Starting phenix.real_space_refine on Wed Feb 12 12:28:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbz_27318/02_2025/8dbz_27318.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbz_27318/02_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_27318/02_2025/8dbz_27318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbz_27318/02_2025/8dbz_27318.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbz_27318/02_2025/8dbz_27318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbz_27318/02_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-5592/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: 4.83, 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: 1.85 Conformation dependent library (CDL) restraints added in 1.3 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: 1.20 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: 2.25 Time building geometry restraints manager: 2.18 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: 0.430 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.370 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:2.720 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 8087 Z= 0.225 Angle : 0.732 8.438 11050 Z= 0.408 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 *********************** 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 : 0.949 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: 0.2275 time to fit residues: 38.8762 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 : 0.880 ------------------------------------------------------------------------------- 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 = 0.4504 r_free = 0.4504 target = 0.194857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.164044 restraints weight = 14078.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.165690 restraints weight = 11558.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.166689 restraints weight = 9921.441| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 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 8087 Z= 0.268 Angle : 0.674 8.752 11050 Z= 0.362 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 *********************** 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 : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 THR cc_start: 0.6577 (p) cc_final: 0.5942 (p) REVERT: A 231 GLU cc_start: 0.6764 (tm-30) cc_final: 0.6093 (tt0) REVERT: A 276 MET cc_start: 0.7580 (tpp) cc_final: 0.7109 (tpp) REVERT: A 308 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7248 (m) REVERT: A 356 LYS cc_start: 0.7500 (mttm) cc_final: 0.7083 (ttmm) REVERT: D 46 GLU cc_start: 0.5073 (pt0) cc_final: 0.4226 (mm-30) REVERT: D 106 TYR cc_start: 0.5080 (t80) cc_final: 0.2759 (t80) REVERT: B 29 TYR cc_start: 0.2486 (m-80) cc_final: 0.1939 (m-80) REVERT: B 80 TYR cc_start: 0.8008 (m-80) cc_final: 0.7740 (m-80) REVERT: B 98 ARG cc_start: 0.7384 (ptm-80) cc_final: 0.7153 (ptm160) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.1924 time to fit residues: 34.5647 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 : 0.842 ------------------------------------------------------------------------------- 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: 3.9990 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 98 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 40.0000 chunk 62 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.4526 r_free = 0.4526 target = 0.197566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.166450 restraints weight = 14956.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.167906 restraints weight = 12203.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.169379 restraints weight = 10599.138| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8087 Z= 0.214 Angle : 0.629 8.402 11050 Z= 0.334 Chirality : 0.046 0.190 1322 Planarity : 0.005 0.056 1455 Dihedral : 5.612 62.720 1248 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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: -1.39 (0.25), residues: 1160 helix: -0.05 (0.70), residues: 57 sheet: -0.65 (0.25), residues: 438 loop : -1.17 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 36 HIS 0.003 0.001 HIS A 69 PHE 0.015 0.002 PHE E 72 TYR 0.025 0.002 TYR C 41 ARG 0.005 0.001 ARG A 333 *********************** 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 131 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.8069 (tmm) cc_final: 0.7601 (tpp) REVERT: A 231 GLU cc_start: 0.6867 (tm-30) cc_final: 0.5959 (tp30) REVERT: A 276 MET cc_start: 0.7385 (tpp) cc_final: 0.6856 (tpp) REVERT: A 356 LYS cc_start: 0.7417 (mttm) cc_final: 0.6994 (ttmm) REVERT: D 46 GLU cc_start: 0.5375 (pt0) cc_final: 0.4776 (mm-30) REVERT: D 106 TYR cc_start: 0.5020 (t80) cc_final: 0.2433 (t80) REVERT: B 51 ILE cc_start: 0.7914 (tp) cc_final: 0.7666 (tp) REVERT: B 80 TYR cc_start: 0.8077 (m-80) cc_final: 0.7864 (m-80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1927 time to fit residues: 34.5983 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 : 0.914 ------------------------------------------------------------------------------- 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: 7.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4525 r_free = 0.4525 target = 0.197296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.166678 restraints weight = 14229.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.168211 restraints weight = 11597.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.169494 restraints weight = 9949.459| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 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 0.042 8087 Z= 0.204 Angle : 0.612 8.321 11050 Z= 0.324 Chirality : 0.046 0.189 1322 Planarity : 0.005 0.058 1455 Dihedral : 5.528 64.119 1248 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 0.15 % Allowed : 5.47 % Favored : 94.38 % 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: -1.36 (0.26), residues: 1160 helix: 0.16 (0.70), residues: 59 sheet: -0.63 (0.25), residues: 446 loop : -1.18 (0.26), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 36 HIS 0.002 0.001 HIS A 351 PHE 0.018 0.002 PHE E 72 TYR 0.036 0.002 TYR E 92 ARG 0.004 0.000 ARG A 268 *********************** 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 131 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.6858 (tm-30) cc_final: 0.5962 (tt0) REVERT: A 276 MET cc_start: 0.7383 (tpp) cc_final: 0.6854 (tpp) REVERT: A 356 LYS cc_start: 0.7383 (mttm) cc_final: 0.7011 (ttmm) REVERT: D 46 GLU cc_start: 0.5159 (pt0) cc_final: 0.4954 (mm-30) REVERT: D 106 TYR cc_start: 0.4947 (t80) cc_final: 0.2422 (t80) REVERT: E 32 ARG cc_start: 0.4868 (tpt170) cc_final: 0.3759 (tpm170) REVERT: B 51 ILE cc_start: 0.7872 (tp) cc_final: 0.7596 (tp) REVERT: B 80 TYR cc_start: 0.8066 (m-80) cc_final: 0.7841 (m-80) REVERT: B 105 TYR cc_start: 0.6633 (t80) cc_final: 0.5550 (t80) REVERT: B 106 PHE cc_start: 0.6456 (OUTLIER) cc_final: 0.5271 (m-10) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1811 time to fit residues: 33.6858 Evaluate side-chains 111 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 4 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 22 optimal weight: 0.0060 chunk 111 optimal weight: 7.9990 chunk 95 optimal weight: 40.0000 chunk 108 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 overall best weight: 2.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS E 1 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.191765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.158764 restraints weight = 14553.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.160568 restraints weight = 11769.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.161672 restraints weight = 10020.232| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8087 Z= 0.360 Angle : 0.728 8.076 11050 Z= 0.383 Chirality : 0.048 0.219 1322 Planarity : 0.005 0.069 1455 Dihedral : 6.074 65.881 1248 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.67 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % 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: -1.70 (0.25), residues: 1160 helix: 0.02 (0.70), residues: 59 sheet: -0.82 (0.25), residues: 449 loop : -1.45 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP E 36 HIS 0.004 0.001 HIS A 69 PHE 0.028 0.003 PHE E 72 TYR 0.024 0.003 TYR C 41 ARG 0.006 0.001 ARG B 38 *********************** 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 126 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.7694 (m) cc_final: 0.7119 (p) REVERT: A 231 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6139 (tp30) REVERT: A 266 ASP cc_start: 0.6095 (t0) cc_final: 0.5827 (t0) REVERT: A 276 MET cc_start: 0.7888 (tpp) cc_final: 0.7558 (tpp) REVERT: D 106 TYR cc_start: 0.5805 (t80) cc_final: 0.3143 (t80) REVERT: B 51 ILE cc_start: 0.8047 (tp) cc_final: 0.7831 (tp) REVERT: B 80 TYR cc_start: 0.8274 (m-80) cc_final: 0.8015 (m-80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1850 time to fit residues: 32.8265 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 : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 103 optimal weight: 50.0000 chunk 109 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 92 optimal weight: 30.0000 chunk 21 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.193906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.161359 restraints weight = 14544.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.163252 restraints weight = 11838.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.164032 restraints weight = 10046.401| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8087 Z= 0.288 Angle : 0.680 8.994 11050 Z= 0.357 Chirality : 0.047 0.214 1322 Planarity : 0.005 0.064 1455 Dihedral : 5.956 66.678 1248 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.16 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: -1.66 (0.25), residues: 1160 helix: 0.02 (0.70), residues: 59 sheet: -0.75 (0.25), residues: 446 loop : -1.45 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP E 36 HIS 0.004 0.001 HIS B 104 PHE 0.030 0.002 PHE E 72 TYR 0.025 0.003 TYR C 41 ARG 0.003 0.001 ARG B 98 *********************** 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 129 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.7722 (m) cc_final: 0.7314 (p) REVERT: A 276 MET cc_start: 0.7715 (tpp) cc_final: 0.7077 (tpp) REVERT: D 106 TYR cc_start: 0.5477 (t80) cc_final: 0.2818 (t80) REVERT: B 29 TYR cc_start: 0.1547 (m-80) cc_final: 0.1017 (m-80) REVERT: B 80 TYR cc_start: 0.8273 (m-80) cc_final: 0.7962 (m-80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2013 time to fit residues: 35.7678 Evaluate side-chains 102 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 81 optimal weight: 0.0040 chunk 89 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.198457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.166317 restraints weight = 14371.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.167751 restraints weight = 11355.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.169452 restraints weight = 9785.473| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8087 Z= 0.205 Angle : 0.644 8.137 11050 Z= 0.337 Chirality : 0.046 0.176 1322 Planarity : 0.005 0.070 1455 Dihedral : 5.638 67.085 1248 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: -1.46 (0.25), residues: 1160 helix: -0.34 (0.65), residues: 66 sheet: -0.64 (0.25), residues: 456 loop : -1.25 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP E 36 HIS 0.003 0.001 HIS B 104 PHE 0.028 0.002 PHE E 72 TYR 0.024 0.002 TYR C 41 ARG 0.009 0.001 ARG E 18 *********************** 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 133 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 LEU cc_start: 0.7381 (mt) cc_final: 0.7113 (mt) REVERT: A 276 MET cc_start: 0.7528 (tpp) cc_final: 0.6890 (tpp) REVERT: D 106 TYR cc_start: 0.5123 (t80) cc_final: 0.2448 (t80) REVERT: B 29 TYR cc_start: 0.1319 (m-80) cc_final: 0.0742 (m-80) REVERT: B 51 ILE cc_start: 0.7729 (tp) cc_final: 0.7515 (tp) REVERT: B 80 TYR cc_start: 0.8108 (m-80) cc_final: 0.7797 (m-80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1826 time to fit residues: 34.0728 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 : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 55 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.199867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.167949 restraints weight = 14455.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.169982 restraints weight = 11404.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.171723 restraints weight = 9574.189| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8087 Z= 0.198 Angle : 0.635 7.538 11050 Z= 0.331 Chirality : 0.046 0.171 1322 Planarity : 0.005 0.071 1455 Dihedral : 5.549 67.153 1248 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % 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 (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: -1.37 (0.26), residues: 1160 helix: -0.25 (0.64), residues: 66 sheet: -0.60 (0.25), residues: 442 loop : -1.16 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP E 36 HIS 0.004 0.001 HIS B 104 PHE 0.036 0.002 PHE E 72 TYR 0.031 0.002 TYR E 37 ARG 0.011 0.001 ARG B 98 *********************** 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 117 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8486 (mptt) cc_final: 0.8171 (mmtt) REVERT: A 234 LEU cc_start: 0.7437 (mt) cc_final: 0.7184 (mt) REVERT: A 276 MET cc_start: 0.7389 (tpp) cc_final: 0.6734 (tpp) REVERT: E 32 ARG cc_start: 0.5616 (tpt170) cc_final: 0.4228 (tpp-160) REVERT: B 29 TYR cc_start: 0.1288 (m-80) cc_final: 0.0808 (m-80) REVERT: B 51 ILE cc_start: 0.7701 (tp) cc_final: 0.7459 (tp) REVERT: B 80 TYR cc_start: 0.8147 (m-80) cc_final: 0.7922 (m-80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1841 time to fit residues: 30.1741 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 : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 20.0000 chunk 49 optimal weight: 0.0770 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 overall best weight: 3.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN D 65 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.187852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.156045 restraints weight = 14581.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.157599 restraints weight = 12067.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.158514 restraints weight = 10510.269| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 8087 Z= 0.461 Angle : 0.823 9.247 11050 Z= 0.434 Chirality : 0.052 0.232 1322 Planarity : 0.006 0.090 1455 Dihedral : 6.509 70.226 1248 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: -1.87 (0.25), residues: 1160 helix: -0.27 (0.69), residues: 59 sheet: -1.05 (0.26), residues: 399 loop : -1.45 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.005 TRP E 36 HIS 0.008 0.002 HIS B 104 PHE 0.051 0.004 PHE E 72 TYR 0.034 0.004 TYR B 105 ARG 0.007 0.001 ARG B 98 *********************** 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 : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.5718 (mm110) cc_final: 0.5469 (mt0) REVERT: A 276 MET cc_start: 0.8059 (tpp) cc_final: 0.7815 (tpp) REVERT: D 106 TYR cc_start: 0.6038 (t80) cc_final: 0.3262 (t80) REVERT: B 29 TYR cc_start: 0.0903 (m-80) cc_final: 0.0407 (m-80) REVERT: B 112 TYR cc_start: 0.7744 (p90) cc_final: 0.7541 (p90) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1923 time to fit residues: 31.3973 Evaluate side-chains 91 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4510 r_free = 0.4510 target = 0.195520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.164167 restraints weight = 13914.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.165968 restraints weight = 11425.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.166846 restraints weight = 9751.791| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8087 Z= 0.237 Angle : 0.684 8.501 11050 Z= 0.357 Chirality : 0.047 0.185 1322 Planarity : 0.005 0.081 1455 Dihedral : 6.009 69.983 1248 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % 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 (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: -1.76 (0.25), residues: 1160 helix: -0.54 (0.66), residues: 65 sheet: -0.89 (0.26), residues: 422 loop : -1.40 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP E 36 HIS 0.004 0.001 HIS B 104 PHE 0.043 0.002 PHE E 72 TYR 0.036 0.003 TYR E 37 ARG 0.008 0.001 ARG B 98 ********************** 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 127 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8566 (mptt) cc_final: 0.8240 (mmtt) REVERT: A 103 GLN cc_start: 0.5644 (mm110) cc_final: 0.5411 (mt0) REVERT: A 145 THR cc_start: 0.7077 (p) cc_final: 0.6847 (p) REVERT: A 231 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6414 (tt0) REVERT: A 234 LEU cc_start: 0.7258 (mt) cc_final: 0.7007 (mt) REVERT: A 276 MET cc_start: 0.7656 (tpp) cc_final: 0.6993 (tpp) REVERT: A 324 MET cc_start: 0.4025 (mmm) cc_final: 0.3463 (mmm) REVERT: B 29 TYR cc_start: 0.0480 (m-80) cc_final: 0.0040 (m-80) REVERT: B 51 ILE cc_start: 0.7839 (tp) cc_final: 0.7620 (tp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2114 time to fit residues: 36.5559 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 : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 104 optimal weight: 40.0000 chunk 8 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 ** 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 = 0.4427 r_free = 0.4427 target = 0.187665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.158124 restraints weight = 14527.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.155740 restraints weight = 13255.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156838 restraints weight = 12381.680| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 8087 Z= 0.473 Angle : 0.850 10.656 11050 Z= 0.449 Chirality : 0.052 0.235 1322 Planarity : 0.006 0.065 1455 Dihedral : 6.670 70.508 1248 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -2.09 (0.25), residues: 1160 helix: -0.52 (0.68), residues: 59 sheet: -1.07 (0.26), residues: 414 loop : -1.70 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRP E 36 HIS 0.007 0.002 HIS B 104 PHE 0.046 0.004 PHE E 72 TYR 0.031 0.004 TYR E 92 ARG 0.006 0.001 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2892.03 seconds wall clock time: 52 minutes 22.14 seconds (3142.14 seconds total)