Starting phenix.real_space_refine on Fri Dec 8 03:46:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x93_22098/12_2023/6x93_22098.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x93_22098/12_2023/6x93_22098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x93_22098/12_2023/6x93_22098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x93_22098/12_2023/6x93_22098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x93_22098/12_2023/6x93_22098.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x93_22098/12_2023/6x93_22098.pdb" } resolution = 3.5 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= 0.048 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 27 5.16 5 C 4267 2.51 5 N 1238 2.21 5 O 1314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 197": "OD1" <-> "OD2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 159": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6846 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1003 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1572 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1504 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 170} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 877 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 Chain: "E" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 981 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 847 Unresolved non-hydrogen dihedrals: 561 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 9, 'PHE:plan': 9, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 371 Chain: "F" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 909 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 169} Link IDs: {'PTRANS': 12, 'TRANS': 170} Chain breaks: 2 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 856 Unresolved non-hydrogen dihedrals: 568 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 10, 'PHE:plan': 10, 'GLU:plan': 14, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 402 Time building chain proxies: 4.23, per 1000 atoms: 0.62 Number of scatterers: 6846 At special positions: 0 Unit cell: (95.942, 101.332, 136.906, 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 27 16.00 O 1314 8.00 N 1238 7.00 C 4267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 12 " - pdb=" SG CYS A 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 54 " distance=2.02 Simple disulfide: pdb=" SG CYS B 181 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 209 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 17 sheets defined 28.7% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 14 through 17 Processing helix chain 'A' and resid 18 through 41 removed outlier: 3.913A pdb=" N ARG A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 55 removed outlier: 4.027A pdb=" N GLU A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 removed outlier: 3.676A pdb=" N SER A 66 " --> pdb=" O CYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 4.217A pdb=" N ASN A 82 " --> pdb=" O PRO A 78 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 107 removed outlier: 3.970A pdb=" N LEU A 94 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 4.045A pdb=" N LEU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 4.791A pdb=" N TYR A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 160 removed outlier: 4.229A pdb=" N ARG A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 4.331A pdb=" N ASP B 68 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 135 through 140 removed outlier: 4.118A pdb=" N PHE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.781A pdb=" N GLY B 175 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 removed outlier: 3.554A pdb=" N LYS C 35 " --> pdb=" O VAL C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'D' and resid 14 through 41 removed outlier: 3.524A pdb=" N TYR D 18 " --> pdb=" O HIS D 14 " (cutoff:3.500A) Proline residue: D 20 - end of helix removed outlier: 3.697A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 55 removed outlier: 3.988A pdb=" N GLU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 74 removed outlier: 3.701A pdb=" N GLN D 63 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER D 66 " --> pdb=" O CYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 84 removed outlier: 4.228A pdb=" N ASN D 82 " --> pdb=" O PRO D 78 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 105 removed outlier: 3.749A pdb=" N LEU D 94 " --> pdb=" O HIS D 90 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 101 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 131 removed outlier: 3.952A pdb=" N GLN D 123 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 4.453A pdb=" N TYR D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 160 removed outlier: 3.504A pdb=" N MET D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 159 " --> pdb=" O THR D 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 68 through 70 No H-bonds generated for 'chain 'E' and resid 68 through 70' Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 171 through 176 removed outlier: 3.922A pdb=" N GLY E 175 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 35 removed outlier: 3.590A pdb=" N LYS F 35 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 49 removed outlier: 4.158A pdb=" N GLN F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 148 Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 16 removed outlier: 3.772A pdb=" N GLU B 14 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 21 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 16 " --> pdb=" O HIS B 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 55 removed outlier: 8.179A pdb=" N ASN B 49 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ARG B 42 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE B 51 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N LEU B 40 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN B 53 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL B 38 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG B 80 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 78 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA B 81 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASN B 89 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP B 83 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N HIS B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113 removed outlier: 3.596A pdb=" N GLU B 112 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.545A pdb=" N VAL B 164 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 52 through 53 removed outlier: 4.123A pdb=" N ALA C 91 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 117 through 120 Processing sheet with id=AA7, first strand: chain 'C' and resid 135 through 136 removed outlier: 4.613A pdb=" N TRP C 143 " --> pdb=" O ILE C 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 156 Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.119A pdb=" N SER E 10 " --> pdb=" O THR E 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AB2, first strand: chain 'E' and resid 49 through 50 removed outlier: 3.609A pdb=" N ARG E 78 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY E 74 " --> pdb=" O TYR E 43 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 86 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 49 through 50 removed outlier: 3.609A pdb=" N ARG E 78 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY E 74 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 112 through 113 Processing sheet with id=AB5, first strand: chain 'E' and resid 161 through 164 removed outlier: 3.621A pdb=" N PHE E 180 " --> pdb=" O ILE E 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 52 through 54 Processing sheet with id=AB7, first strand: chain 'F' and resid 117 through 120 removed outlier: 3.616A pdb=" N MET F 129 " --> pdb=" O GLU F 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 155 through 156 243 hydrogen bonds defined for protein. 639 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: 1.61 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2405 1.35 - 1.48: 1706 1.48 - 1.61: 2799 1.61 - 1.74: 0 1.74 - 1.87: 41 Bond restraints: 6951 Sorted by residual: bond pdb=" CG LEU A 23 " pdb=" CD2 LEU A 23 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.81e+00 bond pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " ideal model delta sigma weight residual 1.808 1.873 -0.065 3.30e-02 9.18e+02 3.91e+00 bond pdb=" CG LEU A 60 " pdb=" CD1 LEU A 60 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.31e+00 bond pdb=" CB TRP A 104 " pdb=" CG TRP A 104 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.15e+00 bond pdb=" C GLU C 182 " pdb=" N PRO C 183 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.12e+00 ... (remaining 6946 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.17: 190 106.17 - 113.19: 3719 113.19 - 120.21: 2516 120.21 - 127.23: 3020 127.23 - 134.25: 72 Bond angle restraints: 9517 Sorted by residual: angle pdb=" N GLU E 101 " pdb=" CA GLU E 101 " pdb=" C GLU E 101 " ideal model delta sigma weight residual 113.50 106.83 6.67 1.23e+00 6.61e-01 2.94e+01 angle pdb=" C ALA D 152 " pdb=" N TYR D 153 " pdb=" CA TYR D 153 " ideal model delta sigma weight residual 121.58 111.34 10.24 1.95e+00 2.63e-01 2.76e+01 angle pdb=" N GLN E 56 " pdb=" CA GLN E 56 " pdb=" C GLN E 56 " ideal model delta sigma weight residual 112.23 106.29 5.94 1.26e+00 6.30e-01 2.22e+01 angle pdb=" CA TYR B 70 " pdb=" CB TYR B 70 " pdb=" CG TYR B 70 " ideal model delta sigma weight residual 113.90 105.55 8.35 1.80e+00 3.09e-01 2.15e+01 angle pdb=" N VAL E 79 " pdb=" CA VAL E 79 " pdb=" C VAL E 79 " ideal model delta sigma weight residual 108.81 101.31 7.50 1.62e+00 3.81e-01 2.14e+01 ... (remaining 9512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3835 17.91 - 35.83: 242 35.83 - 53.74: 47 53.74 - 71.65: 8 71.65 - 89.56: 3 Dihedral angle restraints: 4135 sinusoidal: 1081 harmonic: 3054 Sorted by residual: dihedral pdb=" CA LEU C 50 " pdb=" C LEU C 50 " pdb=" N THR C 51 " pdb=" CA THR C 51 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA CYS B 54 " pdb=" C CYS B 54 " pdb=" N SER B 55 " pdb=" CA SER B 55 " ideal model delta harmonic sigma weight residual 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA CYS E 54 " pdb=" C CYS E 54 " pdb=" N SER E 55 " pdb=" CA SER E 55 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 4132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 727 0.047 - 0.095: 285 0.095 - 0.142: 104 0.142 - 0.189: 19 0.189 - 0.237: 5 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CG LEU A 46 " pdb=" CB LEU A 46 " pdb=" CD1 LEU A 46 " pdb=" CD2 LEU A 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA LYS C 81 " pdb=" N LYS C 81 " pdb=" C LYS C 81 " pdb=" CB LYS C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE B 21 " pdb=" CA ILE B 21 " pdb=" CG1 ILE B 21 " pdb=" CG2 ILE B 21 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1137 not shown) Planarity restraints: 1273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 148 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" C ASN D 148 " -0.067 2.00e-02 2.50e+03 pdb=" O ASN D 148 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR D 149 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 190 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C SER E 190 " -0.063 2.00e-02 2.50e+03 pdb=" O SER E 190 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG E 191 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 182 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" CD GLU C 182 " 0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU C 182 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU C 182 " -0.019 2.00e-02 2.50e+03 ... (remaining 1270 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 638 2.72 - 3.26: 7117 3.26 - 3.81: 10480 3.81 - 4.35: 12114 4.35 - 4.90: 19981 Nonbonded interactions: 50330 Sorted by model distance: nonbonded pdb=" N GLU A 75 " pdb=" OE1 GLU A 75 " model vdw 2.173 2.520 nonbonded pdb=" OG1 THR C 51 " pdb=" OE1 GLN C 68 " model vdw 2.196 2.440 nonbonded pdb=" O VAL F 191 " pdb=" N SER F 205 " model vdw 2.200 2.520 nonbonded pdb=" OD2 ASP A 100 " pdb=" OG SER C 80 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASN C 138 " pdb=" N GLU C 141 " model vdw 2.226 2.520 ... (remaining 50325 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 12 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 or (resid 18 through 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 or (resid 59 through 60 and (name N or na \ me CA or name C or name O or name CB )) or resid 61 or (resid 62 through 94 and \ (name N or name CA or name C or name O or name CB )) or resid 95 or (resid 96 th \ rough 107 and (name N or name CA or name C or name O or name CB )) or resid 108 \ or resid 125 through 160)) selection = (chain 'D' and (resid 12 through 107 or resid 114 or (resid 117 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 126 through 134 and (name N o \ r name CA or name C or name O or name CB )) or resid 135 or (resid 136 through 1 \ 60 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and ((resid 4 through 43 and (name N or name CA or name C or name O o \ r name CB )) or resid 44 or (resid 45 through 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 or (resid 75 through 83 and (name N or nam \ e CA or name C or name O or name CB )) or resid 84 or (resid 85 through 106 and \ (name N or name CA or name C or name O or name CB )) or resid 107 or (resid 108 \ through 115 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 6 or (resid 117 through 119 and (name N or name CA or name C or name O or name C \ B )) or resid 120 or (resid 121 through 174 and (name N or name CA or name C or \ name O or name CB )) or resid 175 or (resid 176 through 177 and (name N or name \ CA or name C or name O or name CB )) or (resid 178 through 194 and (name N or na \ me CA or name C or name O or name CB )) or resid 195 or (resid 196 through 206 a \ nd (name N or name CA or name C or name O or name CB )))) selection = chain 'E' } ncs_group { reference = (chain 'C' and ((resid 21 through 47 and (name N or name CA or name C or name O \ or name CB )) or resid 48 or (resid 49 through 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 or (resid 84 through 113 and (name N or n \ ame CA or name C or name O or name CB )) or resid 114 or (resid 115 through 116 \ and (name N or name CA or name C or name O or name CB )) or resid 117 or (resid \ 118 through 192 and (name N or name CA or name C or name O or name CB )) or resi \ d 193 or (resid 194 through 201 and (name N or name CA or name C or name O or na \ me CB )) or resid 202 or (resid 203 through 214 and (name N or name CA or name C \ or name O or name CB )))) selection = chain 'F' } 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=0.50 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: 0.730 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: 3.900 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.020 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 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 : 0.007 0.072 6951 Z= 0.493 Angle : 1.132 10.236 9517 Z= 0.685 Chirality : 0.058 0.237 1140 Planarity : 0.007 0.071 1273 Dihedral : 13.578 89.561 2116 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.42 % Allowed : 7.98 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.23), residues: 1014 helix: -2.54 (0.27), residues: 239 sheet: -1.61 (0.33), residues: 193 loop : -2.21 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 100 HIS 0.011 0.002 HIS C 85 PHE 0.022 0.003 PHE C 105 TYR 0.028 0.003 TYR D 153 ARG 0.012 0.002 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 101 average time/residue: 0.2191 time to fit residues: 28.8173 Evaluate side-chains 70 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 20.0000 chunk 76 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.0020 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 HIS ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6951 Z= 0.225 Angle : 0.681 8.545 9517 Z= 0.378 Chirality : 0.045 0.153 1140 Planarity : 0.004 0.037 1273 Dihedral : 6.176 22.137 1075 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.57 % Allowed : 15.55 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.24), residues: 1014 helix: -1.59 (0.31), residues: 235 sheet: -1.84 (0.31), residues: 215 loop : -1.83 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 90 HIS 0.006 0.001 HIS A 14 PHE 0.044 0.002 PHE C 62 TYR 0.032 0.002 TYR D 153 ARG 0.006 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 94 average time/residue: 0.1893 time to fit residues: 23.8373 Evaluate side-chains 81 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.635 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0864 time to fit residues: 3.1335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 82 ASN B 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6951 Z= 0.336 Angle : 0.733 7.637 9517 Z= 0.409 Chirality : 0.047 0.249 1140 Planarity : 0.004 0.035 1273 Dihedral : 6.336 24.841 1075 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.52 % Allowed : 19.33 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.24), residues: 1014 helix: -1.63 (0.31), residues: 237 sheet: -2.20 (0.30), residues: 237 loop : -1.87 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 184 HIS 0.008 0.001 HIS C 85 PHE 0.023 0.002 PHE C 62 TYR 0.026 0.002 TYR D 153 ARG 0.004 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 85 average time/residue: 0.2160 time to fit residues: 25.2110 Evaluate side-chains 75 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0706 time to fit residues: 2.4787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6951 Z= 0.208 Angle : 0.622 7.117 9517 Z= 0.339 Chirality : 0.044 0.205 1140 Planarity : 0.003 0.027 1273 Dihedral : 5.740 23.107 1075 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.36 % Allowed : 19.33 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.24), residues: 1014 helix: -1.11 (0.33), residues: 237 sheet: -2.11 (0.31), residues: 227 loop : -1.91 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 184 HIS 0.006 0.001 HIS A 14 PHE 0.017 0.001 PHE C 62 TYR 0.028 0.001 TYR D 153 ARG 0.004 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.1822 time to fit residues: 23.2756 Evaluate side-chains 87 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1156 time to fit residues: 2.9808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 0.0980 chunk 67 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6951 Z= 0.220 Angle : 0.619 6.822 9517 Z= 0.337 Chirality : 0.044 0.189 1140 Planarity : 0.003 0.027 1273 Dihedral : 5.576 25.594 1075 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.20 % Allowed : 19.12 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.24), residues: 1014 helix: -0.93 (0.33), residues: 239 sheet: -2.23 (0.33), residues: 198 loop : -1.93 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 184 HIS 0.005 0.001 HIS A 14 PHE 0.013 0.002 PHE C 62 TYR 0.021 0.002 TYR D 153 ARG 0.003 0.001 ARG B 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 99 average time/residue: 0.1662 time to fit residues: 22.9757 Evaluate side-chains 84 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0556 time to fit residues: 1.7425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 30.0000 chunk 19 optimal weight: 0.0470 chunk 57 optimal weight: 0.0010 chunk 24 optimal weight: 8.9990 chunk 97 optimal weight: 0.0770 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 0.0170 overall best weight: 0.2280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6951 Z= 0.154 Angle : 0.576 8.706 9517 Z= 0.307 Chirality : 0.042 0.182 1140 Planarity : 0.003 0.028 1273 Dihedral : 5.110 31.970 1075 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.26 % Allowed : 20.80 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.25), residues: 1014 helix: -0.36 (0.35), residues: 239 sheet: -1.64 (0.37), residues: 174 loop : -1.85 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 159 HIS 0.006 0.001 HIS A 14 PHE 0.015 0.001 PHE C 62 TYR 0.013 0.001 TYR D 153 ARG 0.005 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 92 average time/residue: 0.1993 time to fit residues: 24.6178 Evaluate side-chains 84 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0747 time to fit residues: 1.7128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6951 Z= 0.358 Angle : 0.726 8.648 9517 Z= 0.401 Chirality : 0.047 0.184 1140 Planarity : 0.004 0.032 1273 Dihedral : 6.002 35.533 1075 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.84 % Allowed : 24.79 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.24), residues: 1014 helix: -1.06 (0.33), residues: 240 sheet: -2.01 (0.34), residues: 218 loop : -1.98 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 152 HIS 0.005 0.001 HIS A 14 PHE 0.019 0.003 PHE A 71 TYR 0.020 0.003 TYR B 70 ARG 0.005 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 79 average time/residue: 0.2104 time to fit residues: 22.8471 Evaluate side-chains 74 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0682 time to fit residues: 1.3654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 88 optimal weight: 40.0000 chunk 93 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6951 Z= 0.226 Angle : 0.643 9.949 9517 Z= 0.347 Chirality : 0.044 0.168 1140 Planarity : 0.003 0.032 1273 Dihedral : 5.583 40.855 1075 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.05 % Allowed : 25.42 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.25), residues: 1014 helix: -0.79 (0.34), residues: 235 sheet: -2.09 (0.34), residues: 204 loop : -1.85 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 184 HIS 0.005 0.001 HIS A 14 PHE 0.016 0.002 PHE D 146 TYR 0.017 0.002 TYR D 153 ARG 0.006 0.001 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 0.1965 time to fit residues: 20.5603 Evaluate side-chains 77 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0748 time to fit residues: 1.7021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 59 optimal weight: 0.1980 chunk 95 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6951 Z= 0.393 Angle : 0.783 10.489 9517 Z= 0.431 Chirality : 0.048 0.198 1140 Planarity : 0.004 0.035 1273 Dihedral : 6.516 50.346 1075 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 1.47 % Allowed : 25.63 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.24), residues: 1014 helix: -1.54 (0.32), residues: 238 sheet: -2.21 (0.33), residues: 222 loop : -2.14 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 90 HIS 0.004 0.001 HIS C 85 PHE 0.016 0.002 PHE A 71 TYR 0.029 0.003 TYR D 153 ARG 0.006 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.1846 time to fit residues: 19.3231 Evaluate side-chains 77 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0918 time to fit residues: 1.9337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6951 Z= 0.217 Angle : 0.669 11.121 9517 Z= 0.355 Chirality : 0.044 0.162 1140 Planarity : 0.003 0.033 1273 Dihedral : 5.835 51.623 1075 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.84 % Allowed : 25.63 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.25), residues: 1014 helix: -1.05 (0.33), residues: 238 sheet: -2.16 (0.34), residues: 207 loop : -2.03 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 184 HIS 0.005 0.001 HIS A 14 PHE 0.015 0.002 PHE D 146 TYR 0.015 0.002 TYR D 153 ARG 0.003 0.000 ARG B 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 79 average time/residue: 0.1915 time to fit residues: 20.6393 Evaluate side-chains 78 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0722 time to fit residues: 1.5473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 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 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.142565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.125845 restraints weight = 27403.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.127460 restraints weight = 17566.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.128549 restraints weight = 13356.974| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6951 Z= 0.196 Angle : 0.656 11.920 9517 Z= 0.342 Chirality : 0.043 0.166 1140 Planarity : 0.003 0.031 1273 Dihedral : 5.506 50.805 1075 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.63 % Allowed : 26.68 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.25), residues: 1014 helix: -0.61 (0.35), residues: 232 sheet: -2.19 (0.34), residues: 217 loop : -1.95 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 184 HIS 0.005 0.001 HIS A 14 PHE 0.015 0.001 PHE D 146 TYR 0.017 0.001 TYR D 153 ARG 0.003 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1595.63 seconds wall clock time: 29 minutes 41.73 seconds (1781.73 seconds total)