Starting phenix.real_space_refine on Thu May 15 08:41:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itr_60876/05_2025/9itr_60876.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itr_60876/05_2025/9itr_60876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itr_60876/05_2025/9itr_60876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itr_60876/05_2025/9itr_60876.map" model { file = "/net/cci-nas-00/data/ceres_data/9itr_60876/05_2025/9itr_60876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itr_60876/05_2025/9itr_60876.cif" } resolution = 4.6 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= 0.009 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 23 5.16 5 C 8409 2.51 5 N 2263 2.21 5 O 2341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13036 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 480 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "J" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "K" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "N" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "O" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "P" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "Q" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "T" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1759 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 14, 'TRANS': 234} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 106 Chain: "Z" Number of atoms: 1855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1855 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 14, 'TRANS': 237} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "Y" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1158 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 1, 'TRANS': 151} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "V" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1123 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 149} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "U" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1047 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 1, 'TRANS': 148} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "X" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1069 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 1, 'TRANS': 150} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Time building chain proxies: 8.22, per 1000 atoms: 0.63 Number of scatterers: 13036 At special positions: 0 Unit cell: (94.86, 143.22, 223.2, 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 23 16.00 O 2341 8.00 N 2263 7.00 C 8409 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 1 sheets defined 87.0% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'H' and resid 3 through 38 removed outlier: 3.875A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix removed outlier: 4.484A pdb=" N GLY H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 72 removed outlier: 3.737A pdb=" N VAL H 46 " --> pdb=" O GLU H 42 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 37 removed outlier: 4.537A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Proline residue: I 20 - end of helix removed outlier: 4.066A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG I 37 " --> pdb=" O GLN I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 72 Processing helix chain 'J' and resid 3 through 19 Processing helix chain 'J' and resid 20 through 38 Processing helix chain 'J' and resid 41 through 72 Processing helix chain 'K' and resid 3 through 38 removed outlier: 3.609A pdb=" N VAL K 7 " --> pdb=" O GLY K 3 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY K 19 " --> pdb=" O LEU K 15 " (cutoff:3.500A) Proline residue: K 20 - end of helix Processing helix chain 'K' and resid 41 through 72 removed outlier: 3.806A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 38 removed outlier: 3.762A pdb=" N VAL L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) Proline residue: L 20 - end of helix Processing helix chain 'L' and resid 41 through 71 removed outlier: 3.723A pdb=" N GLY L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 38 removed outlier: 3.522A pdb=" N VAL M 7 " --> pdb=" O GLY M 3 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix removed outlier: 4.574A pdb=" N GLY M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 72 removed outlier: 3.674A pdb=" N ILE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 17 through 38 Processing helix chain 'N' and resid 41 through 72 Processing helix chain 'O' and resid 3 through 38 Proline residue: O 20 - end of helix removed outlier: 4.281A pdb=" N GLY O 23 " --> pdb=" O GLY O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 72 removed outlier: 3.667A pdb=" N ALA O 58 " --> pdb=" O ALA O 54 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 Processing helix chain 'P' and resid 17 through 38 removed outlier: 4.061A pdb=" N GLY P 25 " --> pdb=" O GLY P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 72 removed outlier: 3.639A pdb=" N GLY P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 3.550A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Proline residue: Q 20 - end of helix removed outlier: 3.511A pdb=" N ASN Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 72 removed outlier: 3.912A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 71 removed outlier: 5.032A pdb=" N ILE T 56 " --> pdb=" O PHE T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 97 Processing helix chain 'T' and resid 106 through 124 removed outlier: 3.506A pdb=" N GLY T 124 " --> pdb=" O GLY T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 190 through 212 removed outlier: 3.822A pdb=" N ALA T 212 " --> pdb=" O TRP T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 220 removed outlier: 3.977A pdb=" N TYR T 217 " --> pdb=" O GLY T 214 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS T 220 " --> pdb=" O TYR T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 268 removed outlier: 3.919A pdb=" N ILE T 233 " --> pdb=" O SER T 229 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE T 234 " --> pdb=" O PHE T 230 " (cutoff:3.500A) Proline residue: T 243 - end of helix removed outlier: 4.660A pdb=" N ILE T 254 " --> pdb=" O LEU T 250 " (cutoff:3.500A) Processing helix chain 'T' and resid 272 through 304 removed outlier: 4.611A pdb=" N PHE T 276 " --> pdb=" O LEU T 272 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 20 through 25 removed outlier: 4.018A pdb=" N PHE Z 24 " --> pdb=" O ALA Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 71 removed outlier: 4.046A pdb=" N VAL Z 54 " --> pdb=" O ASN Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 99 Processing helix chain 'Z' and resid 102 through 124 removed outlier: 3.507A pdb=" N ALA Z 106 " --> pdb=" O TYR Z 102 " (cutoff:3.500A) Proline residue: Z 108 - end of helix removed outlier: 3.625A pdb=" N VAL Z 117 " --> pdb=" O ILE Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 214 removed outlier: 3.534A pdb=" N THR Z 194 " --> pdb=" O ASP Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 214 through 220 Processing helix chain 'Z' and resid 231 through 268 Proline residue: Z 243 - end of helix removed outlier: 3.818A pdb=" N ILE Z 254 " --> pdb=" O LEU Z 250 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 304 removed outlier: 3.737A pdb=" N PHE Z 285 " --> pdb=" O VAL Z 281 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR Z 304 " --> pdb=" O ASN Z 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 26 Processing helix chain 'Y' and resid 29 through 82 removed outlier: 4.013A pdb=" N MET Y 34 " --> pdb=" O TYR Y 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU Y 39 " --> pdb=" O ASN Y 35 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU Y 58 " --> pdb=" O VAL Y 54 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA Y 59 " --> pdb=" O ARG Y 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN Y 60 " --> pdb=" O GLU Y 56 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN Y 82 " --> pdb=" O LYS Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 139 removed outlier: 4.185A pdb=" N GLU Y 91 " --> pdb=" O ALA Y 87 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE Y 95 " --> pdb=" O GLU Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 140 through 147 Processing helix chain 'Y' and resid 148 through 158 removed outlier: 3.508A pdb=" N ILE Y 153 " --> pdb=" O HIS Y 149 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 29 removed outlier: 3.565A pdb=" N ILE V 16 " --> pdb=" O ILE V 12 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA V 27 " --> pdb=" O PHE V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 112 removed outlier: 4.097A pdb=" N ARG V 73 " --> pdb=" O ILE V 69 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN V 74 " --> pdb=" O ALA V 70 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU V 75 " --> pdb=" O ARG V 71 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE V 79 " --> pdb=" O GLU V 75 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU V 107 " --> pdb=" O GLU V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 120 Processing helix chain 'V' and resid 126 through 135 removed outlier: 3.743A pdb=" N VAL V 132 " --> pdb=" O ILE V 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 158 removed outlier: 3.982A pdb=" N SER V 156 " --> pdb=" O LEU V 152 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 41 removed outlier: 3.531A pdb=" N ASN U 17 " --> pdb=" O ALA U 13 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA U 27 " --> pdb=" O PHE U 23 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Proline residue: U 32 - end of helix Processing helix chain 'U' and resid 45 through 123 removed outlier: 3.784A pdb=" N ASP U 50 " --> pdb=" O GLU U 46 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA U 51 " --> pdb=" O SER U 47 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR U 65 " --> pdb=" O ALA U 61 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN U 89 " --> pdb=" O GLU U 85 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU U 91 " --> pdb=" O ALA U 87 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA U 92 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU U 93 " --> pdb=" O GLN U 89 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS U 106 " --> pdb=" O ALA U 102 " (cutoff:3.500A) Processing helix chain 'U' and resid 123 through 140 removed outlier: 3.524A pdb=" N THR U 133 " --> pdb=" O ALA U 129 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 156 removed outlier: 3.680A pdb=" N SER U 156 " --> pdb=" O LEU U 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 30 removed outlier: 3.753A pdb=" N ALA X 27 " --> pdb=" O PHE X 23 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU X 28 " --> pdb=" O ILE X 24 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR X 30 " --> pdb=" O ARG X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 148 removed outlier: 3.625A pdb=" N ASP X 50 " --> pdb=" O GLU X 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA X 51 " --> pdb=" O SER X 47 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN X 60 " --> pdb=" O GLU X 56 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG X 63 " --> pdb=" O ALA X 59 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN X 90 " --> pdb=" O ARG X 86 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU X 101 " --> pdb=" O GLN X 97 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN X 115 " --> pdb=" O ALA X 111 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU X 116 " --> pdb=" O GLN X 112 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU X 121 " --> pdb=" O ARG X 117 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA X 124 " --> pdb=" O MET X 120 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS X 125 " --> pdb=" O LEU X 121 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER X 126 " --> pdb=" O SER X 122 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN X 127 " --> pdb=" O GLU X 123 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP X 130 " --> pdb=" O SER X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 156 removed outlier: 3.705A pdb=" N ALA X 154 " --> pdb=" O ASP X 150 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU X 155 " --> pdb=" O ALA X 151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 39 through 41 1233 hydrogen bonds defined for protein. 3687 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: 3.83 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4082 1.34 - 1.45: 1573 1.45 - 1.57: 7499 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 13200 Sorted by residual: bond pdb=" N ILE T 39 " pdb=" CA ILE T 39 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.08e-02 8.57e+03 1.08e+01 bond pdb=" N VAL T 303 " pdb=" CA VAL T 303 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.72e+00 bond pdb=" N VAL X 33 " pdb=" CA VAL X 33 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.64e+00 bond pdb=" N PHE T 40 " pdb=" CA PHE T 40 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.09e-02 8.42e+03 8.34e+00 bond pdb=" N LEU V 140 " pdb=" CA LEU V 140 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.16e-02 7.43e+03 8.14e+00 ... (remaining 13195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 17059 1.64 - 3.28: 717 3.28 - 4.92: 110 4.92 - 6.56: 30 6.56 - 8.19: 6 Bond angle restraints: 17922 Sorted by residual: angle pdb=" N ILE Q 41 " pdb=" CA ILE Q 41 " pdb=" C ILE Q 41 " ideal model delta sigma weight residual 112.43 105.26 7.17 9.20e-01 1.18e+00 6.07e+01 angle pdb=" N ILE N 41 " pdb=" CA ILE N 41 " pdb=" C ILE N 41 " ideal model delta sigma weight residual 111.91 105.61 6.30 8.90e-01 1.26e+00 5.00e+01 angle pdb=" C CYS T 135 " pdb=" CA CYS T 135 " pdb=" CB CYS T 135 " ideal model delta sigma weight residual 116.54 110.80 5.74 1.15e+00 7.56e-01 2.49e+01 angle pdb=" C ALA U 158 " pdb=" CA ALA U 158 " pdb=" CB ALA U 158 " ideal model delta sigma weight residual 116.54 111.57 4.97 1.15e+00 7.56e-01 1.87e+01 angle pdb=" C PHE Z 221 " pdb=" CA PHE Z 221 " pdb=" CB PHE Z 221 " ideal model delta sigma weight residual 117.23 111.52 5.71 1.36e+00 5.41e-01 1.76e+01 ... (remaining 17917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 7038 16.92 - 33.84: 616 33.84 - 50.76: 116 50.76 - 67.68: 15 67.68 - 84.60: 12 Dihedral angle restraints: 7797 sinusoidal: 2666 harmonic: 5131 Sorted by residual: dihedral pdb=" CA PHE T 52 " pdb=" C PHE T 52 " pdb=" N VAL T 53 " pdb=" CA VAL T 53 " ideal model delta harmonic sigma weight residual 180.00 155.67 24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLN V 112 " pdb=" C GLN V 112 " pdb=" N ALA V 113 " pdb=" CA ALA V 113 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA T 212 " pdb=" C ALA T 212 " pdb=" N LEU T 213 " pdb=" CA LEU T 213 " ideal model delta harmonic sigma weight residual 180.00 160.40 19.60 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 7794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2030 0.095 - 0.190: 144 0.190 - 0.284: 13 0.284 - 0.379: 0 0.379 - 0.474: 1 Chirality restraints: 2188 Sorted by residual: chirality pdb=" CB ILE P 18 " pdb=" CA ILE P 18 " pdb=" CG1 ILE P 18 " pdb=" CG2 ILE P 18 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CB ILE O 41 " pdb=" CA ILE O 41 " pdb=" CG1 ILE O 41 " pdb=" CG2 ILE O 41 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE M 18 " pdb=" CA ILE M 18 " pdb=" CG1 ILE M 18 " pdb=" CG2 ILE M 18 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2185 not shown) Planarity restraints: 2335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 62 " 0.013 2.00e-02 2.50e+03 1.76e-02 5.43e+00 pdb=" CG PHE K 62 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE K 62 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE K 62 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE K 62 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE K 62 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE K 62 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 19 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO Q 20 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO Q 20 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO Q 20 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY L 23 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C GLY L 23 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY L 23 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE L 24 " -0.011 2.00e-02 2.50e+03 ... (remaining 2332 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2441 2.76 - 3.29: 15334 3.29 - 3.83: 23745 3.83 - 4.36: 27120 4.36 - 4.90: 42779 Nonbonded interactions: 111419 Sorted by model distance: nonbonded pdb=" O SER Q 29 " pdb=" NE2 GLN Q 33 " model vdw 2.223 3.120 nonbonded pdb=" O GLU X 123 " pdb=" OG SER X 126 " model vdw 2.225 3.040 nonbonded pdb=" NH2 ARG O 37 " pdb=" O GLN P 33 " model vdw 2.251 3.120 nonbonded pdb=" O ARG O 44 " pdb=" OG1 THR O 47 " model vdw 2.263 3.040 nonbonded pdb=" O LEU P 6 " pdb=" OG1 THR P 9 " model vdw 2.267 3.040 ... (remaining 111414 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 'H' selection = (chain 'I' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'J' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'K' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'L' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'M' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'N' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'O' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'P' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'Q' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) } ncs_group { reference = chain 'T' selection = (chain 'Z' and ((resid 19 through 41 and (name N or name CA or name C or name O \ or name CB )) or resid 42 through 72 or (resid 73 through 78 and (name N or name \ CA or name C or name O or name CB )) or resid 79 or (resid 80 and (name N or na \ me CA or name C or name O or name CB )) or resid 81 through 136 or resid 174 thr \ ough 182 or (resid 183 through 189 and (name N or name CA or name C or name O or \ name CB )) or resid 190 through 216 or (resid 217 through 225 and (name N or na \ me CA or name C or name O or name CB )) or resid 226 through 304)) } ncs_group { reference = (chain 'U' and resid 10 through 158) selection = (chain 'V' and ((resid 10 through 39 and (name N or name CA or name C or name O \ or name CB )) or resid 40 through 148 or (resid 149 through 158 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'X' and (resid 10 through 136 or (resid 137 through 140 and (name N or na \ me CA or name C or name O or name CB )) or resid 141 through 158)) selection = (chain 'Y' and ((resid 10 through 39 and (name N or name CA or name C or name O \ or name CB )) or resid 40 through 136 or (resid 137 through 140 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 141 through 147 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 or (resid 149 through 1 \ 58 and (name N or name CA or name C or name O or name CB )))) } 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: 3.020 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.530 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.005 0.059 13200 Z= 0.287 Angle : 0.754 8.194 17922 Z= 0.472 Chirality : 0.052 0.474 2188 Planarity : 0.004 0.051 2335 Dihedral : 13.780 84.596 4493 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1782 helix: 0.26 (0.13), residues: 1432 sheet: None (None), residues: 0 loop : -1.59 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Z 208 HIS 0.001 0.000 HIS V 149 PHE 0.040 0.002 PHE K 62 TYR 0.013 0.001 TYR X 65 ARG 0.003 0.000 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.19538 ( 1233) hydrogen bonds : angle 6.54537 ( 3687) covalent geometry : bond 0.00463 (13200) covalent geometry : angle 0.75422 (17922) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 TYR cc_start: 0.9573 (m-80) cc_final: 0.9373 (m-80) REVERT: I 15 LEU cc_start: 0.9493 (tp) cc_final: 0.9137 (tp) REVERT: I 51 ILE cc_start: 0.9590 (pt) cc_final: 0.9305 (pt) REVERT: I 53 ILE cc_start: 0.9699 (pt) cc_final: 0.9448 (pt) REVERT: I 57 GLU cc_start: 0.9034 (mp0) cc_final: 0.8038 (tp30) REVERT: J 55 PHE cc_start: 0.9791 (m-80) cc_final: 0.9408 (m-80) REVERT: J 59 LEU cc_start: 0.9529 (mm) cc_final: 0.9284 (mm) REVERT: J 62 PHE cc_start: 0.9321 (m-80) cc_final: 0.8984 (m-80) REVERT: J 68 PHE cc_start: 0.8828 (m-10) cc_final: 0.8554 (m-10) REVERT: K 15 LEU cc_start: 0.9247 (tp) cc_final: 0.9040 (tp) REVERT: K 55 PHE cc_start: 0.9375 (m-10) cc_final: 0.9129 (m-80) REVERT: K 57 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8775 (pt0) REVERT: K 62 PHE cc_start: 0.9472 (m-80) cc_final: 0.9083 (m-80) REVERT: L 27 ILE cc_start: 0.9678 (mm) cc_final: 0.9465 (mt) REVERT: M 49 MET cc_start: 0.9597 (ppp) cc_final: 0.9370 (ppp) REVERT: M 50 PHE cc_start: 0.8805 (m-10) cc_final: 0.8432 (m-10) REVERT: M 62 PHE cc_start: 0.9445 (m-80) cc_final: 0.8827 (m-80) REVERT: N 50 PHE cc_start: 0.9466 (m-80) cc_final: 0.9116 (m-80) REVERT: N 57 GLU cc_start: 0.9547 (mt-10) cc_final: 0.9321 (pt0) REVERT: N 68 PHE cc_start: 0.9218 (m-10) cc_final: 0.8940 (m-80) REVERT: O 15 LEU cc_start: 0.9805 (tp) cc_final: 0.9585 (tp) REVERT: O 47 THR cc_start: 0.9670 (p) cc_final: 0.9432 (p) REVERT: O 50 PHE cc_start: 0.9648 (m-10) cc_final: 0.9043 (m-80) REVERT: O 62 PHE cc_start: 0.8900 (t80) cc_final: 0.8302 (t80) REVERT: O 66 ILE cc_start: 0.9532 (mm) cc_final: 0.9207 (mm) REVERT: O 68 PHE cc_start: 0.9502 (m-80) cc_final: 0.9061 (m-80) REVERT: P 15 LEU cc_start: 0.9514 (tp) cc_final: 0.9299 (tp) REVERT: P 55 PHE cc_start: 0.9460 (m-80) cc_final: 0.9158 (m-80) REVERT: Q 55 PHE cc_start: 0.9355 (m-80) cc_final: 0.9066 (m-80) REVERT: T 122 TRP cc_start: 0.8900 (m-10) cc_final: 0.8683 (m-90) REVERT: T 241 VAL cc_start: 0.9424 (p) cc_final: 0.9210 (p) REVERT: T 244 PHE cc_start: 0.9251 (m-80) cc_final: 0.8967 (m-80) REVERT: T 277 TYR cc_start: 0.9252 (m-80) cc_final: 0.8793 (m-10) REVERT: T 287 GLN cc_start: 0.9642 (mp10) cc_final: 0.9296 (mp10) REVERT: T 291 PHE cc_start: 0.9515 (t80) cc_final: 0.9191 (t80) REVERT: Z 95 PHE cc_start: 0.9645 (m-10) cc_final: 0.9436 (m-80) REVERT: Z 206 GLU cc_start: 0.9310 (pp20) cc_final: 0.9025 (pp20) REVERT: Z 248 PHE cc_start: 0.9247 (m-10) cc_final: 0.9006 (m-80) REVERT: Z 251 PHE cc_start: 0.9233 (t80) cc_final: 0.8338 (t80) REVERT: Z 255 PHE cc_start: 0.9389 (t80) cc_final: 0.9135 (t80) REVERT: Y 34 MET cc_start: 0.9589 (mpp) cc_final: 0.9257 (mpp) REVERT: Y 120 MET cc_start: 0.9675 (mmp) cc_final: 0.9464 (mmp) REVERT: X 117 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7920 (mtt180) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2168 time to fit residues: 116.6273 Evaluate side-chains 285 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 30.0000 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 72 optimal weight: 50.0000 chunk 140 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 97 GLN V 112 GLN ** V 127 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 = 0.3593 r_free = 0.3593 target = 0.074002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.064325 restraints weight = 138691.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.065515 restraints weight = 76079.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.066303 restraints weight = 48040.345| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13200 Z= 0.189 Angle : 0.623 8.907 17922 Z= 0.348 Chirality : 0.042 0.188 2188 Planarity : 0.005 0.044 2335 Dihedral : 4.399 25.688 1925 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.69 % Allowed : 6.23 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 1782 helix: 0.56 (0.13), residues: 1475 sheet: -1.92 (1.96), residues: 10 loop : -2.09 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 208 HIS 0.002 0.001 HIS V 149 PHE 0.042 0.002 PHE I 62 TYR 0.012 0.001 TYR T 277 ARG 0.009 0.001 ARG V 43 Details of bonding type rmsd hydrogen bonds : bond 0.05557 ( 1233) hydrogen bonds : angle 4.78522 ( 3687) covalent geometry : bond 0.00363 (13200) covalent geometry : angle 0.62307 (17922) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 352 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 TYR cc_start: 0.9524 (m-80) cc_final: 0.9181 (m-80) REVERT: H 53 ILE cc_start: 0.9774 (tt) cc_final: 0.9526 (tt) REVERT: H 62 PHE cc_start: 0.9586 (m-80) cc_final: 0.9383 (m-80) REVERT: I 15 LEU cc_start: 0.9445 (tp) cc_final: 0.9126 (tp) REVERT: J 38 ASN cc_start: 0.9421 (t0) cc_final: 0.9068 (t0) REVERT: J 59 LEU cc_start: 0.9505 (mm) cc_final: 0.9237 (mm) REVERT: J 62 PHE cc_start: 0.9190 (m-80) cc_final: 0.8859 (m-80) REVERT: J 68 PHE cc_start: 0.8830 (m-10) cc_final: 0.8538 (m-10) REVERT: K 15 LEU cc_start: 0.9234 (tp) cc_final: 0.8996 (tp) REVERT: K 55 PHE cc_start: 0.9319 (m-10) cc_final: 0.9068 (m-80) REVERT: K 57 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8818 (pt0) REVERT: K 62 PHE cc_start: 0.9470 (m-80) cc_final: 0.9156 (m-80) REVERT: L 9 THR cc_start: 0.9535 (t) cc_final: 0.9310 (m) REVERT: L 70 ILE cc_start: 0.6938 (mt) cc_final: 0.6652 (mt) REVERT: M 50 PHE cc_start: 0.8783 (m-10) cc_final: 0.8530 (t80) REVERT: M 62 PHE cc_start: 0.9346 (m-80) cc_final: 0.8806 (m-80) REVERT: N 32 VAL cc_start: 0.9506 (p) cc_final: 0.9296 (p) REVERT: N 49 MET cc_start: 0.9155 (ppp) cc_final: 0.8896 (ppp) REVERT: N 50 PHE cc_start: 0.9279 (m-80) cc_final: 0.8999 (m-80) REVERT: N 57 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9260 (pt0) REVERT: O 15 LEU cc_start: 0.9793 (tp) cc_final: 0.9550 (tp) REVERT: O 32 VAL cc_start: 0.9749 (p) cc_final: 0.9421 (p) REVERT: O 37 ARG cc_start: 0.8897 (ppt170) cc_final: 0.8305 (ppt170) REVERT: O 50 PHE cc_start: 0.9667 (m-10) cc_final: 0.9076 (m-80) REVERT: O 68 PHE cc_start: 0.9413 (m-80) cc_final: 0.8958 (m-80) REVERT: P 55 PHE cc_start: 0.9464 (m-80) cc_final: 0.8939 (m-80) REVERT: Q 55 PHE cc_start: 0.9269 (m-80) cc_final: 0.9053 (m-80) REVERT: T 241 VAL cc_start: 0.9317 (p) cc_final: 0.9028 (p) REVERT: T 244 PHE cc_start: 0.9267 (m-80) cc_final: 0.8937 (m-80) REVERT: T 258 GLU cc_start: 0.9220 (pp20) cc_final: 0.9013 (pp20) REVERT: T 277 TYR cc_start: 0.9250 (m-80) cc_final: 0.8793 (m-10) REVERT: T 291 PHE cc_start: 0.9631 (t80) cc_final: 0.9273 (t80) REVERT: Z 206 GLU cc_start: 0.9274 (pp20) cc_final: 0.9015 (pp20) REVERT: Z 248 PHE cc_start: 0.9237 (m-10) cc_final: 0.9001 (m-80) REVERT: Z 251 PHE cc_start: 0.9224 (t80) cc_final: 0.8262 (t80) REVERT: Z 255 PHE cc_start: 0.9547 (t80) cc_final: 0.9259 (t80) REVERT: Z 264 MET cc_start: 0.8717 (ptt) cc_final: 0.8481 (ptt) REVERT: Z 277 TYR cc_start: 0.9631 (m-80) cc_final: 0.9122 (m-80) REVERT: Y 34 MET cc_start: 0.9545 (mpp) cc_final: 0.9215 (mpp) REVERT: Y 120 MET cc_start: 0.9615 (mmp) cc_final: 0.9389 (mmp) REVERT: X 117 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7725 (mtt180) REVERT: X 120 MET cc_start: 0.9422 (mpp) cc_final: 0.8631 (tpt) outliers start: 8 outliers final: 4 residues processed: 359 average time/residue: 0.2138 time to fit residues: 114.5699 Evaluate side-chains 285 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 281 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 81 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 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 = 0.3290 r_free = 0.3290 target = 0.050199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.040671 restraints weight = 123757.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.041565 restraints weight = 90603.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.042154 restraints weight = 71111.453| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13200 Z= 0.165 Angle : 0.627 8.800 17922 Z= 0.345 Chirality : 0.043 0.208 2188 Planarity : 0.004 0.053 2335 Dihedral : 4.415 26.348 1925 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.26 % Allowed : 5.88 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1782 helix: 0.57 (0.13), residues: 1474 sheet: -1.83 (1.96), residues: 10 loop : -2.03 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 208 HIS 0.001 0.000 HIS V 149 PHE 0.028 0.002 PHE N 62 TYR 0.009 0.001 TYR Y 65 ARG 0.007 0.000 ARG V 73 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 1233) hydrogen bonds : angle 4.70094 ( 3687) covalent geometry : bond 0.00324 (13200) covalent geometry : angle 0.62688 (17922) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 343 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 TYR cc_start: 0.9539 (m-80) cc_final: 0.8874 (m-80) REVERT: H 55 PHE cc_start: 0.9701 (m-80) cc_final: 0.9484 (m-80) REVERT: H 62 PHE cc_start: 0.9637 (m-80) cc_final: 0.9420 (m-80) REVERT: I 15 LEU cc_start: 0.9439 (tp) cc_final: 0.9133 (tp) REVERT: I 35 ILE cc_start: 0.9093 (tp) cc_final: 0.8869 (tp) REVERT: I 40 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8260 (mp0) REVERT: I 51 ILE cc_start: 0.9517 (pt) cc_final: 0.9253 (pt) REVERT: J 47 THR cc_start: 0.9653 (p) cc_final: 0.9408 (p) REVERT: J 50 PHE cc_start: 0.9388 (m-80) cc_final: 0.9091 (m-80) REVERT: J 59 LEU cc_start: 0.9546 (mm) cc_final: 0.9270 (mm) REVERT: J 62 PHE cc_start: 0.9225 (m-80) cc_final: 0.8888 (m-80) REVERT: K 27 ILE cc_start: 0.9488 (mt) cc_final: 0.9274 (mt) REVERT: K 55 PHE cc_start: 0.9324 (m-10) cc_final: 0.9103 (m-80) REVERT: K 57 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8851 (pt0) REVERT: K 62 PHE cc_start: 0.9504 (m-80) cc_final: 0.9156 (m-80) REVERT: L 9 THR cc_start: 0.9535 (t) cc_final: 0.9301 (m) REVERT: L 26 ILE cc_start: 0.9761 (tp) cc_final: 0.9533 (tt) REVERT: L 70 ILE cc_start: 0.6961 (mt) cc_final: 0.6664 (mt) REVERT: M 50 PHE cc_start: 0.8734 (m-10) cc_final: 0.8477 (t80) REVERT: M 55 PHE cc_start: 0.9564 (m-80) cc_final: 0.9354 (m-80) REVERT: M 62 PHE cc_start: 0.9348 (m-80) cc_final: 0.8866 (m-80) REVERT: N 15 LEU cc_start: 0.9390 (tp) cc_final: 0.9187 (tp) REVERT: N 32 VAL cc_start: 0.9448 (p) cc_final: 0.9239 (p) REVERT: N 49 MET cc_start: 0.9273 (ppp) cc_final: 0.9067 (ppp) REVERT: N 50 PHE cc_start: 0.9310 (m-80) cc_final: 0.9086 (m-80) REVERT: N 57 GLU cc_start: 0.9531 (mt-10) cc_final: 0.9227 (pt0) REVERT: O 32 VAL cc_start: 0.9743 (p) cc_final: 0.9486 (p) REVERT: O 37 ARG cc_start: 0.8802 (ppt170) cc_final: 0.8425 (ppt170) REVERT: O 47 THR cc_start: 0.9670 (p) cc_final: 0.9456 (p) REVERT: O 50 PHE cc_start: 0.9699 (m-80) cc_final: 0.9086 (m-80) REVERT: O 62 PHE cc_start: 0.8895 (t80) cc_final: 0.8536 (t80) REVERT: O 68 PHE cc_start: 0.9329 (m-80) cc_final: 0.8894 (m-80) REVERT: P 55 PHE cc_start: 0.9454 (m-80) cc_final: 0.8938 (m-80) REVERT: T 241 VAL cc_start: 0.9409 (p) cc_final: 0.9146 (p) REVERT: T 244 PHE cc_start: 0.9285 (m-80) cc_final: 0.8986 (m-80) REVERT: T 277 TYR cc_start: 0.9181 (m-80) cc_final: 0.8658 (m-10) REVERT: T 285 PHE cc_start: 0.9592 (m-80) cc_final: 0.9227 (m-80) REVERT: T 291 PHE cc_start: 0.9599 (t80) cc_final: 0.9360 (t80) REVERT: Z 206 GLU cc_start: 0.9268 (pp20) cc_final: 0.9016 (pp20) REVERT: Z 248 PHE cc_start: 0.9217 (m-10) cc_final: 0.8967 (m-80) REVERT: Z 251 PHE cc_start: 0.9169 (t80) cc_final: 0.8259 (t80) REVERT: Z 255 PHE cc_start: 0.9512 (t80) cc_final: 0.9292 (t80) REVERT: Z 264 MET cc_start: 0.8636 (ptt) cc_final: 0.8350 (ptt) REVERT: Z 277 TYR cc_start: 0.9665 (m-80) cc_final: 0.9117 (m-80) REVERT: Y 120 MET cc_start: 0.9601 (mmp) cc_final: 0.9358 (mmp) REVERT: V 127 GLN cc_start: 0.9398 (pt0) cc_final: 0.9101 (pm20) REVERT: U 131 LEU cc_start: 0.9627 (mm) cc_final: 0.9266 (pp) REVERT: X 117 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7996 (mtt180) REVERT: X 120 MET cc_start: 0.9204 (mpp) cc_final: 0.8750 (tmm) REVERT: X 130 ASP cc_start: 0.9613 (m-30) cc_final: 0.9264 (p0) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 0.2074 time to fit residues: 107.1991 Evaluate side-chains 282 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 72 optimal weight: 50.0000 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 192 ASN ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 ASN ** V 127 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 = 0.3275 r_free = 0.3275 target = 0.049654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.040257 restraints weight = 122941.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.041017 restraints weight = 91016.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.041794 restraints weight = 73460.311| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13200 Z= 0.181 Angle : 0.647 9.488 17922 Z= 0.354 Chirality : 0.044 0.238 2188 Planarity : 0.004 0.066 2335 Dihedral : 4.374 26.002 1925 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.52 % Allowed : 3.98 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 1782 helix: 0.62 (0.13), residues: 1485 sheet: -1.90 (1.92), residues: 10 loop : -1.98 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 208 HIS 0.002 0.001 HIS V 149 PHE 0.033 0.002 PHE N 62 TYR 0.010 0.001 TYR T 277 ARG 0.007 0.000 ARG T 249 Details of bonding type rmsd hydrogen bonds : bond 0.04904 ( 1233) hydrogen bonds : angle 4.61450 ( 3687) covalent geometry : bond 0.00353 (13200) covalent geometry : angle 0.64702 (17922) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 342 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 TYR cc_start: 0.9466 (m-80) cc_final: 0.8804 (m-80) REVERT: H 55 PHE cc_start: 0.9661 (m-80) cc_final: 0.9439 (m-80) REVERT: H 62 PHE cc_start: 0.9621 (m-80) cc_final: 0.9397 (m-80) REVERT: I 15 LEU cc_start: 0.9436 (tp) cc_final: 0.9112 (tp) REVERT: I 49 MET cc_start: 0.9576 (ptt) cc_final: 0.9227 (tmm) REVERT: J 59 LEU cc_start: 0.9543 (mm) cc_final: 0.9271 (mm) REVERT: J 62 PHE cc_start: 0.9244 (m-10) cc_final: 0.8914 (m-80) REVERT: J 68 PHE cc_start: 0.8664 (m-10) cc_final: 0.8429 (m-10) REVERT: K 51 ILE cc_start: 0.9015 (pt) cc_final: 0.8655 (pt) REVERT: K 55 PHE cc_start: 0.9315 (m-10) cc_final: 0.9076 (m-80) REVERT: K 62 PHE cc_start: 0.9518 (m-80) cc_final: 0.9131 (m-80) REVERT: L 9 THR cc_start: 0.9510 (t) cc_final: 0.9256 (m) REVERT: L 26 ILE cc_start: 0.9704 (tp) cc_final: 0.9471 (tt) REVERT: L 70 ILE cc_start: 0.7102 (mt) cc_final: 0.6786 (mt) REVERT: M 50 PHE cc_start: 0.8767 (m-10) cc_final: 0.8500 (t80) REVERT: M 62 PHE cc_start: 0.9391 (m-80) cc_final: 0.8934 (m-80) REVERT: N 49 MET cc_start: 0.9275 (ppp) cc_final: 0.9075 (ppp) REVERT: N 50 PHE cc_start: 0.9316 (m-80) cc_final: 0.9086 (m-80) REVERT: N 57 GLU cc_start: 0.9563 (mt-10) cc_final: 0.9299 (mt-10) REVERT: O 32 VAL cc_start: 0.9748 (p) cc_final: 0.9521 (p) REVERT: O 50 PHE cc_start: 0.9717 (m-80) cc_final: 0.9106 (m-80) REVERT: O 68 PHE cc_start: 0.9318 (m-80) cc_final: 0.8863 (m-80) REVERT: P 55 PHE cc_start: 0.9395 (m-80) cc_final: 0.8994 (m-80) REVERT: Q 55 PHE cc_start: 0.9305 (m-80) cc_final: 0.8958 (m-80) REVERT: T 241 VAL cc_start: 0.9430 (p) cc_final: 0.9131 (m) REVERT: T 244 PHE cc_start: 0.9309 (m-80) cc_final: 0.9034 (m-80) REVERT: T 277 TYR cc_start: 0.9169 (m-80) cc_final: 0.8622 (m-10) REVERT: T 285 PHE cc_start: 0.9601 (m-80) cc_final: 0.9249 (m-80) REVERT: T 291 PHE cc_start: 0.9604 (t80) cc_final: 0.9324 (t80) REVERT: Z 206 GLU cc_start: 0.9265 (pp20) cc_final: 0.8994 (pp20) REVERT: Z 248 PHE cc_start: 0.9206 (m-10) cc_final: 0.8967 (m-80) REVERT: Z 251 PHE cc_start: 0.9195 (t80) cc_final: 0.8319 (t80) REVERT: Z 277 TYR cc_start: 0.9664 (m-80) cc_final: 0.9185 (m-80) REVERT: Y 34 MET cc_start: 0.9524 (mpp) cc_final: 0.9146 (mpp) REVERT: Y 120 MET cc_start: 0.9605 (mmp) cc_final: 0.9330 (mmp) REVERT: V 88 LYS cc_start: 0.9857 (pttp) cc_final: 0.9614 (pttp) REVERT: V 127 GLN cc_start: 0.9496 (pt0) cc_final: 0.9042 (pm20) REVERT: X 117 ARG cc_start: 0.8336 (mtt180) cc_final: 0.8059 (mtt180) REVERT: X 120 MET cc_start: 0.9235 (mpp) cc_final: 0.8508 (tpt) REVERT: X 130 ASP cc_start: 0.9616 (m-30) cc_final: 0.9273 (p0) outliers start: 6 outliers final: 2 residues processed: 346 average time/residue: 0.2101 time to fit residues: 109.3810 Evaluate side-chains 280 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 278 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 32 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 4 optimal weight: 0.0570 chunk 118 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 GLN ** V 127 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 = 0.3298 r_free = 0.3298 target = 0.050711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.041093 restraints weight = 119473.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.041884 restraints weight = 88115.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042707 restraints weight = 70559.224| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13200 Z= 0.149 Angle : 0.644 8.969 17922 Z= 0.346 Chirality : 0.044 0.199 2188 Planarity : 0.004 0.053 2335 Dihedral : 4.389 26.502 1925 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.26 % Allowed : 3.20 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1782 helix: 0.71 (0.13), residues: 1469 sheet: -1.80 (1.95), residues: 10 loop : -2.16 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.001 0.000 HIS V 149 PHE 0.052 0.002 PHE J 50 TYR 0.011 0.001 TYR T 277 ARG 0.013 0.000 ARG U 63 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 1233) hydrogen bonds : angle 4.51972 ( 3687) covalent geometry : bond 0.00295 (13200) covalent geometry : angle 0.64378 (17922) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 349 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 26 ILE cc_start: 0.9324 (tp) cc_final: 0.9096 (tt) REVERT: H 48 TYR cc_start: 0.9490 (m-80) cc_final: 0.8841 (m-80) REVERT: I 15 LEU cc_start: 0.9351 (tp) cc_final: 0.9036 (tp) REVERT: I 40 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8203 (mp0) REVERT: I 49 MET cc_start: 0.9516 (ptt) cc_final: 0.9242 (tmm) REVERT: J 68 PHE cc_start: 0.8576 (m-10) cc_final: 0.8355 (m-80) REVERT: K 27 ILE cc_start: 0.9494 (mt) cc_final: 0.9284 (mt) REVERT: K 48 TYR cc_start: 0.8619 (m-10) cc_final: 0.7960 (m-80) REVERT: K 51 ILE cc_start: 0.9050 (pt) cc_final: 0.8644 (pt) REVERT: K 55 PHE cc_start: 0.9320 (m-10) cc_final: 0.9099 (m-80) REVERT: K 62 PHE cc_start: 0.9510 (m-80) cc_final: 0.9132 (m-80) REVERT: L 26 ILE cc_start: 0.9642 (tp) cc_final: 0.9385 (tt) REVERT: M 50 PHE cc_start: 0.8687 (m-10) cc_final: 0.8462 (t80) REVERT: M 62 PHE cc_start: 0.9406 (m-80) cc_final: 0.8927 (m-80) REVERT: N 15 LEU cc_start: 0.9237 (tp) cc_final: 0.9025 (tp) REVERT: N 57 GLU cc_start: 0.9550 (mt-10) cc_final: 0.9307 (mt-10) REVERT: N 68 PHE cc_start: 0.9305 (m-80) cc_final: 0.9095 (m-80) REVERT: O 32 VAL cc_start: 0.9707 (p) cc_final: 0.9470 (p) REVERT: O 50 PHE cc_start: 0.9741 (m-80) cc_final: 0.9137 (m-80) REVERT: O 68 PHE cc_start: 0.9253 (m-80) cc_final: 0.8788 (m-80) REVERT: P 55 PHE cc_start: 0.9411 (m-80) cc_final: 0.9019 (m-80) REVERT: Q 55 PHE cc_start: 0.9276 (m-80) cc_final: 0.8968 (m-80) REVERT: T 241 VAL cc_start: 0.9441 (p) cc_final: 0.9210 (p) REVERT: T 244 PHE cc_start: 0.9240 (m-80) cc_final: 0.8971 (m-80) REVERT: T 277 TYR cc_start: 0.9160 (m-80) cc_final: 0.8613 (m-10) REVERT: T 285 PHE cc_start: 0.9627 (m-80) cc_final: 0.9326 (m-80) REVERT: T 290 ILE cc_start: 0.9609 (pt) cc_final: 0.9327 (pt) REVERT: T 291 PHE cc_start: 0.9602 (t80) cc_final: 0.9285 (t80) REVERT: Z 206 GLU cc_start: 0.9304 (pp20) cc_final: 0.9042 (pp20) REVERT: Z 248 PHE cc_start: 0.9153 (m-10) cc_final: 0.8861 (m-80) REVERT: Z 251 PHE cc_start: 0.9257 (t80) cc_final: 0.8469 (t80) REVERT: Z 277 TYR cc_start: 0.9691 (m-80) cc_final: 0.9210 (m-80) REVERT: Y 34 MET cc_start: 0.9476 (mpp) cc_final: 0.9129 (mpp) REVERT: Y 120 MET cc_start: 0.9627 (mmp) cc_final: 0.9137 (ttt) REVERT: V 120 MET cc_start: 0.9221 (ptp) cc_final: 0.8697 (ptp) REVERT: V 127 GLN cc_start: 0.9522 (pt0) cc_final: 0.9094 (pm20) REVERT: U 131 LEU cc_start: 0.9632 (mm) cc_final: 0.9280 (pp) REVERT: X 120 MET cc_start: 0.9112 (mpp) cc_final: 0.8486 (tpt) REVERT: X 130 ASP cc_start: 0.9632 (m-30) cc_final: 0.9303 (p0) outliers start: 3 outliers final: 0 residues processed: 352 average time/residue: 0.2113 time to fit residues: 111.7846 Evaluate side-chains 287 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 134 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 GLN ** V 127 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 = 0.3292 r_free = 0.3292 target = 0.050561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.041044 restraints weight = 123528.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.041853 restraints weight = 91241.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.042656 restraints weight = 72993.380| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13200 Z= 0.155 Angle : 0.645 9.015 17922 Z= 0.349 Chirality : 0.044 0.260 2188 Planarity : 0.004 0.063 2335 Dihedral : 4.340 26.194 1925 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1782 helix: 0.70 (0.13), residues: 1498 sheet: -1.90 (1.95), residues: 10 loop : -1.86 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 PHE 0.051 0.002 PHE H 62 TYR 0.009 0.001 TYR T 277 ARG 0.010 0.000 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 1233) hydrogen bonds : angle 4.46861 ( 3687) covalent geometry : bond 0.00316 (13200) covalent geometry : angle 0.64461 (17922) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 TYR cc_start: 0.9426 (m-80) cc_final: 0.9106 (m-80) REVERT: I 15 LEU cc_start: 0.9351 (tp) cc_final: 0.9008 (tp) REVERT: I 40 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8165 (mp0) REVERT: J 59 LEU cc_start: 0.9533 (mm) cc_final: 0.9279 (mm) REVERT: J 62 PHE cc_start: 0.9216 (m-10) cc_final: 0.8928 (m-80) REVERT: K 48 TYR cc_start: 0.8675 (m-10) cc_final: 0.7986 (m-80) REVERT: K 51 ILE cc_start: 0.9037 (pt) cc_final: 0.8603 (pt) REVERT: K 55 PHE cc_start: 0.9303 (m-10) cc_final: 0.9079 (m-80) REVERT: K 62 PHE cc_start: 0.9512 (m-80) cc_final: 0.9127 (m-80) REVERT: L 9 THR cc_start: 0.9502 (t) cc_final: 0.9279 (m) REVERT: L 26 ILE cc_start: 0.9703 (tp) cc_final: 0.9476 (tt) REVERT: M 50 PHE cc_start: 0.8687 (m-10) cc_final: 0.8471 (t80) REVERT: M 62 PHE cc_start: 0.9392 (m-80) cc_final: 0.8908 (m-80) REVERT: N 15 LEU cc_start: 0.9283 (tp) cc_final: 0.9067 (tp) REVERT: N 49 MET cc_start: 0.9284 (ppp) cc_final: 0.9068 (ppp) REVERT: N 50 PHE cc_start: 0.9241 (m-80) cc_final: 0.8907 (m-80) REVERT: N 57 GLU cc_start: 0.9585 (mt-10) cc_final: 0.9337 (mt-10) REVERT: N 68 PHE cc_start: 0.9278 (m-80) cc_final: 0.9061 (m-80) REVERT: O 50 PHE cc_start: 0.9734 (m-80) cc_final: 0.9103 (m-80) REVERT: O 62 PHE cc_start: 0.8965 (t80) cc_final: 0.8698 (t80) REVERT: O 68 PHE cc_start: 0.9221 (m-80) cc_final: 0.8750 (m-80) REVERT: P 49 MET cc_start: 0.9476 (ptp) cc_final: 0.9269 (ptp) REVERT: P 55 PHE cc_start: 0.9398 (m-80) cc_final: 0.9110 (m-80) REVERT: Q 55 PHE cc_start: 0.9248 (m-80) cc_final: 0.8936 (m-80) REVERT: T 244 PHE cc_start: 0.9298 (m-80) cc_final: 0.8999 (m-80) REVERT: T 277 TYR cc_start: 0.9120 (m-80) cc_final: 0.8535 (m-10) REVERT: T 285 PHE cc_start: 0.9569 (m-80) cc_final: 0.9303 (m-80) REVERT: T 287 GLN cc_start: 0.9489 (mp-120) cc_final: 0.9208 (mm-40) REVERT: T 291 PHE cc_start: 0.9566 (t80) cc_final: 0.9287 (t80) REVERT: Z 206 GLU cc_start: 0.9260 (pp20) cc_final: 0.8987 (pp20) REVERT: Z 251 PHE cc_start: 0.9191 (t80) cc_final: 0.8352 (t80) REVERT: Z 277 TYR cc_start: 0.9654 (m-80) cc_final: 0.9269 (m-80) REVERT: Y 34 MET cc_start: 0.9470 (mpp) cc_final: 0.9095 (mpp) REVERT: Y 120 MET cc_start: 0.9608 (mmp) cc_final: 0.9361 (mmp) REVERT: V 120 MET cc_start: 0.9189 (ptp) cc_final: 0.8769 (ptp) REVERT: V 127 GLN cc_start: 0.9444 (pt0) cc_final: 0.9045 (pm20) REVERT: X 120 MET cc_start: 0.9205 (mpp) cc_final: 0.8494 (tpt) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.2225 time to fit residues: 115.2162 Evaluate side-chains 278 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 150 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.075806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.066038 restraints weight = 136440.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.067277 restraints weight = 75284.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.068107 restraints weight = 47636.850| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13200 Z= 0.155 Angle : 0.674 10.341 17922 Z= 0.364 Chirality : 0.045 0.321 2188 Planarity : 0.005 0.097 2335 Dihedral : 4.387 26.431 1925 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1782 helix: 0.69 (0.13), residues: 1487 sheet: None (None), residues: 0 loop : -1.99 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.001 0.000 HIS V 149 PHE 0.038 0.002 PHE N 62 TYR 0.008 0.001 TYR O 48 ARG 0.008 0.000 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 1233) hydrogen bonds : angle 4.53931 ( 3687) covalent geometry : bond 0.00319 (13200) covalent geometry : angle 0.67409 (17922) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 26 ILE cc_start: 0.9469 (tp) cc_final: 0.9223 (tt) REVERT: H 48 TYR cc_start: 0.9391 (m-80) cc_final: 0.8675 (m-80) REVERT: H 62 PHE cc_start: 0.9584 (m-80) cc_final: 0.9383 (m-80) REVERT: I 35 ILE cc_start: 0.8947 (tp) cc_final: 0.8718 (tp) REVERT: K 5 ASN cc_start: 0.9453 (p0) cc_final: 0.9176 (p0) REVERT: K 27 ILE cc_start: 0.9524 (mt) cc_final: 0.9312 (mt) REVERT: K 48 TYR cc_start: 0.8757 (m-10) cc_final: 0.8051 (m-80) REVERT: K 51 ILE cc_start: 0.9005 (pt) cc_final: 0.8506 (pt) REVERT: K 55 PHE cc_start: 0.9258 (m-10) cc_final: 0.9011 (m-80) REVERT: K 57 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8851 (pt0) REVERT: K 62 PHE cc_start: 0.9431 (m-80) cc_final: 0.9056 (m-80) REVERT: L 9 THR cc_start: 0.9478 (t) cc_final: 0.9244 (m) REVERT: L 26 ILE cc_start: 0.9789 (tp) cc_final: 0.9537 (tt) REVERT: L 70 ILE cc_start: 0.6789 (mt) cc_final: 0.6567 (mt) REVERT: M 27 ILE cc_start: 0.9679 (pt) cc_final: 0.9382 (mm) REVERT: M 50 PHE cc_start: 0.8650 (m-10) cc_final: 0.8423 (t80) REVERT: M 62 PHE cc_start: 0.9344 (m-80) cc_final: 0.8868 (m-80) REVERT: N 15 LEU cc_start: 0.9129 (tp) cc_final: 0.8915 (tp) REVERT: N 49 MET cc_start: 0.9214 (ppp) cc_final: 0.8917 (ppp) REVERT: N 50 PHE cc_start: 0.9169 (m-80) cc_final: 0.8754 (m-80) REVERT: N 57 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9227 (mt-10) REVERT: N 68 PHE cc_start: 0.9322 (m-80) cc_final: 0.9109 (m-80) REVERT: O 50 PHE cc_start: 0.9727 (m-80) cc_final: 0.9108 (m-80) REVERT: O 62 PHE cc_start: 0.8926 (t80) cc_final: 0.8616 (t80) REVERT: O 68 PHE cc_start: 0.9201 (m-80) cc_final: 0.8722 (m-80) REVERT: P 55 PHE cc_start: 0.9376 (m-80) cc_final: 0.9056 (m-80) REVERT: Q 55 PHE cc_start: 0.9187 (m-80) cc_final: 0.8889 (m-80) REVERT: T 244 PHE cc_start: 0.9238 (m-80) cc_final: 0.8880 (m-80) REVERT: T 261 LEU cc_start: 0.9772 (tp) cc_final: 0.9548 (mm) REVERT: T 277 TYR cc_start: 0.9044 (m-80) cc_final: 0.8558 (m-80) REVERT: T 285 PHE cc_start: 0.9577 (m-80) cc_final: 0.9326 (m-80) REVERT: T 287 GLN cc_start: 0.9463 (mp-120) cc_final: 0.9178 (mp10) REVERT: T 290 ILE cc_start: 0.9626 (pt) cc_final: 0.9334 (pt) REVERT: T 291 PHE cc_start: 0.9591 (t80) cc_final: 0.9184 (t80) REVERT: Z 92 TYR cc_start: 0.9598 (t80) cc_final: 0.9384 (t80) REVERT: Z 206 GLU cc_start: 0.9267 (pp20) cc_final: 0.8985 (pp20) REVERT: Z 251 PHE cc_start: 0.9232 (t80) cc_final: 0.8416 (t80) REVERT: Z 277 TYR cc_start: 0.9583 (m-80) cc_final: 0.9167 (m-80) REVERT: Y 34 MET cc_start: 0.9504 (mpp) cc_final: 0.9112 (mpp) REVERT: Y 120 MET cc_start: 0.9590 (mmp) cc_final: 0.9347 (mmp) REVERT: V 127 GLN cc_start: 0.9462 (pt0) cc_final: 0.9074 (pm20) REVERT: U 84 GLN cc_start: 0.9396 (mp10) cc_final: 0.9169 (mp10) REVERT: U 131 LEU cc_start: 0.9612 (mm) cc_final: 0.9224 (pp) REVERT: X 115 GLN cc_start: 0.9621 (pm20) cc_final: 0.9395 (pm20) REVERT: X 120 MET cc_start: 0.9333 (mpp) cc_final: 0.8533 (tpt) outliers start: 1 outliers final: 1 residues processed: 342 average time/residue: 0.2081 time to fit residues: 106.4432 Evaluate side-chains 284 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 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 = 0.3602 r_free = 0.3602 target = 0.074751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.065003 restraints weight = 137729.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.066217 restraints weight = 76191.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.067044 restraints weight = 48324.975| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13200 Z= 0.168 Angle : 0.687 14.844 17922 Z= 0.368 Chirality : 0.046 0.353 2188 Planarity : 0.004 0.053 2335 Dihedral : 4.369 25.978 1925 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1782 helix: 0.73 (0.13), residues: 1495 sheet: None (None), residues: 0 loop : -1.81 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.001 0.000 HIS Y 149 PHE 0.030 0.002 PHE I 62 TYR 0.010 0.001 TYR X 65 ARG 0.018 0.000 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 1233) hydrogen bonds : angle 4.57505 ( 3687) covalent geometry : bond 0.00343 (13200) covalent geometry : angle 0.68740 (17922) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 TYR cc_start: 0.9423 (m-80) cc_final: 0.8704 (m-80) REVERT: H 62 PHE cc_start: 0.9603 (m-80) cc_final: 0.9392 (m-80) REVERT: I 35 ILE cc_start: 0.9076 (tp) cc_final: 0.8862 (tp) REVERT: J 59 LEU cc_start: 0.9524 (mm) cc_final: 0.9238 (mm) REVERT: J 68 PHE cc_start: 0.8598 (m-10) cc_final: 0.8242 (m-80) REVERT: K 51 ILE cc_start: 0.8980 (pt) cc_final: 0.8556 (pt) REVERT: K 55 PHE cc_start: 0.9214 (m-10) cc_final: 0.8953 (m-80) REVERT: K 62 PHE cc_start: 0.9464 (m-80) cc_final: 0.9086 (m-80) REVERT: L 9 THR cc_start: 0.9477 (t) cc_final: 0.9248 (m) REVERT: L 26 ILE cc_start: 0.9774 (tp) cc_final: 0.9567 (tt) REVERT: L 70 ILE cc_start: 0.6762 (mt) cc_final: 0.6526 (mt) REVERT: M 27 ILE cc_start: 0.9680 (pt) cc_final: 0.9382 (mm) REVERT: M 50 PHE cc_start: 0.8664 (m-10) cc_final: 0.8421 (t80) REVERT: M 62 PHE cc_start: 0.9383 (m-80) cc_final: 0.9038 (m-80) REVERT: N 49 MET cc_start: 0.9230 (ppp) cc_final: 0.8969 (ptt) REVERT: N 57 GLU cc_start: 0.9602 (mt-10) cc_final: 0.9297 (mt-10) REVERT: N 68 PHE cc_start: 0.9359 (m-80) cc_final: 0.9155 (m-80) REVERT: O 50 PHE cc_start: 0.9729 (m-80) cc_final: 0.9137 (m-80) REVERT: O 62 PHE cc_start: 0.8988 (t80) cc_final: 0.8679 (t80) REVERT: O 68 PHE cc_start: 0.9239 (m-80) cc_final: 0.8743 (m-80) REVERT: P 55 PHE cc_start: 0.9417 (m-80) cc_final: 0.9105 (m-80) REVERT: Q 55 PHE cc_start: 0.9205 (m-80) cc_final: 0.8917 (m-80) REVERT: T 244 PHE cc_start: 0.9274 (m-80) cc_final: 0.8935 (m-80) REVERT: T 261 LEU cc_start: 0.9773 (tp) cc_final: 0.9543 (mm) REVERT: T 277 TYR cc_start: 0.9113 (m-80) cc_final: 0.8645 (m-80) REVERT: T 285 PHE cc_start: 0.9585 (m-80) cc_final: 0.9305 (m-80) REVERT: T 287 GLN cc_start: 0.9482 (mp-120) cc_final: 0.9150 (mm-40) REVERT: T 290 ILE cc_start: 0.9627 (pt) cc_final: 0.9338 (pt) REVERT: T 291 PHE cc_start: 0.9635 (t80) cc_final: 0.9230 (t80) REVERT: Z 92 TYR cc_start: 0.9605 (t80) cc_final: 0.9402 (t80) REVERT: Z 206 GLU cc_start: 0.9294 (pp20) cc_final: 0.9008 (pp20) REVERT: Z 248 PHE cc_start: 0.9183 (m-10) cc_final: 0.8982 (m-80) REVERT: Z 251 PHE cc_start: 0.9217 (t80) cc_final: 0.8234 (t80) REVERT: Z 277 TYR cc_start: 0.9632 (m-80) cc_final: 0.9161 (m-80) REVERT: Y 34 MET cc_start: 0.9500 (mpp) cc_final: 0.9099 (mpp) REVERT: Y 91 GLU cc_start: 0.9616 (tm-30) cc_final: 0.8690 (mm-30) REVERT: Y 106 LYS cc_start: 0.9522 (ptpp) cc_final: 0.9111 (ptpt) REVERT: Y 120 MET cc_start: 0.9598 (mmp) cc_final: 0.9327 (mmp) REVERT: V 120 MET cc_start: 0.9224 (ptp) cc_final: 0.8856 (ptp) REVERT: V 127 GLN cc_start: 0.9391 (pt0) cc_final: 0.9168 (pm20) REVERT: X 120 MET cc_start: 0.9394 (mpp) cc_final: 0.8626 (tpt) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2239 time to fit residues: 115.1007 Evaluate side-chains 274 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 146 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 145 optimal weight: 0.2980 chunk 140 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 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 = 0.3305 r_free = 0.3305 target = 0.051105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041686 restraints weight = 119913.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.042547 restraints weight = 88982.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.043299 restraints weight = 71099.284| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13200 Z= 0.155 Angle : 0.697 14.304 17922 Z= 0.372 Chirality : 0.046 0.255 2188 Planarity : 0.004 0.060 2335 Dihedral : 4.434 27.576 1925 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.20), residues: 1782 helix: 0.74 (0.13), residues: 1487 sheet: None (None), residues: 0 loop : -1.99 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 208 HIS 0.001 0.000 HIS V 149 PHE 0.040 0.002 PHE J 50 TYR 0.009 0.001 TYR X 65 ARG 0.011 0.000 ARG V 73 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 1233) hydrogen bonds : angle 4.53156 ( 3687) covalent geometry : bond 0.00322 (13200) covalent geometry : angle 0.69666 (17922) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 TYR cc_start: 0.9453 (m-80) cc_final: 0.8771 (m-80) REVERT: H 55 PHE cc_start: 0.9703 (m-80) cc_final: 0.9492 (m-80) REVERT: H 62 PHE cc_start: 0.9647 (m-80) cc_final: 0.9437 (m-80) REVERT: I 35 ILE cc_start: 0.9093 (tp) cc_final: 0.8835 (tp) REVERT: I 50 PHE cc_start: 0.9270 (m-80) cc_final: 0.8954 (m-80) REVERT: J 62 PHE cc_start: 0.9076 (m-80) cc_final: 0.8856 (m-80) REVERT: J 68 PHE cc_start: 0.8592 (m-10) cc_final: 0.8358 (m-80) REVERT: K 48 TYR cc_start: 0.8646 (m-10) cc_final: 0.7945 (m-80) REVERT: K 51 ILE cc_start: 0.9026 (pt) cc_final: 0.8605 (pt) REVERT: K 55 PHE cc_start: 0.9224 (m-10) cc_final: 0.8925 (m-80) REVERT: K 57 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8799 (pt0) REVERT: K 62 PHE cc_start: 0.9481 (m-80) cc_final: 0.9157 (m-80) REVERT: L 9 THR cc_start: 0.9483 (t) cc_final: 0.9255 (m) REVERT: L 53 ILE cc_start: 0.9071 (pt) cc_final: 0.8865 (pt) REVERT: L 70 ILE cc_start: 0.6882 (mt) cc_final: 0.6645 (mt) REVERT: M 27 ILE cc_start: 0.9700 (pt) cc_final: 0.9368 (mm) REVERT: M 50 PHE cc_start: 0.8690 (m-10) cc_final: 0.8423 (t80) REVERT: M 62 PHE cc_start: 0.9450 (m-80) cc_final: 0.9042 (m-80) REVERT: N 15 LEU cc_start: 0.9265 (tp) cc_final: 0.9044 (tp) REVERT: N 47 THR cc_start: 0.9551 (p) cc_final: 0.9335 (p) REVERT: N 50 PHE cc_start: 0.9303 (m-10) cc_final: 0.8985 (m-80) REVERT: N 57 GLU cc_start: 0.9649 (mt-10) cc_final: 0.9337 (mt-10) REVERT: O 50 PHE cc_start: 0.9744 (m-80) cc_final: 0.9148 (m-80) REVERT: O 62 PHE cc_start: 0.8987 (t80) cc_final: 0.8642 (t80) REVERT: O 68 PHE cc_start: 0.9218 (m-80) cc_final: 0.8698 (m-80) REVERT: P 49 MET cc_start: 0.9631 (ptp) cc_final: 0.9403 (ptp) REVERT: P 55 PHE cc_start: 0.9410 (m-80) cc_final: 0.9121 (m-80) REVERT: Q 55 PHE cc_start: 0.9235 (m-80) cc_final: 0.8947 (m-80) REVERT: T 244 PHE cc_start: 0.9284 (m-80) cc_final: 0.8989 (m-80) REVERT: T 261 LEU cc_start: 0.9770 (tp) cc_final: 0.9554 (mm) REVERT: T 277 TYR cc_start: 0.9002 (m-80) cc_final: 0.8568 (m-80) REVERT: T 285 PHE cc_start: 0.9572 (m-80) cc_final: 0.9322 (m-80) REVERT: T 287 GLN cc_start: 0.9472 (mp-120) cc_final: 0.9077 (mm-40) REVERT: T 290 ILE cc_start: 0.9603 (pt) cc_final: 0.9285 (pt) REVERT: T 291 PHE cc_start: 0.9580 (t80) cc_final: 0.9249 (t80) REVERT: Z 92 TYR cc_start: 0.9520 (t80) cc_final: 0.9303 (t80) REVERT: Z 206 GLU cc_start: 0.9257 (pp20) cc_final: 0.8985 (pp20) REVERT: Z 248 PHE cc_start: 0.9201 (m-10) cc_final: 0.8989 (m-80) REVERT: Z 249 ARG cc_start: 0.9414 (ptp-170) cc_final: 0.8840 (ptp90) REVERT: Z 251 PHE cc_start: 0.9212 (t80) cc_final: 0.8313 (t80) REVERT: Z 277 TYR cc_start: 0.9643 (m-80) cc_final: 0.9146 (m-80) REVERT: Y 34 MET cc_start: 0.9439 (mpp) cc_final: 0.9035 (mpp) REVERT: Y 91 GLU cc_start: 0.9502 (tm-30) cc_final: 0.8738 (mm-30) REVERT: Y 120 MET cc_start: 0.9614 (mmp) cc_final: 0.9303 (mmp) REVERT: V 120 MET cc_start: 0.9122 (ptp) cc_final: 0.8830 (ptp) REVERT: V 127 GLN cc_start: 0.9403 (pt0) cc_final: 0.8971 (pm20) REVERT: X 120 MET cc_start: 0.9225 (mpp) cc_final: 0.8552 (tpt) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.2074 time to fit residues: 104.4726 Evaluate side-chains 283 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.071352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.063322 restraints weight = 139286.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.064575 restraints weight = 76453.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.065432 restraints weight = 48458.487| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13200 Z= 0.183 Angle : 0.705 13.297 17922 Z= 0.382 Chirality : 0.046 0.258 2188 Planarity : 0.005 0.060 2335 Dihedral : 4.401 28.184 1925 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1782 helix: 0.77 (0.13), residues: 1487 sheet: None (None), residues: 0 loop : -1.99 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Z 208 HIS 0.001 0.001 HIS V 149 PHE 0.062 0.002 PHE J 50 TYR 0.011 0.001 TYR X 65 ARG 0.013 0.001 ARG V 73 Details of bonding type rmsd hydrogen bonds : bond 0.04614 ( 1233) hydrogen bonds : angle 4.59654 ( 3687) covalent geometry : bond 0.00376 (13200) covalent geometry : angle 0.70524 (17922) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 TYR cc_start: 0.9422 (m-80) cc_final: 0.8722 (m-80) REVERT: H 55 PHE cc_start: 0.9653 (m-80) cc_final: 0.9449 (m-80) REVERT: H 62 PHE cc_start: 0.9594 (m-80) cc_final: 0.9372 (m-80) REVERT: I 35 ILE cc_start: 0.9166 (tp) cc_final: 0.8947 (tp) REVERT: J 40 GLU cc_start: 0.8872 (tp30) cc_final: 0.8391 (tp30) REVERT: J 57 GLU cc_start: 0.9623 (mt-10) cc_final: 0.9248 (mt-10) REVERT: J 68 PHE cc_start: 0.8690 (m-10) cc_final: 0.8392 (m-80) REVERT: K 5 ASN cc_start: 0.9483 (p0) cc_final: 0.9231 (p0) REVERT: K 51 ILE cc_start: 0.8970 (pt) cc_final: 0.8536 (pt) REVERT: K 55 PHE cc_start: 0.9213 (m-10) cc_final: 0.8911 (m-80) REVERT: K 62 PHE cc_start: 0.9489 (m-80) cc_final: 0.9154 (m-80) REVERT: L 9 THR cc_start: 0.9476 (t) cc_final: 0.9239 (m) REVERT: L 70 ILE cc_start: 0.6821 (mt) cc_final: 0.6581 (mt) REVERT: M 50 PHE cc_start: 0.8717 (m-10) cc_final: 0.8451 (t80) REVERT: M 62 PHE cc_start: 0.9443 (m-80) cc_final: 0.8952 (m-80) REVERT: N 47 THR cc_start: 0.9536 (p) cc_final: 0.9254 (p) REVERT: N 49 MET cc_start: 0.9347 (ppp) cc_final: 0.9055 (ppp) REVERT: N 50 PHE cc_start: 0.9348 (m-10) cc_final: 0.8920 (m-80) REVERT: N 57 GLU cc_start: 0.9568 (mt-10) cc_final: 0.9249 (mt-10) REVERT: N 68 PHE cc_start: 0.9271 (m-80) cc_final: 0.8870 (m-80) REVERT: O 50 PHE cc_start: 0.9740 (m-80) cc_final: 0.9162 (m-80) REVERT: O 62 PHE cc_start: 0.8966 (t80) cc_final: 0.8633 (t80) REVERT: O 68 PHE cc_start: 0.9244 (m-80) cc_final: 0.8755 (m-80) REVERT: P 55 PHE cc_start: 0.9412 (m-80) cc_final: 0.9113 (m-80) REVERT: Q 51 ILE cc_start: 0.9508 (mt) cc_final: 0.9294 (mt) REVERT: Q 55 PHE cc_start: 0.9204 (m-80) cc_final: 0.8906 (m-80) REVERT: T 240 LEU cc_start: 0.9435 (mt) cc_final: 0.9197 (mt) REVERT: T 244 PHE cc_start: 0.9288 (m-80) cc_final: 0.8968 (m-80) REVERT: T 261 LEU cc_start: 0.9767 (tp) cc_final: 0.9547 (mm) REVERT: T 277 TYR cc_start: 0.9084 (m-80) cc_final: 0.8674 (m-80) REVERT: T 285 PHE cc_start: 0.9578 (m-80) cc_final: 0.9316 (m-80) REVERT: T 291 PHE cc_start: 0.9629 (t80) cc_final: 0.9269 (t80) REVERT: Z 248 PHE cc_start: 0.9227 (m-10) cc_final: 0.9006 (m-80) REVERT: Z 251 PHE cc_start: 0.9279 (t80) cc_final: 0.8282 (t80) REVERT: Z 277 TYR cc_start: 0.9633 (m-80) cc_final: 0.9151 (m-80) REVERT: Y 34 MET cc_start: 0.9506 (mpp) cc_final: 0.9126 (mpp) REVERT: Y 91 GLU cc_start: 0.9619 (tm-30) cc_final: 0.8665 (mm-30) REVERT: Y 106 LYS cc_start: 0.9534 (ptpp) cc_final: 0.9120 (ptpt) REVERT: Y 120 MET cc_start: 0.9579 (mmp) cc_final: 0.9290 (mmp) REVERT: V 120 MET cc_start: 0.9219 (ptp) cc_final: 0.8842 (ptp) REVERT: V 127 GLN cc_start: 0.9403 (pt0) cc_final: 0.9178 (pm20) REVERT: X 130 ASP cc_start: 0.9611 (m-30) cc_final: 0.9224 (p0) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2063 time to fit residues: 103.0095 Evaluate side-chains 270 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 105 optimal weight: 30.0000 chunk 165 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 72 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 116 optimal weight: 0.0040 chunk 5 optimal weight: 3.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 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 = 0.3261 r_free = 0.3261 target = 0.049322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.039130 restraints weight = 130027.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.040031 restraints weight = 92383.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.040927 restraints weight = 71749.543| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13200 Z= 0.215 Angle : 0.727 13.505 17922 Z= 0.397 Chirality : 0.047 0.317 2188 Planarity : 0.005 0.076 2335 Dihedral : 4.443 25.507 1925 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 1782 helix: 0.65 (0.13), residues: 1498 sheet: -2.00 (1.91), residues: 10 loop : -1.91 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Z 208 HIS 0.002 0.001 HIS V 149 PHE 0.040 0.002 PHE J 62 TYR 0.013 0.001 TYR X 65 ARG 0.014 0.001 ARG T 249 Details of bonding type rmsd hydrogen bonds : bond 0.04806 ( 1233) hydrogen bonds : angle 4.71084 ( 3687) covalent geometry : bond 0.00428 (13200) covalent geometry : angle 0.72732 (17922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3906.95 seconds wall clock time: 69 minutes 11.82 seconds (4151.82 seconds total)