037 0.002 PHE E 72 TRP 0.022 0.003 TRP B 117 HIS 0.003 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8087) covalent geometry : angle 0.73229 (11050) SS BOND : bond 0.00362 ( 10) SS BOND : angle 2.12005 ( 20) hydrogen bonds : bond 0.31179 ( 243) hydrogen bonds : angle 11.86299 ( 627) *********************** 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 : 0.255 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: 0.7325 (tpp) REVERT: A 356 LYS cc_start: 0.7609 (mttm) cc_final: 0.7349 (ttmm) REVERT: A 363 TRP cc_start: 0.4347 (t60) cc_final: 0.3741 (t60) REVERT: B 51 ILE cc_start: 0.8022 (tp) cc_final: 0.7806 (tp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0965 time to fit residues: 16.5900 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 : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.0870 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4537 r_free = 0.4537 target = 0.198352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.165380 restraints weight = 14755.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.167256 restraints weight = 11503.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.169060 restraints weight = 9723.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.170011 restraints weight = 8510.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.171326 restraints weight = 7789.872| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8097 Z= 0.151 Angle : 0.644 8.381 11070 Z= 0.345 Chirality : 0.046 0.193 1322 Planarity : 0.005 0.069 1455 Dihedral : 5.775 66.485 1248 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 0.30 % Allowed : 5.78 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.26), residues: 1160 helix: -0.29 (0.67), residues: 57 sheet: -0.51 (0.25), residues: 456 loop : -1.08 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 333 TYR 0.029 0.002 TYR C 41 PHE 0.023 0.002 PHE E 72 TRP 0.021 0.002 TRP E 36 HIS 0.004 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8087) covalent geometry : angle 0.64185 (11050) SS BOND : bond 0.00225 ( 10) SS BOND : angle 1.31133 ( 20) hydrogen bonds : bond 0.04671 ( 243) hydrogen bonds : angle 7.57542 ( 627) *********************** 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 131 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 THR cc_start: 0.6455 (p) cc_final: 0.5711 (p) REVERT: A 231 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6074 (tt0) REVERT: A 276 MET cc_start: 0.7380 (tpp) cc_final: 0.6911 (tpp) REVERT: A 308 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.7114 (m) REVERT: A 356 LYS cc_start: 0.7463 (mttm) cc_final: 0.7039 (ttmm) REVERT: D 46 GLU cc_start: 0.4970 (pt0) cc_final: 0.4086 (mm-30) outliers start: 2 outliers final: 0 residues processed: 131 average time/residue: 0.0718 time to fit residues: 13.2391 Evaluate side-chains 104 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.0060 chunk 105 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 overall best weight: 2.5802 ------------------------------------------------------------------------------- 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** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 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 = 0.4474 r_free = 0.4474 target = 0.192780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.160629 restraints weight = 14941.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.162292 restraints weight = 12350.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.163093 restraints weight = 10713.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.163986 restraints weight = 9744.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.164849 restraints weight = 9095.362| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8097 Z= 0.213 Angle : 0.714 8.645 11070 Z= 0.378 Chirality : 0.048 0.216 1322 Planarity : 0.005 0.056 1455 Dihedral : 6.018 62.232 1248 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.33 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.25), residues: 1160 helix: -0.19 (0.71), residues: 57 sheet: -0.88 (0.25), residues: 444 loop : -1.35 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 333 TYR 0.028 0.003 TYR D 111 PHE 0.019 0.002 PHE E 72 TRP 0.037 0.004 TRP B 36 HIS 0.004 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 8087) covalent geometry : angle 0.71002 (11050) SS BOND : bond 0.00549 ( 10) SS BOND : angle 1.81158 ( 20) hydrogen bonds : bond 0.04399 ( 243) hydrogen bonds : angle 7.09615 ( 627) *********************** 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 124 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6046 (tp30) REVERT: A 276 MET cc_start: 0.7646 (tpp) cc_final: 0.7404 (tpp) REVERT: A 356 LYS cc_start: 0.7556 (mttm) cc_final: 0.6927 (ttmm) REVERT: D 106 TYR cc_start: 0.5534 (t80) cc_final: 0.3182 (t80) REVERT: D 113 GLU cc_start: 0.8162 (pm20) cc_final: 0.7404 (tp30) REVERT: B 39 GLN cc_start: 0.6298 (tp40) cc_final: 0.6014 (tt0) REVERT: B 112 TYR cc_start: 0.7690 (p90) cc_final: 0.7429 (p90) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0773 time to fit residues: 13.0738 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 : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 78 optimal weight: 0.4980 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 103 optimal weight: 50.0000 chunk 34 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 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 = 0.4555 r_free = 0.4555 target = 0.199341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.169361 restraints weight = 14720.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.169988 restraints weight = 11905.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.169930 restraints weight = 10993.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.170237 restraints weight = 11183.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.170623 restraints weight = 10215.043| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.2460 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= 0.135 Angle : 0.628 8.984 11070 Z= 0.331 Chirality : 0.046 0.181 1322 Planarity : 0.005 0.066 1455 Dihedral : 5.645 62.893 1248 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 0.15 % Allowed : 4.41 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.25), residues: 1160 helix: 0.10 (0.71), residues: 57 sheet: -0.60 (0.25), residues: 436 loop : -1.25 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.025 0.002 TYR C 41 PHE 0.017 0.002 PHE D 112 TRP 0.030 0.003 TRP E 36 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8087) covalent geometry : angle 0.62545 (11050) SS BOND : bond 0.00267 ( 10) SS BOND : angle 1.53156 ( 20) hydrogen bonds : bond 0.03368 ( 243) hydrogen bonds : angle 6.47771 ( 627) *********************** 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 135 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.6955 (tm-30) cc_final: 0.5954 (tt0) REVERT: A 276 MET cc_start: 0.7353 (tpp) cc_final: 0.6861 (tpp) REVERT: A 356 LYS cc_start: 0.7438 (mttm) cc_final: 0.7143 (ttmm) REVERT: D 106 TYR cc_start: 0.4912 (t80) cc_final: 0.2305 (t80) REVERT: B 105 TYR cc_start: 0.6824 (t80) cc_final: 0.5611 (t80) REVERT: B 106 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.5230 (m-10) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.0737 time to fit residues: 13.8729 Evaluate side-chains 109 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.200558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.167279 restraints weight = 14595.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.169667 restraints weight = 11160.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.171074 restraints weight = 9193.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.172758 restraints weight = 8062.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.173504 restraints weight = 7199.871| |-----------------------------------------------------------------------------| r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8097 Z= 0.125 Angle : 0.619 7.976 11070 Z= 0.325 Chirality : 0.045 0.184 1322 Planarity : 0.005 0.072 1455 Dihedral : 5.477 63.534 1248 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.26), residues: 1160 helix: 0.20 (0.69), residues: 60 sheet: -0.58 (0.25), residues: 448 loop : -1.09 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.022 0.002 TYR C 41 PHE 0.029 0.002 PHE E 72 TRP 0.033 0.002 TRP E 36 HIS 0.003 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8087) covalent geometry : angle 0.61734 (11050) SS BOND : bond 0.00236 ( 10) SS BOND : angle 1.30873 ( 20) hydrogen bonds : bond 0.03224 ( 243) hydrogen bonds : angle 6.01727 ( 627) *********************** REFINEMENT MACRO_CYCLE 5 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 134 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6115 (tt0) REVERT: A 276 MET cc_start: 0.7330 (tpp) cc_final: 0.6778 (tpp) REVERT: A 356 LYS cc_start: 0.7287 (mttm) cc_final: 0.7066 (ttmm) REVERT: D 106 TYR cc_start: 0.4964 (t80) cc_final: 0.2356 (t80) REVERT: E 32 ARG cc_start: 0.4729 (tpt170) cc_final: 0.4128 (tpm170) REVERT: E 108 ILE cc_start: 0.5341 (tt) cc_final: 0.5090 (tt) REVERT: B 51 ILE cc_start: 0.7933 (tp) cc_final: 0.7623 (tp) REVERT: B 80 TYR cc_start: 0.7831 (m-80) cc_final: 0.7601 (m-80) REVERT: B 105 TYR cc_start: 0.6675 (t80) cc_final: 0.5682 (t80) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0722 time to fit residues: 13.8696 Evaluate side-chains 110 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 82 optimal weight: 30.0000 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN D 65 HIS E 1 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.195085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.165010 restraints weight = 14504.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.164123 restraints weight = 12603.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.164326 restraints weight = 11608.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.164842 restraints weight = 10869.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.165514 restraints weight = 10080.236| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.3043 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= 0.174 Angle : 0.664 7.938 11070 Z= 0.350 Chirality : 0.046 0.212 1322 Planarity : 0.005 0.069 1455 Dihedral : 5.768 65.582 1248 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.26), residues: 1160 helix: 0.03 (0.68), residues: 60 sheet: -0.64 (0.25), residues: 451 loop : -1.21 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.024 0.003 TYR C 41 PHE 0.026 0.002 PHE E 72 TRP 0.031 0.003 TRP D 104 HIS 0.003 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8087) covalent geometry : angle 0.65939 (11050) SS BOND : bond 0.00369 ( 10) SS BOND : angle 1.87704 ( 20) hydrogen bonds : bond 0.03544 ( 243) hydrogen bonds : angle 6.16645 ( 627) *********************** REFINEMENT MACRO_CYCLE 6 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: 0 poor density : 124 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8603 (mptt) cc_final: 0.8381 (mmtt) REVERT: A 77 SER cc_start: 0.7643 (m) cc_final: 0.7320 (p) REVERT: A 276 MET cc_start: 0.7486 (tpp) cc_final: 0.6997 (tpp) REVERT: D 106 TYR cc_start: 0.5339 (t80) cc_final: 0.2714 (t80) REVERT: E 32 ARG cc_start: 0.5152 (tpt170) cc_final: 0.4619 (tpm170) REVERT: E 108 ILE cc_start: 0.5430 (tt) cc_final: 0.5177 (tt) REVERT: B 51 ILE cc_start: 0.8005 (tp) cc_final: 0.7754 (tp) REVERT: B 80 TYR cc_start: 0.7996 (m-80) cc_final: 0.7666 (m-80) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0749 time to fit residues: 13.2117 Evaluate side-chains 101 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 chunk 52 optimal weight: 0.6980 chunk 91 optimal weight: 40.0000 chunk 42 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS ** 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 = 0.4517 r_free = 0.4517 target = 0.195884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.166745 restraints weight = 14671.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.165552 restraints weight = 15431.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.166902 restraints weight = 13606.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.167555 restraints weight = 11099.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.167865 restraints weight = 9904.779| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8097 Z= 0.167 Angle : 0.664 7.571 11070 Z= 0.348 Chirality : 0.046 0.203 1322 Planarity : 0.005 0.065 1455 Dihedral : 5.756 67.324 1248 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.25), residues: 1160 helix: -0.51 (0.65), residues: 66 sheet: -0.65 (0.25), residues: 450 loop : -1.31 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 18 TYR 0.028 0.003 TYR C 41 PHE 0.029 0.002 PHE E 72 TRP 0.045 0.004 TRP E 36 HIS 0.004 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8087) covalent geometry : angle 0.66076 (11050) SS BOND : bond 0.00302 ( 10) SS BOND : angle 1.67290 ( 20) hydrogen bonds : bond 0.03392 ( 243) hydrogen bonds : angle 6.06226 ( 627) *********************** REFINEMENT MACRO_CYCLE 7 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 123 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.7555 (m) cc_final: 0.7254 (p) REVERT: A 234 LEU cc_start: 0.7461 (mt) cc_final: 0.7163 (mt) REVERT: A 276 MET cc_start: 0.7655 (tpp) cc_final: 0.7099 (tpp) REVERT: D 106 TYR cc_start: 0.5575 (t80) cc_final: 0.2788 (t80) REVERT: E 76 ILE cc_start: 0.7288 (mt) cc_final: 0.7048 (mt) REVERT: B 80 TYR cc_start: 0.8048 (m-80) cc_final: 0.7617 (m-80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0761 time to fit residues: 13.3836 Evaluate side-chains 98 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 98 optimal weight: 0.0060 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 40.0000 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 overall best weight: 2.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS ** 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 = 0.4496 r_free = 0.4496 target = 0.193982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.160036 restraints weight = 14632.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.162115 restraints weight = 11542.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.163328 restraints weight = 9706.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.164698 restraints weight = 8655.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.165383 restraints weight = 7903.268| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8097 Z= 0.183 Angle : 0.694 8.101 11070 Z= 0.364 Chirality : 0.047 0.204 1322 Planarity : 0.005 0.067 1455 Dihedral : 5.874 68.797 1248 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.25), residues: 1160 helix: -0.50 (0.65), residues: 65 sheet: -0.80 (0.25), residues: 460 loop : -1.31 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 18 TYR 0.028 0.003 TYR C 41 PHE 0.033 0.002 PHE E 72 TRP 0.076 0.004 TRP E 36 HIS 0.004 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 8087) covalent geometry : angle 0.69189 (11050) SS BOND : bond 0.00337 ( 10) SS BOND : angle 1.48056 ( 20) hydrogen bonds : bond 0.03465 ( 243) hydrogen bonds : angle 6.12853 ( 627) *********************** REFINEMENT MACRO_CYCLE 8 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 123 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.7579 (m) cc_final: 0.7252 (p) REVERT: A 234 LEU cc_start: 0.7580 (mt) cc_final: 0.7320 (mt) REVERT: A 276 MET cc_start: 0.7699 (tpp) cc_final: 0.7126 (tpp) REVERT: D 106 TYR cc_start: 0.5738 (t80) cc_final: 0.2851 (t80) REVERT: B 51 ILE cc_start: 0.8023 (tp) cc_final: 0.7782 (tp) REVERT: B 80 TYR cc_start: 0.8111 (m-80) cc_final: 0.7729 (m-80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0808 time to fit residues: 14.0272 Evaluate side-chains 98 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 112 optimal weight: 40.0000 chunk 35 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS ** 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 33 ASN ** 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 = 0.4525 r_free = 0.4525 target = 0.196362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.166792 restraints weight = 13995.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.166411 restraints weight = 12259.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.167317 restraints weight = 10902.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.167734 restraints weight = 10171.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.168038 restraints weight = 9118.283| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8097 Z= 0.146 Angle : 0.661 8.856 11070 Z= 0.346 Chirality : 0.046 0.188 1322 Planarity : 0.005 0.071 1455 Dihedral : 5.736 69.520 1248 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.26), residues: 1160 helix: -0.42 (0.65), residues: 66 sheet: -0.78 (0.25), residues: 460 loop : -1.23 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 98 TYR 0.035 0.003 TYR E 37 PHE 0.047 0.002 PHE E 72 TRP 0.041 0.003 TRP E 36 HIS 0.003 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8087) covalent geometry : angle 0.65892 (11050) SS BOND : bond 0.00305 ( 10) SS BOND : angle 1.44324 ( 20) hydrogen bonds : bond 0.03142 ( 243) hydrogen bonds : angle 5.93294 ( 627) *********************** REFINEMENT MACRO_CYCLE 9 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 118 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 LEU cc_start: 0.7437 (mt) cc_final: 0.7195 (mt) REVERT: A 276 MET cc_start: 0.7625 (tpp) cc_final: 0.7026 (tpp) REVERT: A 356 LYS cc_start: 0.7565 (mttm) cc_final: 0.7236 (ttmm) REVERT: D 106 TYR cc_start: 0.5666 (t80) cc_final: 0.2826 (t80) REVERT: E 108 ILE cc_start: 0.5425 (tt) cc_final: 0.5106 (tt) REVERT: B 51 ILE cc_start: 0.7883 (tp) cc_final: 0.7540 (tp) REVERT: B 80 TYR cc_start: 0.8056 (m-80) cc_final: 0.7563 (m-80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0895 time to fit residues: 14.6915 Evaluate side-chains 95 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** 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 = 0.4485 r_free = 0.4485 target = 0.192831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.160985 restraints weight = 13975.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.162696 restraints weight = 11388.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.163717 restraints weight = 9735.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.164692 restraints weight = 8724.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.164841 restraints weight = 8012.203| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8097 Z= 0.184 Angle : 0.696 8.693 11070 Z= 0.367 Chirality : 0.047 0.201 1322 Planarity : 0.005 0.081 1455 Dihedral : 5.950 70.920 1248 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.25), residues: 1160 helix: -0.67 (0.64), residues: 66 sheet: -0.86 (0.25), residues: 462 loop : -1.38 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 98 TYR 0.027 0.003 TYR C 41 PHE 0.043 0.002 PHE E 72 TRP 0.026 0.003 TRP E 36 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 8087) covalent geometry : angle 0.69434 (11050) SS BOND : bond 0.00304 ( 10) SS BOND : angle 1.38002 ( 20) hydrogen bonds : bond 0.03514 ( 243) hydrogen bonds : angle 6.16296 ( 627) ********************** REFINEMENT MACRO_CYCLE 10 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 114 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6337 (tt0) REVERT: A 234 LEU cc_start: 0.7345 (mt) cc_final: 0.7070 (mt) REVERT: A 276 MET cc_start: 0.7717 (tpp) cc_final: 0.7147 (tpp) REVERT: A 356 LYS cc_start: 0.7813 (mttm) cc_final: 0.7383 (ttmm) REVERT: D 106 TYR cc_start: 0.5686 (t80) cc_final: 0.2757 (t80) REVERT: B 51 ILE cc_start: 0.7985 (tp) cc_final: 0.7708 (tp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0888 time to fit residues: 13.9738 Evaluate side-chains 92 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 88 optimal weight: 40.0000 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** 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 = 0.4457 r_free = 0.4457 target = 0.190166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.157511 restraints weight = 14134.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.159025 restraints weight = 11481.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.160445 restraints weight = 9921.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.160445 restraints weight = 8877.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.160445 restraints weight = 8877.257| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8097 Z= 0.216 Angle : 0.744 9.239 11070 Z= 0.392 Chirality : 0.049 0.213 1322 Planarity : 0.005 0.066 1455 Dihedral : 6.229 72.981 1248 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.25), residues: 1160 helix: -0.15 (0.69), residues: 59 sheet: -1.11 (0.25), residues: 435 loop : -1.34 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.026 0.003 TYR E 37 PHE 0.043 0.003 PHE E 72 TRP 0.030 0.004 TRP D 115 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 8087) covalent geometry : angle 0.74185 (11050) SS BOND : bond 0.00327 ( 10) SS BOND : angle 1.42991 ( 20) hydrogen bonds : bond 0.03799 ( 243) hydrogen bonds : angle 6.43052 ( 627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1484.00 seconds wall clock time: 26 minutes 13.15 seconds (1573.15 seconds total)