Starting phenix.real_space_refine on Thu Sep 18 01:25:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itr_60876/09_2025/9itr_60876.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itr_60876/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9itr_60876/09_2025/9itr_60876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itr_60876/09_2025/9itr_60876.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9itr_60876/09_2025/9itr_60876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itr_60876/09_2025/9itr_60876.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'PHE:plan': 7, 'TYR:plan': 2, 'HIS:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2} 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: {'ARG:plan': 1, 'PHE:plan': 6, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 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: {'ASN:plan1': 2, 'PHE:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 1} 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: {'PHE:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1} 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: {'PHE:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 77 Time building chain proxies: 3.44, per 1000 atoms: 0.26 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: 1.29 Conformation dependent library (CDL) restraints added in 637.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.33 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: 2.19 Time building geometry restraints manager: 1.68 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: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.670 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.870 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG H 37 TYR 0.013 0.001 TYR X 65 PHE 0.040 0.002 PHE K 62 TRP 0.010 0.002 TRP Z 208 HIS 0.001 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00463 (13200) covalent geometry : angle 0.75422 (17922) hydrogen bonds : bond 0.19538 ( 1233) hydrogen bonds : angle 6.54537 ( 3687) *********************** 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 : 0.536 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: 0.1128 time to fit residues: 61.3266 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 : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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** ** X 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 = 0.3280 r_free = 0.3280 target = 0.049713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.040260 restraints weight = 124836.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041168 restraints weight = 90636.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.041950 restraints weight = 70669.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.042436 restraints weight = 59113.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.042754 restraints weight = 51362.505| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13200 Z= 0.183 Angle : 0.624 8.986 17922 Z= 0.347 Chirality : 0.042 0.189 2188 Planarity : 0.005 0.044 2335 Dihedral : 4.401 25.936 1925 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.69 % Allowed : 6.31 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.19), residues: 1782 helix: 0.54 (0.13), residues: 1475 sheet: -1.92 (1.97), residues: 10 loop : -2.09 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 63 TYR 0.013 0.001 TYR T 277 PHE 0.039 0.002 PHE I 62 TRP 0.009 0.002 TRP Z 208 HIS 0.002 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00354 (13200) covalent geometry : angle 0.62372 (17922) hydrogen bonds : bond 0.05371 ( 1233) hydrogen bonds : angle 4.76552 ( 3687) *********************** 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 361 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 353 time to evaluate : 0.518 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: symmetry clash REVERT: H 48 TYR cc_start: 0.9534 (m-80) cc_final: 0.9248 (m-80) REVERT: H 53 ILE cc_start: 0.9763 (tt) cc_final: 0.9562 (tt) REVERT: H 62 PHE cc_start: 0.9614 (m-80) cc_final: 0.9407 (m-80) REVERT: I 15 LEU cc_start: 0.9440 (tp) cc_final: 0.9129 (tp) REVERT: J 38 ASN cc_start: 0.9464 (t0) cc_final: 0.9074 (t0) REVERT: J 59 LEU cc_start: 0.9533 (mm) cc_final: 0.9258 (mm) REVERT: J 62 PHE cc_start: 0.9214 (m-80) cc_final: 0.8883 (m-80) REVERT: J 68 PHE cc_start: 0.8745 (m-10) cc_final: 0.8427 (m-10) REVERT: K 15 LEU cc_start: 0.9214 (tp) cc_final: 0.8982 (tp) REVERT: K 55 PHE cc_start: 0.9358 (m-10) cc_final: 0.9098 (m-80) REVERT: K 57 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8852 (pt0) REVERT: K 62 PHE cc_start: 0.9462 (m-80) cc_final: 0.9164 (m-80) REVERT: L 9 THR cc_start: 0.9536 (t) cc_final: 0.9302 (m) REVERT: L 70 ILE cc_start: 0.7144 (mt) cc_final: 0.6869 (mt) REVERT: M 50 PHE cc_start: 0.8786 (m-10) cc_final: 0.8521 (t80) REVERT: M 55 PHE cc_start: 0.9546 (m-80) cc_final: 0.9235 (m-80) REVERT: M 62 PHE cc_start: 0.9355 (m-80) cc_final: 0.8797 (m-80) REVERT: N 32 VAL cc_start: 0.9410 (p) cc_final: 0.9196 (p) REVERT: N 49 MET cc_start: 0.9225 (ppp) cc_final: 0.9010 (ppp) REVERT: N 50 PHE cc_start: 0.9312 (m-80) cc_final: 0.9094 (m-80) REVERT: N 57 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9218 (pt0) REVERT: O 15 LEU cc_start: 0.9807 (tp) cc_final: 0.9556 (tp) REVERT: O 32 VAL cc_start: 0.9715 (p) cc_final: 0.9382 (p) REVERT: O 37 ARG cc_start: 0.8869 (ppt170) cc_final: 0.8355 (ppt170) REVERT: O 50 PHE cc_start: 0.9686 (m-10) cc_final: 0.9089 (m-80) REVERT: O 68 PHE cc_start: 0.9402 (m-80) cc_final: 0.8951 (m-80) REVERT: P 55 PHE cc_start: 0.9469 (m-80) cc_final: 0.8948 (m-80) REVERT: Q 55 PHE cc_start: 0.9299 (m-80) cc_final: 0.9093 (m-80) REVERT: T 241 VAL cc_start: 0.9378 (p) cc_final: 0.9128 (p) REVERT: T 244 PHE cc_start: 0.9289 (m-80) cc_final: 0.8999 (m-80) REVERT: T 277 TYR cc_start: 0.9228 (m-80) cc_final: 0.8796 (m-10) REVERT: T 291 PHE cc_start: 0.9590 (t80) cc_final: 0.9265 (t80) REVERT: Z 206 GLU cc_start: 0.9221 (pp20) cc_final: 0.8971 (pp20) REVERT: Z 248 PHE cc_start: 0.9225 (m-10) cc_final: 0.8975 (m-80) REVERT: Z 251 PHE cc_start: 0.9179 (t80) cc_final: 0.8287 (t80) REVERT: Z 255 PHE cc_start: 0.9556 (t80) cc_final: 0.9296 (t80) REVERT: Z 277 TYR cc_start: 0.9653 (m-80) cc_final: 0.9164 (m-80) REVERT: Y 34 MET cc_start: 0.9495 (mpp) cc_final: 0.9173 (mpp) REVERT: Y 120 MET cc_start: 0.9618 (mmp) cc_final: 0.9399 (mmp) REVERT: X 115 GLN cc_start: 0.9638 (pm20) cc_final: 0.9228 (pm20) REVERT: X 117 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7907 (mtt180) REVERT: X 119 ARG cc_start: 0.9504 (mmp80) cc_final: 0.9141 (mmp80) REVERT: X 120 MET cc_start: 0.9366 (mpp) cc_final: 0.8710 (tpt) outliers start: 8 outliers final: 4 residues processed: 360 average time/residue: 0.1050 time to fit residues: 56.8861 Evaluate side-chains 284 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 280 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 149 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 81 optimal weight: 50.0000 chunk 165 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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** ** Y 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3579 r_free = 0.3579 target = 0.073294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.063643 restraints weight = 140834.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.064832 restraints weight = 77909.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.065659 restraints weight = 49488.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.066198 restraints weight = 34378.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.066551 restraints weight = 25842.809| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2029 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= 0.196 Angle : 0.640 8.115 17922 Z= 0.356 Chirality : 0.043 0.202 2188 Planarity : 0.004 0.055 2335 Dihedral : 4.412 25.570 1925 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.35 % Allowed : 6.14 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.19), residues: 1782 helix: 0.54 (0.13), residues: 1492 sheet: -1.88 (1.93), residues: 10 loop : -1.94 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG V 73 TYR 0.010 0.001 TYR T 277 PHE 0.029 0.002 PHE I 62 TRP 0.010 0.002 TRP Z 208 HIS 0.001 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00374 (13200) covalent geometry : angle 0.64007 (17922) hydrogen bonds : bond 0.05132 ( 1233) hydrogen bonds : angle 4.73929 ( 3687) *********************** 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 341 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 337 time to evaluate : 0.539 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: H 48 TYR cc_start: 0.9471 (m-80) cc_final: 0.8805 (m-80) REVERT: H 55 PHE cc_start: 0.9717 (m-80) cc_final: 0.9480 (m-80) REVERT: I 15 LEU cc_start: 0.9369 (tp) cc_final: 0.9057 (tp) REVERT: I 35 ILE cc_start: 0.9048 (tp) cc_final: 0.8836 (tp) REVERT: I 49 MET cc_start: 0.9567 (ptt) cc_final: 0.9311 (tmm) REVERT: I 51 ILE cc_start: 0.9532 (pt) cc_final: 0.9297 (pt) REVERT: I 66 ILE cc_start: 0.8916 (mm) cc_final: 0.8689 (mm) REVERT: J 47 THR cc_start: 0.9705 (p) cc_final: 0.9473 (p) REVERT: J 50 PHE cc_start: 0.9403 (m-80) cc_final: 0.9141 (m-80) REVERT: J 59 LEU cc_start: 0.9490 (mm) cc_final: 0.9236 (mm) REVERT: J 62 PHE cc_start: 0.9197 (m-10) cc_final: 0.8856 (m-80) REVERT: K 27 ILE cc_start: 0.9503 (mt) cc_final: 0.9289 (mt) REVERT: K 51 ILE cc_start: 0.9017 (pt) cc_final: 0.8612 (pt) REVERT: K 55 PHE cc_start: 0.9312 (m-10) cc_final: 0.9064 (m-80) REVERT: K 57 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8936 (mt-10) REVERT: K 62 PHE cc_start: 0.9491 (m-80) cc_final: 0.9146 (m-80) REVERT: L 9 THR cc_start: 0.9524 (t) cc_final: 0.9295 (m) REVERT: L 26 ILE cc_start: 0.9767 (tp) cc_final: 0.9530 (tt) REVERT: L 70 ILE cc_start: 0.6596 (mt) cc_final: 0.6291 (mt) REVERT: M 50 PHE cc_start: 0.8748 (m-10) cc_final: 0.8485 (t80) REVERT: M 62 PHE cc_start: 0.9379 (m-80) cc_final: 0.8936 (m-80) REVERT: N 32 VAL cc_start: 0.9481 (p) cc_final: 0.9260 (p) REVERT: N 47 THR cc_start: 0.9645 (p) cc_final: 0.9425 (p) REVERT: N 49 MET cc_start: 0.9136 (ppp) cc_final: 0.8889 (ppp) REVERT: N 50 PHE cc_start: 0.9226 (m-80) cc_final: 0.8975 (m-80) REVERT: N 57 GLU cc_start: 0.9564 (mt-10) cc_final: 0.9346 (mt-10) REVERT: O 32 VAL cc_start: 0.9695 (p) cc_final: 0.9441 (p) REVERT: O 37 ARG cc_start: 0.8716 (ppt170) cc_final: 0.8266 (ppt170) REVERT: O 50 PHE cc_start: 0.9707 (m-80) cc_final: 0.9177 (m-80) REVERT: O 62 PHE cc_start: 0.8913 (t80) cc_final: 0.8538 (t80) REVERT: O 68 PHE cc_start: 0.9360 (m-80) cc_final: 0.8906 (m-80) REVERT: P 55 PHE cc_start: 0.9437 (m-80) cc_final: 0.8925 (m-80) REVERT: T 241 VAL cc_start: 0.9325 (p) cc_final: 0.9058 (p) REVERT: T 244 PHE cc_start: 0.9199 (m-80) cc_final: 0.8942 (m-80) REVERT: T 277 TYR cc_start: 0.9230 (m-80) cc_final: 0.8707 (m-10) REVERT: T 285 PHE cc_start: 0.9646 (m-80) cc_final: 0.9287 (m-80) REVERT: T 291 PHE cc_start: 0.9704 (t80) cc_final: 0.9397 (t80) REVERT: Z 206 GLU cc_start: 0.9346 (pp20) cc_final: 0.9084 (pp20) REVERT: Z 248 PHE cc_start: 0.9158 (m-10) cc_final: 0.8938 (m-80) REVERT: Z 250 LEU cc_start: 0.9482 (mt) cc_final: 0.9258 (mt) REVERT: Z 251 PHE cc_start: 0.9161 (t80) cc_final: 0.8168 (t80) REVERT: Z 255 PHE cc_start: 0.9558 (t80) cc_final: 0.9296 (t80) REVERT: Z 264 MET cc_start: 0.8663 (ptt) cc_final: 0.8362 (ptt) REVERT: Z 277 TYR cc_start: 0.9671 (m-80) cc_final: 0.9109 (m-80) REVERT: Y 106 LYS cc_start: 0.9525 (ptpp) cc_final: 0.9207 (ptpp) REVERT: Y 120 MET cc_start: 0.9610 (mmp) cc_final: 0.9348 (mmp) REVERT: Y 128 ILE cc_start: 0.9193 (pt) cc_final: 0.8982 (pt) REVERT: X 115 GLN cc_start: 0.9618 (pm20) cc_final: 0.9390 (pm20) REVERT: X 117 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7844 (mtt180) REVERT: X 120 MET cc_start: 0.9293 (mpp) cc_final: 0.8687 (tpt) REVERT: X 130 ASP cc_start: 0.9580 (m-30) cc_final: 0.9234 (p0) outliers start: 4 outliers final: 1 residues processed: 340 average time/residue: 0.1036 time to fit residues: 53.5458 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 : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 140 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 38 ASN ** 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 = 0.050677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.040010 restraints weight = 124412.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.041023 restraints weight = 87812.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.041914 restraints weight = 67405.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.042535 restraints weight = 54175.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.042915 restraints weight = 47072.308| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13200 Z= 0.149 Angle : 0.630 9.081 17922 Z= 0.343 Chirality : 0.044 0.187 2188 Planarity : 0.004 0.068 2335 Dihedral : 4.410 26.512 1925 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.26 % Allowed : 4.07 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.19), residues: 1782 helix: 0.69 (0.13), residues: 1471 sheet: None (None), residues: 0 loop : -2.08 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 73 TYR 0.024 0.001 TYR O 48 PHE 0.054 0.002 PHE H 62 TRP 0.008 0.001 TRP Z 208 HIS 0.002 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00298 (13200) covalent geometry : angle 0.63023 (17922) hydrogen bonds : bond 0.04734 ( 1233) hydrogen bonds : angle 4.55225 ( 3687) *********************** 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 350 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 347 time to evaluate : 0.566 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: H 48 TYR cc_start: 0.9445 (m-80) cc_final: 0.8818 (m-80) REVERT: H 55 PHE cc_start: 0.9716 (m-80) cc_final: 0.9471 (m-80) REVERT: I 15 LEU cc_start: 0.9305 (tp) cc_final: 0.8985 (tp) REVERT: I 40 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8212 (mp0) REVERT: I 49 MET cc_start: 0.9508 (ptt) cc_final: 0.9117 (tmm) REVERT: I 51 ILE cc_start: 0.9514 (pt) cc_final: 0.9311 (pt) REVERT: J 40 GLU cc_start: 0.9231 (tp30) cc_final: 0.9004 (mp0) REVERT: J 59 LEU cc_start: 0.9509 (mm) cc_final: 0.9277 (mm) REVERT: J 62 PHE cc_start: 0.9224 (m-10) cc_final: 0.8874 (m-80) REVERT: K 51 ILE cc_start: 0.9063 (pt) cc_final: 0.8753 (pt) REVERT: K 55 PHE cc_start: 0.9328 (m-10) cc_final: 0.9112 (m-80) REVERT: K 62 PHE cc_start: 0.9526 (m-80) cc_final: 0.9151 (m-80) REVERT: L 26 ILE cc_start: 0.9593 (tp) cc_final: 0.9340 (tt) REVERT: M 32 VAL cc_start: 0.9727 (p) cc_final: 0.9500 (p) REVERT: M 50 PHE cc_start: 0.8673 (m-10) cc_final: 0.8387 (t80) REVERT: M 62 PHE cc_start: 0.9414 (m-80) cc_final: 0.8973 (m-80) REVERT: N 15 LEU cc_start: 0.9225 (tp) cc_final: 0.9017 (tp) REVERT: N 32 VAL cc_start: 0.9296 (p) cc_final: 0.9070 (p) REVERT: O 32 VAL cc_start: 0.9685 (p) cc_final: 0.9454 (p) REVERT: O 50 PHE cc_start: 0.9720 (m-80) cc_final: 0.9148 (m-80) REVERT: O 68 PHE cc_start: 0.9345 (m-80) cc_final: 0.8861 (m-80) REVERT: P 49 MET cc_start: 0.9787 (ptt) cc_final: 0.9540 (ptt) REVERT: P 55 PHE cc_start: 0.9332 (m-80) cc_final: 0.8958 (m-80) REVERT: Q 55 PHE cc_start: 0.9119 (m-80) cc_final: 0.8851 (m-80) REVERT: T 241 VAL cc_start: 0.9435 (p) cc_final: 0.9201 (p) REVERT: T 244 PHE cc_start: 0.9196 (m-80) cc_final: 0.8933 (m-80) REVERT: T 277 TYR cc_start: 0.9169 (m-80) cc_final: 0.8600 (m-10) REVERT: T 285 PHE cc_start: 0.9644 (m-80) cc_final: 0.9333 (m-80) REVERT: T 291 PHE cc_start: 0.9657 (t80) cc_final: 0.9369 (t80) REVERT: Z 95 PHE cc_start: 0.9652 (m-80) cc_final: 0.9436 (m-80) REVERT: Z 206 GLU cc_start: 0.9318 (pp20) cc_final: 0.9036 (pp20) REVERT: Z 248 PHE cc_start: 0.9121 (m-10) cc_final: 0.8900 (m-80) REVERT: Z 251 PHE cc_start: 0.9215 (t80) cc_final: 0.8196 (t80) REVERT: Z 255 PHE cc_start: 0.9630 (t80) cc_final: 0.9377 (t80) REVERT: Z 277 TYR cc_start: 0.9703 (m-80) cc_final: 0.9232 (m-80) REVERT: Y 34 MET cc_start: 0.9504 (mpp) cc_final: 0.9120 (mpp) REVERT: Y 120 MET cc_start: 0.9624 (mmp) cc_final: 0.9404 (mmp) REVERT: V 88 LYS cc_start: 0.9865 (pttp) cc_final: 0.9633 (pttm) REVERT: U 131 LEU cc_start: 0.9607 (mm) cc_final: 0.9287 (pp) REVERT: X 120 MET cc_start: 0.9177 (mpp) cc_final: 0.8565 (tpt) REVERT: X 130 ASP cc_start: 0.9615 (m-30) cc_final: 0.9287 (p0) outliers start: 3 outliers final: 1 residues processed: 350 average time/residue: 0.1060 time to fit residues: 55.8890 Evaluate side-chains 282 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 69 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 172 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.050572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.041051 restraints weight = 120911.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.041848 restraints weight = 88896.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.042669 restraints weight = 71403.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.043178 restraints weight = 59558.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.043532 restraints weight = 51967.849| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13200 Z= 0.151 Angle : 0.630 9.634 17922 Z= 0.340 Chirality : 0.043 0.182 2188 Planarity : 0.004 0.053 2335 Dihedral : 4.363 26.180 1925 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.35 % Allowed : 2.85 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.20), residues: 1782 helix: 0.66 (0.13), residues: 1490 sheet: -1.81 (1.95), residues: 10 loop : -1.87 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG U 63 TYR 0.015 0.001 TYR O 48 PHE 0.051 0.002 PHE J 50 TRP 0.008 0.001 TRP Z 208 HIS 0.001 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00301 (13200) covalent geometry : angle 0.62984 (17922) hydrogen bonds : bond 0.04596 ( 1233) hydrogen bonds : angle 4.47446 ( 3687) *********************** 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 349 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 345 time to evaluate : 0.524 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: 0.9431 (m-80) cc_final: 0.8745 (m-80) REVERT: H 55 PHE cc_start: 0.9681 (m-80) cc_final: 0.9451 (m-80) REVERT: H 62 PHE cc_start: 0.9662 (m-80) cc_final: 0.9460 (m-80) REVERT: I 15 LEU cc_start: 0.9381 (tp) cc_final: 0.9049 (tp) REVERT: I 40 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8197 (mp0) REVERT: I 49 MET cc_start: 0.9535 (ptt) cc_final: 0.9279 (tmm) REVERT: I 51 ILE cc_start: 0.9497 (pt) cc_final: 0.9258 (pt) REVERT: J 40 GLU cc_start: 0.9106 (tp30) cc_final: 0.8898 (mp0) REVERT: J 59 LEU cc_start: 0.9529 (mm) cc_final: 0.9277 (mm) REVERT: J 62 PHE cc_start: 0.9198 (m-10) cc_final: 0.8917 (m-80) REVERT: J 68 PHE cc_start: 0.8584 (m-10) cc_final: 0.8322 (m-80) REVERT: K 27 ILE cc_start: 0.9474 (mt) cc_final: 0.9254 (mt) REVERT: K 48 TYR cc_start: 0.8681 (m-10) cc_final: 0.7994 (m-80) REVERT: K 51 ILE cc_start: 0.9035 (pt) cc_final: 0.8611 (pt) REVERT: K 55 PHE cc_start: 0.9310 (m-10) cc_final: 0.9082 (m-80) REVERT: K 62 PHE cc_start: 0.9493 (m-80) cc_final: 0.9105 (m-80) REVERT: L 9 THR cc_start: 0.9494 (t) cc_final: 0.9268 (m) REVERT: L 26 ILE cc_start: 0.9685 (tp) cc_final: 0.9455 (tt) REVERT: M 50 PHE cc_start: 0.8695 (m-10) cc_final: 0.8478 (t80) REVERT: M 62 PHE cc_start: 0.9380 (m-80) cc_final: 0.8896 (m-80) REVERT: N 15 LEU cc_start: 0.9288 (tp) cc_final: 0.9079 (tp) REVERT: N 49 MET cc_start: 0.9298 (ppp) cc_final: 0.9059 (ppp) REVERT: N 50 PHE cc_start: 0.9217 (m-80) cc_final: 0.8883 (m-80) REVERT: O 32 VAL cc_start: 0.9727 (p) cc_final: 0.9496 (p) REVERT: O 47 THR cc_start: 0.9653 (p) cc_final: 0.9434 (p) REVERT: O 50 PHE cc_start: 0.9732 (m-80) cc_final: 0.9105 (m-80) REVERT: O 68 PHE cc_start: 0.9218 (m-80) cc_final: 0.8764 (m-80) REVERT: P 49 MET cc_start: 0.9752 (ptt) cc_final: 0.9489 (ptt) REVERT: P 55 PHE cc_start: 0.9391 (m-80) cc_final: 0.8976 (m-80) REVERT: T 241 VAL cc_start: 0.9406 (p) cc_final: 0.9137 (p) REVERT: T 244 PHE cc_start: 0.9254 (m-80) cc_final: 0.8959 (m-80) REVERT: T 277 TYR cc_start: 0.9143 (m-80) cc_final: 0.8569 (m-10) REVERT: T 285 PHE cc_start: 0.9602 (m-80) cc_final: 0.9297 (m-80) REVERT: T 291 PHE cc_start: 0.9592 (t80) cc_final: 0.9271 (t80) REVERT: Z 95 PHE cc_start: 0.9581 (m-80) cc_final: 0.9370 (m-80) REVERT: Z 206 GLU cc_start: 0.9237 (pp20) cc_final: 0.8975 (pp20) REVERT: Z 251 PHE cc_start: 0.9212 (t80) cc_final: 0.8317 (t80) REVERT: Z 255 PHE cc_start: 0.9552 (t80) cc_final: 0.9287 (t80) REVERT: Z 277 TYR cc_start: 0.9646 (m-80) cc_final: 0.9163 (m-80) REVERT: Y 34 MET cc_start: 0.9455 (mpp) cc_final: 0.9099 (mpp) REVERT: Y 120 MET cc_start: 0.9598 (mmp) cc_final: 0.9357 (mmp) REVERT: V 127 GLN cc_start: 0.9343 (pt0) cc_final: 0.9096 (pm20) REVERT: U 131 LEU cc_start: 0.9635 (mm) cc_final: 0.9266 (pp) REVERT: X 103 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8900 (pp20) REVERT: X 115 GLN cc_start: 0.9636 (pm20) cc_final: 0.9412 (pm20) REVERT: X 130 ASP cc_start: 0.9631 (m-30) cc_final: 0.9272 (p0) outliers start: 4 outliers final: 0 residues processed: 348 average time/residue: 0.1061 time to fit residues: 55.7795 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 : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 126 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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** X 112 GLN 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 = 0.053729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.043784 restraints weight = 144763.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.044751 restraints weight = 108637.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.045442 restraints weight = 86943.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.045838 restraints weight = 72812.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.046413 restraints weight = 64458.647| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13200 Z= 0.177 Angle : 0.647 9.421 17922 Z= 0.353 Chirality : 0.044 0.271 2188 Planarity : 0.005 0.077 2335 Dihedral : 4.375 25.874 1925 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.20), residues: 1782 helix: 0.72 (0.13), residues: 1498 sheet: None (None), residues: 0 loop : -1.79 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 37 TYR 0.013 0.001 TYR O 48 PHE 0.053 0.002 PHE J 50 TRP 0.008 0.001 TRP Z 208 HIS 0.001 0.000 HIS Y 149 Details of bonding type rmsd covalent geometry : bond 0.00358 (13200) covalent geometry : angle 0.64656 (17922) hydrogen bonds : bond 0.04641 ( 1233) hydrogen bonds : angle 4.50195 ( 3687) *********************** 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 340 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 0.521 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: H 26 ILE cc_start: 0.9556 (tp) cc_final: 0.9293 (tt) REVERT: H 48 TYR cc_start: 0.9428 (m-80) cc_final: 0.8758 (m-80) REVERT: H 55 PHE cc_start: 0.9640 (m-80) cc_final: 0.9431 (m-80) REVERT: H 62 PHE cc_start: 0.9666 (m-80) cc_final: 0.9459 (m-80) REVERT: I 15 LEU cc_start: 0.9467 (tp) cc_final: 0.9083 (tp) REVERT: I 49 MET cc_start: 0.9612 (ptt) cc_final: 0.9333 (tmm) REVERT: I 51 ILE cc_start: 0.9547 (pt) cc_final: 0.9346 (pt) REVERT: J 37 ARG cc_start: 0.8455 (mtm-85) cc_final: 0.8089 (ptt-90) REVERT: J 40 GLU cc_start: 0.9146 (tp30) cc_final: 0.8923 (mp0) REVERT: J 57 GLU cc_start: 0.9638 (mt-10) cc_final: 0.9073 (pt0) REVERT: J 59 LEU cc_start: 0.9558 (mm) cc_final: 0.9268 (mm) REVERT: J 62 PHE cc_start: 0.9262 (m-10) cc_final: 0.8886 (m-80) REVERT: J 68 PHE cc_start: 0.8656 (m-10) cc_final: 0.8349 (m-80) REVERT: K 51 ILE cc_start: 0.9013 (pt) cc_final: 0.8592 (pt) REVERT: K 55 PHE cc_start: 0.9242 (m-10) cc_final: 0.8975 (m-80) REVERT: K 62 PHE cc_start: 0.9524 (m-80) cc_final: 0.9151 (m-80) REVERT: L 9 THR cc_start: 0.9497 (t) cc_final: 0.9273 (m) REVERT: L 26 ILE cc_start: 0.9821 (tp) cc_final: 0.9579 (tt) REVERT: L 70 ILE cc_start: 0.6785 (mt) cc_final: 0.6534 (mt) REVERT: M 50 PHE cc_start: 0.8756 (m-10) cc_final: 0.8541 (t80) REVERT: M 62 PHE cc_start: 0.9431 (m-80) cc_final: 0.8967 (m-80) REVERT: N 15 LEU cc_start: 0.9319 (tp) cc_final: 0.9118 (tp) REVERT: N 49 MET cc_start: 0.9312 (ppp) cc_final: 0.9054 (ptt) REVERT: N 68 PHE cc_start: 0.9271 (m-80) cc_final: 0.8936 (m-80) REVERT: O 32 VAL cc_start: 0.9784 (p) cc_final: 0.9550 (p) REVERT: O 50 PHE cc_start: 0.9684 (m-80) cc_final: 0.9037 (m-80) REVERT: O 62 PHE cc_start: 0.8938 (t80) cc_final: 0.8668 (t80) REVERT: O 68 PHE cc_start: 0.9212 (m-80) cc_final: 0.8745 (m-80) REVERT: P 49 MET cc_start: 0.9713 (ptt) cc_final: 0.9495 (ptt) REVERT: P 55 PHE cc_start: 0.9411 (m-80) cc_final: 0.8978 (m-80) REVERT: T 244 PHE cc_start: 0.9341 (m-80) cc_final: 0.9023 (m-80) REVERT: T 277 TYR cc_start: 0.9100 (m-80) cc_final: 0.8532 (m-10) REVERT: T 285 PHE cc_start: 0.9546 (m-80) cc_final: 0.9238 (m-80) REVERT: T 291 PHE cc_start: 0.9567 (t80) cc_final: 0.9221 (t80) REVERT: Z 92 TYR cc_start: 0.9487 (t80) cc_final: 0.9271 (t80) REVERT: Z 206 GLU cc_start: 0.9281 (pp20) cc_final: 0.9029 (pp20) REVERT: Z 248 PHE cc_start: 0.9292 (m-80) cc_final: 0.8919 (m-80) REVERT: Z 250 LEU cc_start: 0.9392 (mt) cc_final: 0.9167 (mt) REVERT: Z 251 PHE cc_start: 0.9060 (t80) cc_final: 0.8267 (t80) REVERT: Z 277 TYR cc_start: 0.9660 (m-80) cc_final: 0.9280 (m-80) REVERT: Y 34 MET cc_start: 0.9488 (mpp) cc_final: 0.9133 (mpp) REVERT: Y 91 GLU cc_start: 0.9597 (tm-30) cc_final: 0.8855 (mm-30) REVERT: Y 120 MET cc_start: 0.9589 (mmp) cc_final: 0.9337 (mmp) REVERT: V 127 GLN cc_start: 0.9479 (pt0) cc_final: 0.8996 (pm20) REVERT: X 120 MET cc_start: 0.9367 (mpp) cc_final: 0.8482 (tpt) REVERT: X 130 ASP cc_start: 0.9636 (m-30) cc_final: 0.9294 (p0) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.1066 time to fit residues: 54.8361 Evaluate side-chains 277 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 2 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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** X 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.072073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.063998 restraints weight = 138790.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.065243 restraints weight = 75096.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.066080 restraints weight = 47421.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.066673 restraints weight = 33020.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.067070 restraints weight = 24366.156| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13200 Z= 0.169 Angle : 0.665 8.424 17922 Z= 0.362 Chirality : 0.045 0.272 2188 Planarity : 0.004 0.050 2335 Dihedral : 4.388 25.994 1925 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.20), residues: 1782 helix: 0.68 (0.13), residues: 1498 sheet: -1.92 (1.92), residues: 10 loop : -1.82 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 117 TYR 0.014 0.001 TYR O 48 PHE 0.039 0.002 PHE L 62 TRP 0.009 0.001 TRP Z 208 HIS 0.001 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00345 (13200) covalent geometry : angle 0.66515 (17922) hydrogen bonds : bond 0.04595 ( 1233) hydrogen bonds : angle 4.54652 ( 3687) *********************** 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 344 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.517 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: 0.9390 (m-80) cc_final: 0.8735 (m-80) REVERT: H 55 PHE cc_start: 0.9695 (m-80) cc_final: 0.9482 (m-80) REVERT: I 15 LEU cc_start: 0.9247 (tp) cc_final: 0.8927 (tp) REVERT: I 49 MET cc_start: 0.9534 (ptt) cc_final: 0.9171 (tmm) REVERT: I 51 ILE cc_start: 0.9528 (pt) cc_final: 0.9318 (pt) REVERT: J 59 LEU cc_start: 0.9477 (mm) cc_final: 0.9233 (mm) REVERT: J 62 PHE cc_start: 0.9204 (m-10) cc_final: 0.8937 (m-80) REVERT: K 51 ILE cc_start: 0.9033 (pt) cc_final: 0.8679 (pt) REVERT: K 55 PHE cc_start: 0.9273 (m-10) cc_final: 0.9038 (m-80) REVERT: K 62 PHE cc_start: 0.9515 (m-80) cc_final: 0.9163 (m-80) REVERT: L 9 THR cc_start: 0.9460 (t) cc_final: 0.9247 (m) REVERT: L 26 ILE cc_start: 0.9654 (tp) cc_final: 0.9428 (tt) REVERT: L 70 ILE cc_start: 0.5897 (mt) cc_final: 0.5677 (mt) REVERT: M 50 PHE cc_start: 0.8631 (m-10) cc_final: 0.8387 (t80) REVERT: M 62 PHE cc_start: 0.9483 (m-80) cc_final: 0.9128 (m-80) REVERT: N 47 THR cc_start: 0.9641 (p) cc_final: 0.9354 (p) REVERT: N 50 PHE cc_start: 0.9228 (m-10) cc_final: 0.8941 (m-80) REVERT: N 68 PHE cc_start: 0.9378 (m-80) cc_final: 0.9071 (m-80) REVERT: O 47 THR cc_start: 0.9709 (p) cc_final: 0.9504 (p) REVERT: O 50 PHE cc_start: 0.9735 (m-80) cc_final: 0.9211 (m-80) REVERT: O 62 PHE cc_start: 0.9040 (t80) cc_final: 0.8746 (t80) REVERT: O 68 PHE cc_start: 0.9299 (m-80) cc_final: 0.8801 (m-80) REVERT: P 49 MET cc_start: 0.9762 (ptt) cc_final: 0.9555 (ptt) REVERT: P 55 PHE cc_start: 0.9365 (m-80) cc_final: 0.9074 (m-80) REVERT: T 244 PHE cc_start: 0.9181 (m-80) cc_final: 0.8902 (m-80) REVERT: T 261 LEU cc_start: 0.9787 (tp) cc_final: 0.9541 (mm) REVERT: T 277 TYR cc_start: 0.9168 (m-80) cc_final: 0.8694 (m-80) REVERT: T 285 PHE cc_start: 0.9639 (m-80) cc_final: 0.9374 (m-80) REVERT: T 291 PHE cc_start: 0.9748 (t80) cc_final: 0.9476 (t80) REVERT: Z 206 GLU cc_start: 0.9441 (pp20) cc_final: 0.9183 (pp20) REVERT: Z 248 PHE cc_start: 0.9255 (m-80) cc_final: 0.8997 (m-80) REVERT: Z 251 PHE cc_start: 0.9260 (t80) cc_final: 0.8401 (t80) REVERT: Z 277 TYR cc_start: 0.9694 (m-80) cc_final: 0.9253 (m-80) REVERT: Y 34 MET cc_start: 0.9503 (mpp) cc_final: 0.9155 (mpp) REVERT: Y 91 GLU cc_start: 0.9570 (tm-30) cc_final: 0.8683 (mm-30) REVERT: Y 120 MET cc_start: 0.9627 (mmp) cc_final: 0.9389 (mmp) REVERT: V 127 GLN cc_start: 0.9573 (pt0) cc_final: 0.9086 (pm20) REVERT: X 115 GLN cc_start: 0.9608 (pm20) cc_final: 0.9383 (pm20) REVERT: X 120 MET cc_start: 0.9292 (mpp) cc_final: 0.8521 (tpt) REVERT: X 130 ASP cc_start: 0.9577 (m-30) cc_final: 0.9202 (p0) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1062 time to fit residues: 55.1890 Evaluate side-chains 281 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 119 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 112 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.076201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.066245 restraints weight = 134584.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.067457 restraints weight = 74196.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.068316 restraints weight = 47390.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.068866 restraints weight = 32780.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.069277 restraints weight = 24390.672| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2974 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= 0.153 Angle : 0.697 16.069 17922 Z= 0.370 Chirality : 0.046 0.333 2188 Planarity : 0.004 0.056 2335 Dihedral : 4.441 26.448 1925 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.20), residues: 1782 helix: 0.68 (0.13), residues: 1504 sheet: -1.80 (1.97), residues: 10 loop : -1.81 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 37 TYR 0.016 0.001 TYR O 48 PHE 0.044 0.002 PHE J 50 TRP 0.008 0.001 TRP Z 208 HIS 0.001 0.000 HIS Y 149 Details of bonding type rmsd covalent geometry : bond 0.00316 (13200) covalent geometry : angle 0.69679 (17922) hydrogen bonds : bond 0.04523 ( 1233) hydrogen bonds : angle 4.52402 ( 3687) *********************** 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 341 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.559 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: 0.9491 (tp) cc_final: 0.9217 (tt) REVERT: H 48 TYR cc_start: 0.9390 (m-80) cc_final: 0.8673 (m-80) REVERT: H 55 PHE cc_start: 0.9640 (m-80) cc_final: 0.9378 (m-80) REVERT: I 15 LEU cc_start: 0.9383 (tp) cc_final: 0.9038 (tp) REVERT: I 35 ILE cc_start: 0.8948 (tp) cc_final: 0.8679 (tp) REVERT: I 49 MET cc_start: 0.9559 (ptt) cc_final: 0.9228 (ppp) REVERT: I 51 ILE cc_start: 0.9482 (pt) cc_final: 0.9274 (pt) REVERT: J 47 THR cc_start: 0.9611 (p) cc_final: 0.9403 (p) REVERT: J 59 LEU cc_start: 0.9512 (mm) cc_final: 0.9175 (mm) REVERT: J 68 PHE cc_start: 0.8509 (m-80) cc_final: 0.8137 (m-80) REVERT: K 5 ASN cc_start: 0.9447 (p0) cc_final: 0.9166 (p0) REVERT: K 51 ILE cc_start: 0.8961 (pt) cc_final: 0.8515 (pt) REVERT: K 55 PHE cc_start: 0.9165 (m-10) cc_final: 0.8882 (m-80) REVERT: K 57 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8835 (pt0) REVERT: K 62 PHE cc_start: 0.9455 (m-80) cc_final: 0.9073 (m-80) REVERT: L 9 THR cc_start: 0.9468 (t) cc_final: 0.9217 (m) REVERT: L 70 ILE cc_start: 0.7031 (mt) cc_final: 0.6807 (mt) REVERT: M 27 ILE cc_start: 0.9662 (pt) cc_final: 0.9357 (mm) REVERT: M 50 PHE cc_start: 0.8662 (m-10) cc_final: 0.8437 (t80) REVERT: M 62 PHE cc_start: 0.9416 (m-80) cc_final: 0.9028 (m-80) REVERT: N 15 LEU cc_start: 0.9118 (tp) cc_final: 0.8898 (tp) REVERT: N 47 THR cc_start: 0.9547 (p) cc_final: 0.9253 (p) REVERT: N 49 MET cc_start: 0.9282 (ppp) cc_final: 0.8974 (ppp) REVERT: N 50 PHE cc_start: 0.9337 (m-10) cc_final: 0.8880 (m-80) REVERT: N 62 PHE cc_start: 0.9527 (m-80) cc_final: 0.9313 (m-80) REVERT: N 68 PHE cc_start: 0.9281 (m-80) cc_final: 0.8968 (m-80) REVERT: O 50 PHE cc_start: 0.9710 (m-80) cc_final: 0.9120 (m-80) REVERT: O 62 PHE cc_start: 0.8919 (t80) cc_final: 0.8600 (t80) REVERT: O 68 PHE cc_start: 0.9178 (m-80) cc_final: 0.8697 (m-80) REVERT: P 49 MET cc_start: 0.9694 (ptt) cc_final: 0.9482 (ptt) REVERT: P 55 PHE cc_start: 0.9351 (m-80) cc_final: 0.9016 (m-80) REVERT: T 244 PHE cc_start: 0.9207 (m-80) cc_final: 0.8971 (m-80) REVERT: T 261 LEU cc_start: 0.9746 (tp) cc_final: 0.9523 (mm) REVERT: T 277 TYR cc_start: 0.8993 (m-80) cc_final: 0.8548 (m-80) REVERT: T 285 PHE cc_start: 0.9547 (m-80) cc_final: 0.9256 (m-80) REVERT: T 290 ILE cc_start: 0.9638 (pt) cc_final: 0.9328 (pt) REVERT: T 291 PHE cc_start: 0.9567 (t80) cc_final: 0.9183 (t80) REVERT: Z 206 GLU cc_start: 0.9232 (pp20) cc_final: 0.8973 (pp20) REVERT: Z 248 PHE cc_start: 0.9296 (m-80) cc_final: 0.9009 (m-80) REVERT: Z 250 LEU cc_start: 0.9398 (mt) cc_final: 0.8974 (mt) REVERT: Z 251 PHE cc_start: 0.9192 (t80) cc_final: 0.8315 (t80) REVERT: Z 277 TYR cc_start: 0.9583 (m-80) cc_final: 0.9104 (m-80) REVERT: Z 287 GLN cc_start: 0.9674 (pm20) cc_final: 0.9120 (pm20) REVERT: Y 34 MET cc_start: 0.9490 (mpp) cc_final: 0.9087 (mpp) REVERT: Y 120 MET cc_start: 0.9569 (mmp) cc_final: 0.9315 (mmp) REVERT: V 127 GLN cc_start: 0.9354 (pt0) cc_final: 0.8909 (pm20) REVERT: U 105 LEU cc_start: 0.9013 (mt) cc_final: 0.8618 (mt) REVERT: X 120 MET cc_start: 0.9433 (mpp) cc_final: 0.8394 (tpt) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1084 time to fit residues: 55.5902 Evaluate side-chains 284 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 32 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.075777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.065864 restraints weight = 136158.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.067091 restraints weight = 75315.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.067950 restraints weight = 48043.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.068475 restraints weight = 33233.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.068934 restraints weight = 25106.736| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13200 Z= 0.159 Angle : 0.709 16.254 17922 Z= 0.379 Chirality : 0.046 0.322 2188 Planarity : 0.005 0.095 2335 Dihedral : 4.435 26.176 1925 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.20), residues: 1782 helix: 0.72 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -1.85 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG T 249 TYR 0.016 0.001 TYR O 48 PHE 0.034 0.002 PHE J 62 TRP 0.009 0.001 TRP Z 208 HIS 0.001 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00331 (13200) covalent geometry : angle 0.70899 (17922) hydrogen bonds : bond 0.04510 ( 1233) hydrogen bonds : angle 4.55965 ( 3687) *********************** 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 340 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.544 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: 0.9397 (m-80) cc_final: 0.8685 (m-80) REVERT: H 55 PHE cc_start: 0.9629 (m-80) cc_final: 0.9400 (m-80) REVERT: I 15 LEU cc_start: 0.9360 (tp) cc_final: 0.9003 (tp) REVERT: I 35 ILE cc_start: 0.9006 (tp) cc_final: 0.8750 (tp) REVERT: I 49 MET cc_start: 0.9603 (ptt) cc_final: 0.9200 (tmm) REVERT: I 51 ILE cc_start: 0.9548 (pt) cc_final: 0.9322 (pt) REVERT: J 68 PHE cc_start: 0.8527 (m-80) cc_final: 0.8186 (m-80) REVERT: K 5 ASN cc_start: 0.9458 (p0) cc_final: 0.9181 (p0) REVERT: K 48 TYR cc_start: 0.8849 (m-10) cc_final: 0.8141 (m-80) REVERT: K 51 ILE cc_start: 0.8970 (pt) cc_final: 0.8455 (pt) REVERT: K 55 PHE cc_start: 0.9183 (m-10) cc_final: 0.8879 (m-80) REVERT: K 62 PHE cc_start: 0.9464 (m-80) cc_final: 0.9117 (m-80) REVERT: L 9 THR cc_start: 0.9468 (t) cc_final: 0.9218 (m) REVERT: L 27 ILE cc_start: 0.9661 (tt) cc_final: 0.9313 (pt) REVERT: L 70 ILE cc_start: 0.6933 (mt) cc_final: 0.6694 (mt) REVERT: M 27 ILE cc_start: 0.9658 (pt) cc_final: 0.9373 (mm) REVERT: M 50 PHE cc_start: 0.8697 (m-10) cc_final: 0.8436 (t80) REVERT: M 62 PHE cc_start: 0.9429 (m-80) cc_final: 0.9045 (m-80) REVERT: N 15 LEU cc_start: 0.9105 (tp) cc_final: 0.8878 (tp) REVERT: N 47 THR cc_start: 0.9521 (p) cc_final: 0.9197 (p) REVERT: N 49 MET cc_start: 0.9282 (ppp) cc_final: 0.8978 (ppp) REVERT: N 50 PHE cc_start: 0.9359 (m-10) cc_final: 0.8909 (m-80) REVERT: N 62 PHE cc_start: 0.9383 (m-80) cc_final: 0.9149 (m-80) REVERT: N 68 PHE cc_start: 0.9275 (m-80) cc_final: 0.8880 (m-80) REVERT: O 50 PHE cc_start: 0.9720 (m-80) cc_final: 0.9107 (m-80) REVERT: O 62 PHE cc_start: 0.8920 (t80) cc_final: 0.8571 (t80) REVERT: O 68 PHE cc_start: 0.9194 (m-80) cc_final: 0.8732 (m-80) REVERT: P 49 MET cc_start: 0.9678 (ptt) cc_final: 0.9440 (ptt) REVERT: P 55 PHE cc_start: 0.9366 (m-80) cc_final: 0.9080 (m-80) REVERT: T 244 PHE cc_start: 0.9069 (m-80) cc_final: 0.8721 (m-80) REVERT: T 261 LEU cc_start: 0.9748 (tp) cc_final: 0.9527 (mm) REVERT: T 277 TYR cc_start: 0.9002 (m-80) cc_final: 0.8589 (m-80) REVERT: T 285 PHE cc_start: 0.9558 (m-80) cc_final: 0.9308 (m-80) REVERT: T 290 ILE cc_start: 0.9601 (pt) cc_final: 0.9297 (pt) REVERT: T 291 PHE cc_start: 0.9523 (t80) cc_final: 0.9113 (t80) REVERT: Z 206 GLU cc_start: 0.9235 (pp20) cc_final: 0.8965 (pp20) REVERT: Z 248 PHE cc_start: 0.9311 (m-80) cc_final: 0.9037 (m-80) REVERT: Z 251 PHE cc_start: 0.9224 (t80) cc_final: 0.8438 (t80) REVERT: Z 277 TYR cc_start: 0.9582 (m-80) cc_final: 0.9093 (m-80) REVERT: Y 34 MET cc_start: 0.9493 (mpp) cc_final: 0.9105 (mpp) REVERT: Y 91 GLU cc_start: 0.9624 (tm-30) cc_final: 0.8679 (mm-30) REVERT: Y 120 MET cc_start: 0.9569 (mmp) cc_final: 0.9307 (mmp) REVERT: V 120 MET cc_start: 0.9282 (ptp) cc_final: 0.8855 (ptp) REVERT: V 127 GLN cc_start: 0.9362 (pt0) cc_final: 0.8912 (pm20) REVERT: X 107 GLU cc_start: 0.9542 (mt-10) cc_final: 0.9318 (mt-10) REVERT: X 115 GLN cc_start: 0.9632 (pm20) cc_final: 0.9251 (pm20) REVERT: X 118 ILE cc_start: 0.9605 (pt) cc_final: 0.8830 (pt) REVERT: X 119 ARG cc_start: 0.9329 (mmp-170) cc_final: 0.9072 (mmp80) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.1082 time to fit residues: 55.2262 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 : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** ** 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 = 0.3289 r_free = 0.3289 target = 0.050842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.041600 restraints weight = 122795.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042386 restraints weight = 90656.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.043067 restraints weight = 72421.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.043690 restraints weight = 60749.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.044019 restraints weight = 53105.742| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13200 Z= 0.168 Angle : 0.719 15.402 17922 Z= 0.387 Chirality : 0.048 0.447 2188 Planarity : 0.004 0.062 2335 Dihedral : 4.428 26.105 1925 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.20), residues: 1782 helix: 0.77 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -2.04 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 37 TYR 0.016 0.001 TYR O 48 PHE 0.044 0.002 PHE J 50 TRP 0.009 0.001 TRP Z 208 HIS 0.001 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00359 (13200) covalent geometry : angle 0.71934 (17922) hydrogen bonds : bond 0.04558 ( 1233) hydrogen bonds : angle 4.60344 ( 3687) ********************** 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 335 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.616 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: H 48 TYR cc_start: 0.9457 (m-80) cc_final: 0.8756 (m-80) REVERT: H 55 PHE cc_start: 0.9708 (m-80) cc_final: 0.9467 (m-80) REVERT: I 15 LEU cc_start: 0.9371 (tp) cc_final: 0.9042 (tp) REVERT: I 35 ILE cc_start: 0.9151 (tp) cc_final: 0.8925 (tp) REVERT: I 49 MET cc_start: 0.9604 (ptt) cc_final: 0.9287 (tmm) REVERT: J 62 PHE cc_start: 0.9320 (m-80) cc_final: 0.9030 (m-80) REVERT: J 68 PHE cc_start: 0.8536 (m-80) cc_final: 0.8159 (m-80) REVERT: K 5 ASN cc_start: 0.9554 (p0) cc_final: 0.9298 (p0) REVERT: K 51 ILE cc_start: 0.8994 (pt) cc_final: 0.8624 (pt) REVERT: K 55 PHE cc_start: 0.9262 (m-10) cc_final: 0.8959 (m-80) REVERT: L 9 THR cc_start: 0.9472 (t) cc_final: 0.9229 (m) REVERT: L 26 ILE cc_start: 0.9738 (tp) cc_final: 0.9519 (tt) REVERT: L 27 ILE cc_start: 0.9735 (tt) cc_final: 0.9310 (pt) REVERT: L 70 ILE cc_start: 0.7026 (mt) cc_final: 0.6808 (mt) REVERT: M 27 ILE cc_start: 0.9667 (pt) cc_final: 0.9383 (mm) REVERT: M 50 PHE cc_start: 0.8703 (m-10) cc_final: 0.8416 (t80) REVERT: M 62 PHE cc_start: 0.9474 (m-80) cc_final: 0.9037 (m-80) REVERT: N 15 LEU cc_start: 0.9262 (tp) cc_final: 0.9053 (tp) REVERT: N 47 THR cc_start: 0.9529 (p) cc_final: 0.9188 (p) REVERT: N 49 MET cc_start: 0.9360 (ppp) cc_final: 0.9144 (ppp) REVERT: N 50 PHE cc_start: 0.9382 (m-10) cc_final: 0.9016 (m-80) REVERT: N 68 PHE cc_start: 0.9259 (m-80) cc_final: 0.8846 (m-80) REVERT: O 50 PHE cc_start: 0.9760 (m-80) cc_final: 0.9181 (m-80) REVERT: O 62 PHE cc_start: 0.8983 (t80) cc_final: 0.8637 (t80) REVERT: O 68 PHE cc_start: 0.9239 (m-80) cc_final: 0.8746 (m-80) REVERT: P 49 MET cc_start: 0.9735 (ptt) cc_final: 0.9508 (ptt) REVERT: P 55 PHE cc_start: 0.9388 (m-80) cc_final: 0.9027 (m-80) REVERT: T 244 PHE cc_start: 0.9118 (m-80) cc_final: 0.8834 (m-80) REVERT: T 261 LEU cc_start: 0.9764 (tp) cc_final: 0.9537 (mm) REVERT: T 277 TYR cc_start: 0.9020 (m-80) cc_final: 0.8581 (m-80) REVERT: T 285 PHE cc_start: 0.9586 (m-80) cc_final: 0.9375 (m-80) REVERT: T 290 ILE cc_start: 0.9575 (pt) cc_final: 0.9247 (pt) REVERT: T 291 PHE cc_start: 0.9547 (t80) cc_final: 0.9203 (t80) REVERT: Z 206 GLU cc_start: 0.9262 (pp20) cc_final: 0.8998 (pp20) REVERT: Z 248 PHE cc_start: 0.9342 (m-80) cc_final: 0.9052 (m-80) REVERT: Z 251 PHE cc_start: 0.9207 (t80) cc_final: 0.8486 (t80) REVERT: Z 277 TYR cc_start: 0.9647 (m-80) cc_final: 0.9128 (m-80) REVERT: Y 34 MET cc_start: 0.9457 (mpp) cc_final: 0.9076 (mpp) REVERT: Y 91 GLU cc_start: 0.9566 (tm-30) cc_final: 0.8756 (mm-30) REVERT: Y 120 MET cc_start: 0.9608 (mmp) cc_final: 0.9357 (mmp) REVERT: V 120 MET cc_start: 0.9249 (ptp) cc_final: 0.8820 (ptp) REVERT: V 127 GLN cc_start: 0.9410 (pt0) cc_final: 0.8955 (pm20) REVERT: U 88 LYS cc_start: 0.9692 (pttm) cc_final: 0.9454 (pttm) REVERT: X 115 GLN cc_start: 0.9718 (pm20) cc_final: 0.9394 (pm20) REVERT: X 118 ILE cc_start: 0.9543 (pt) cc_final: 0.9044 (pt) REVERT: X 119 ARG cc_start: 0.9446 (mmp-170) cc_final: 0.9217 (mmp80) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.1070 time to fit residues: 54.2209 Evaluate side-chains 277 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 78 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 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 = 0.3307 r_free = 0.3307 target = 0.051645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.042183 restraints weight = 119513.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.042983 restraints weight = 89415.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.043839 restraints weight = 71810.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.044327 restraints weight = 59536.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.044637 restraints weight = 52465.177| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13200 Z= 0.156 Angle : 0.724 14.595 17922 Z= 0.387 Chirality : 0.047 0.391 2188 Planarity : 0.004 0.054 2335 Dihedral : 4.432 26.454 1925 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.20), residues: 1782 helix: 0.73 (0.13), residues: 1473 sheet: None (None), residues: 0 loop : -1.98 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG T 249 TYR 0.016 0.001 TYR O 48 PHE 0.039 0.002 PHE J 62 TRP 0.009 0.001 TRP Z 208 HIS 0.001 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00328 (13200) covalent geometry : angle 0.72361 (17922) hydrogen bonds : bond 0.04470 ( 1233) hydrogen bonds : angle 4.56228 ( 3687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.18 seconds wall clock time: 40 minutes 19.00 seconds (2419.00 seconds total)