Starting phenix.real_space_refine on Thu Feb 22 05:06:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrg_22445/02_2024/7jrg_22445_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrg_22445/02_2024/7jrg_22445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrg_22445/02_2024/7jrg_22445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrg_22445/02_2024/7jrg_22445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrg_22445/02_2024/7jrg_22445_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrg_22445/02_2024/7jrg_22445_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.059 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: 7 Type Number sf(0) Gaussians Fe 6 7.16 5 Zn 2 6.06 5 P 38 5.49 5 S 132 5.16 5 C 21324 2.51 5 N 5352 2.21 5 O 6076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 320": "NH1" <-> "NH2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 87": "OD1" <-> "OD2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ASP 201": "OD1" <-> "OD2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D ARG 298": "NH1" <-> "NH2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F ARG 68": "NH1" <-> "NH2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 29": "OD1" <-> "OD2" Residue "H ASP 8": "OD1" <-> "OD2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 14": "OE1" <-> "OE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 68": "OD1" <-> "OD2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 128": "OE1" <-> "OE2" Residue "M GLU 148": "OE1" <-> "OE2" Residue "M GLU 158": "OE1" <-> "OE2" Residue "M TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 183": "OD1" <-> "OD2" Residue "M ASP 212": "OD1" <-> "OD2" Residue "M GLU 222": "OE1" <-> "OE2" Residue "M PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 231": "OD1" <-> "OD2" Residue "M TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 286": "OE1" <-> "OE2" Residue "M GLU 290": "OE1" <-> "OE2" Residue "M PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 386": "OE1" <-> "OE2" Residue "M PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 451": "OD1" <-> "OD2" Residue "M TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 519": "NH1" <-> "NH2" Residue "M TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 56": "OD1" <-> "OD2" Residue "N ASP 66": "OD1" <-> "OD2" Residue "N PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 137": "NH1" <-> "NH2" Residue "N GLU 156": "OE1" <-> "OE2" Residue "N TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 200": "OE1" <-> "OE2" Residue "N GLU 233": "OE1" <-> "OE2" Residue "N GLU 267": "OE1" <-> "OE2" Residue "N GLU 303": "OE1" <-> "OE2" Residue "N PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 451": "OE1" <-> "OE2" Residue "N PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 497": "OE1" <-> "OE2" Residue "O ARG 4": "NH1" <-> "NH2" Residue "O PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 72": "OE1" <-> "OE2" Residue "O ARG 76": "NH1" <-> "NH2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O ARG 85": "NH1" <-> "NH2" Residue "O TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 116": "NH1" <-> "NH2" Residue "O GLU 117": "OE1" <-> "OE2" Residue "O ARG 184": "NH1" <-> "NH2" Residue "O TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O ASP 293": "OD1" <-> "OD2" Residue "O ARG 320": "NH1" <-> "NH2" Residue "O PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 67": "OE1" <-> "OE2" Residue "P ASP 87": "OD1" <-> "OD2" Residue "P ARG 92": "NH1" <-> "NH2" Residue "P ARG 93": "NH1" <-> "NH2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 125": "OE1" <-> "OE2" Residue "P ASP 137": "OD1" <-> "OD2" Residue "P PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 148": "NH1" <-> "NH2" Residue "P ARG 167": "NH1" <-> "NH2" Residue "P ASP 177": "OD1" <-> "OD2" Residue "P ARG 185": "NH1" <-> "NH2" Residue "P PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 244": "OE1" <-> "OE2" Residue "P ASP 250": "OD1" <-> "OD2" Residue "P ARG 266": "NH1" <-> "NH2" Residue "P PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 298": "NH1" <-> "NH2" Residue "P ASP 303": "OD1" <-> "OD2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 142": "OD1" <-> "OD2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R ARG 65": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 40": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 66": "OE1" <-> "OE2" Residue "S ARG 71": "NH1" <-> "NH2" Residue "T GLU 27": "OE1" <-> "OE2" Residue "T TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 39": "OD1" <-> "OD2" Residue "T TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 39": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32930 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3838 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 464} Chain: "B" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3471 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 428} Chain: "C" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3104 Classifications: {'peptide': 388} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 362} Chain: "D" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1910 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 227} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 965 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 108} Chain: "G" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 578 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "H" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "K" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 218 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "M" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3838 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 464} Chain: "N" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3456 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 28, 'TRANS': 426} Chain: "O" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3104 Classifications: {'peptide': 388} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 362} Chain: "P" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1910 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 227} Chain: "Q" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 574 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "R" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 959 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "S" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 578 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "T" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "V" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 476 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "W" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 226 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {' ZN': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "C" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 415 Unusual residues: {'3PE': 6, 'CDL': 2, 'HEM': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 177 Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "M" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 156 Unusual residues: {' ZN': 1, '3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "O" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 420 Unusual residues: {'3PE': 5, 'CDL': 2, 'HEM': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 121 Chain: "P" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "S" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "W" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Time building chain proxies: 17.07, per 1000 atoms: 0.52 Number of scatterers: 32930 At special positions: 0 Unit cell: (129.146, 151.642, 167.473, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 6 26.01 S 132 16.00 P 38 15.00 O 6076 8.00 N 5352 7.00 C 21324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 17 " - pdb=" SG CYS H 59 " distance=2.03 Simple disulfide: pdb=" SG CYS H 31 " - pdb=" SG CYS H 45 " distance=2.02 Simple disulfide: pdb=" SG CYS T 17 " - pdb=" SG CYS T 59 " distance=2.02 Simple disulfide: pdb=" SG CYS T 21 " - pdb=" SG CYS T 55 " distance=2.03 Simple disulfide: pdb=" SG CYS T 31 " - pdb=" SG CYS T 45 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.39 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 137 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 141 " pdb=" ZN M 601 " pdb="ZN ZN M 601 " - pdb=" NE2 HIS M 137 " pdb="ZN ZN M 601 " - pdb=" NE2 HIS M 141 " 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7432 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 15 sheets defined 53.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.28 Creating SS restraints... Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 183 through 198 removed outlier: 3.517A pdb=" N VAL A 186 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Proline residue: A 187 - end of helix Processing helix chain 'A' and resid 204 through 220 Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.967A pdb=" N THR A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.974A pdb=" N ILE A 349 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 409 through 428 removed outlier: 3.717A pdb=" N LEU A 412 " --> pdb=" O PRO A 409 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASP A 413 " --> pdb=" O ASP A 410 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 426 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 449 Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 485 through 495 Processing helix chain 'A' and resid 515 through 521 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 169 through 181 Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 208 through 220 Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 241 through 251 Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 392 through 407 Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 455 through 464 Processing helix chain 'B' and resid 467 through 479 Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'C' and resid 14 through 24 removed outlier: 4.676A pdb=" N THR C 18 " --> pdb=" O PRO C 14 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 57 removed outlier: 4.106A pdb=" N GLY C 43 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 Processing helix chain 'C' and resid 81 through 109 Processing helix chain 'C' and resid 117 through 138 Processing helix chain 'C' and resid 144 through 157 removed outlier: 3.635A pdb=" N ALA C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 172 Processing helix chain 'C' and resid 179 through 210 Proline residue: C 193 - end of helix Processing helix chain 'C' and resid 230 through 251 removed outlier: 3.977A pdb=" N LYS C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 263 Processing helix chain 'C' and resid 279 through 290 Proline residue: C 283 - end of helix Processing helix chain 'C' and resid 294 through 313 removed outlier: 3.618A pdb=" N PHE C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Proline residue: C 312 - end of helix Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 326 through 347 removed outlier: 3.977A pdb=" N CYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 381 removed outlier: 3.892A pdb=" N PHE C 369 " --> pdb=" O PHE C 365 " (cutoff:3.500A) Proline residue: C 373 - end of helix removed outlier: 4.467A pdb=" N GLY C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 386 No H-bonds generated for 'chain 'C' and resid 383 through 386' Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 88 through 100 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 113 through 116 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 163 through 169 Processing helix chain 'D' and resid 181 through 184 No H-bonds generated for 'chain 'D' and resid 181 through 184' Processing helix chain 'D' and resid 188 through 197 Processing helix chain 'D' and resid 244 through 259 Processing helix chain 'D' and resid 263 through 293 Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 108 through 136 removed outlier: 3.515A pdb=" N TYR E 112 " --> pdb=" O ARG E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'F' and resid 15 through 31 Processing helix chain 'F' and resid 35 through 38 Processing helix chain 'F' and resid 41 through 44 No H-bonds generated for 'chain 'F' and resid 41 through 44' Processing helix chain 'F' and resid 46 through 53 Processing helix chain 'F' and resid 56 through 75 Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'F' and resid 95 through 110 Processing helix chain 'G' and resid 24 through 27 No H-bonds generated for 'chain 'G' and resid 24 through 27' Processing helix chain 'G' and resid 30 through 39 Processing helix chain 'G' and resid 42 through 70 Proline residue: G 51 - end of helix Processing helix chain 'H' and resid 9 through 20 Proline residue: H 19 - end of helix Processing helix chain 'H' and resid 22 through 38 Processing helix chain 'H' and resid 46 through 67 Proline residue: H 62 - end of helix removed outlier: 3.775A pdb=" N PHE H 65 " --> pdb=" O ALA H 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 20 Processing helix chain 'J' and resid 24 through 53 Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'K' and resid 17 through 38 Processing helix chain 'M' and resid 49 through 65 Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'M' and resid 125 through 127 No H-bonds generated for 'chain 'M' and resid 125 through 127' Processing helix chain 'M' and resid 133 through 143 removed outlier: 4.315A pdb=" N ALA M 136 " --> pdb=" O ASN M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 162 Processing helix chain 'M' and resid 186 through 198 Processing helix chain 'M' and resid 204 through 219 Processing helix chain 'M' and resid 225 through 237 Processing helix chain 'M' and resid 251 through 256 removed outlier: 4.332A pdb=" N THR M 256 " --> pdb=" O GLN M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 269 Processing helix chain 'M' and resid 272 through 274 No H-bonds generated for 'chain 'M' and resid 272 through 274' Processing helix chain 'M' and resid 285 through 295 Processing helix chain 'M' and resid 306 through 311 Processing helix chain 'M' and resid 348 through 357 Processing helix chain 'M' and resid 374 through 382 Processing helix chain 'M' and resid 412 through 428 Processing helix chain 'M' and resid 432 through 449 Processing helix chain 'M' and resid 454 through 466 Processing helix chain 'M' and resid 473 through 481 Processing helix chain 'M' and resid 485 through 495 Processing helix chain 'M' and resid 515 through 521 Processing helix chain 'N' and resid 118 through 124 Processing helix chain 'N' and resid 135 through 145 Processing helix chain 'N' and resid 166 through 181 removed outlier: 3.882A pdb=" N VAL N 169 " --> pdb=" O LYS N 166 " (cutoff:3.500A) Proline residue: N 170 - end of helix removed outlier: 3.519A pdb=" N GLU N 174 " --> pdb=" O GLN N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 203 Processing helix chain 'N' and resid 208 through 220 Processing helix chain 'N' and resid 233 through 238 Processing helix chain 'N' and resid 241 through 251 Processing helix chain 'N' and resid 254 through 256 No H-bonds generated for 'chain 'N' and resid 254 through 256' Processing helix chain 'N' and resid 266 through 277 Proline residue: N 275 - end of helix Processing helix chain 'N' and resid 322 through 335 Processing helix chain 'N' and resid 353 through 361 Processing helix chain 'N' and resid 392 through 405 Processing helix chain 'N' and resid 414 through 431 Processing helix chain 'N' and resid 435 through 449 Processing helix chain 'N' and resid 455 through 464 Processing helix chain 'N' and resid 467 through 479 Processing helix chain 'N' and resid 490 through 492 No H-bonds generated for 'chain 'N' and resid 490 through 492' Processing helix chain 'N' and resid 496 through 500 Processing helix chain 'O' and resid 10 through 12 No H-bonds generated for 'chain 'O' and resid 10 through 12' Processing helix chain 'O' and resid 17 through 24 Processing helix chain 'O' and resid 35 through 57 Processing helix chain 'O' and resid 67 through 76 Processing helix chain 'O' and resid 81 through 109 Processing helix chain 'O' and resid 117 through 138 Processing helix chain 'O' and resid 144 through 159 removed outlier: 4.139A pdb=" N ALA O 157 " --> pdb=" O ILE O 153 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER O 158 " --> pdb=" O THR O 154 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA O 159 " --> pdb=" O SER O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 172 Processing helix chain 'O' and resid 179 through 209 Proline residue: O 193 - end of helix Processing helix chain 'O' and resid 227 through 251 removed outlier: 6.966A pdb=" N TYR O 232 " --> pdb=" O TYR O 228 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS O 234 " --> pdb=" O TYR O 230 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 263 Processing helix chain 'O' and resid 279 through 290 Proline residue: O 283 - end of helix Processing helix chain 'O' and resid 294 through 310 Processing helix chain 'O' and resid 322 through 324 No H-bonds generated for 'chain 'O' and resid 322 through 324' Processing helix chain 'O' and resid 326 through 347 removed outlier: 4.043A pdb=" N CYS O 347 " --> pdb=" O GLY O 343 " (cutoff:3.500A) Processing helix chain 'O' and resid 354 through 370 removed outlier: 3.823A pdb=" N PHE O 363 " --> pdb=" O GLN O 359 " (cutoff:3.500A) Processing helix chain 'O' and resid 372 through 384 Proline residue: O 383 - end of helix Processing helix chain 'P' and resid 64 through 68 Processing helix chain 'P' and resid 88 through 101 Processing helix chain 'P' and resid 113 through 116 Processing helix chain 'P' and resid 123 through 132 Processing helix chain 'P' and resid 163 through 169 Processing helix chain 'P' and resid 188 through 197 Processing helix chain 'P' and resid 244 through 259 Processing helix chain 'P' and resid 263 through 296 removed outlier: 4.587A pdb=" N VAL P 294 " --> pdb=" O LEU P 290 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LEU P 295 " --> pdb=" O ARG P 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 84 Processing helix chain 'Q' and resid 110 through 137 Processing helix chain 'Q' and resid 141 through 147 Processing helix chain 'R' and resid 15 through 31 Processing helix chain 'R' and resid 36 through 38 No H-bonds generated for 'chain 'R' and resid 36 through 38' Processing helix chain 'R' and resid 41 through 44 No H-bonds generated for 'chain 'R' and resid 41 through 44' Processing helix chain 'R' and resid 46 through 53 Processing helix chain 'R' and resid 56 through 75 Processing helix chain 'R' and resid 81 through 85 Processing helix chain 'R' and resid 95 through 110 Processing helix chain 'S' and resid 17 through 19 No H-bonds generated for 'chain 'S' and resid 17 through 19' Processing helix chain 'S' and resid 30 through 70 removed outlier: 6.232A pdb=" N ILE S 43 " --> pdb=" O SER S 39 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N SER S 44 " --> pdb=" O GLU S 40 " (cutoff:3.500A) Proline residue: S 51 - end of helix Processing helix chain 'T' and resid 9 through 20 Proline residue: T 19 - end of helix Processing helix chain 'T' and resid 22 through 38 Processing helix chain 'T' and resid 46 through 59 Processing helix chain 'T' and resid 61 through 67 removed outlier: 4.216A pdb=" N PHE T 65 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 20 Processing helix chain 'V' and resid 24 through 53 Processing helix chain 'W' and resid 16 through 37 Processing helix chain 'W' and resid 41 through 45 Processing sheet with id= A, first strand: chain 'A' and resid 93 through 98 removed outlier: 3.651A pdb=" N ARG A 103 " --> pdb=" O MET A 275 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 321 through 325 removed outlier: 6.299A pdb=" N ILE A 503 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N MET A 324 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA A 505 " --> pdb=" O MET A 324 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 337 through 339 removed outlier: 3.518A pdb=" N PHE A 401 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 78 through 82 Processing sheet with id= E, first strand: chain 'B' and resid 221 through 223 removed outlier: 3.760A pdb=" N VAL B 292 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 296 through 301 Processing sheet with id= G, first strand: chain 'C' and resid 27 through 29 Processing sheet with id= H, first strand: chain 'D' and resid 134 through 139 removed outlier: 3.673A pdb=" N PHE D 146 " --> pdb=" O ASP D 137 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 94 through 98 removed outlier: 3.786A pdb=" N ARG M 103 " --> pdb=" O MET M 275 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY M 281 " --> pdb=" O GLU M 107 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR M 116 " --> pdb=" O SER M 280 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'M' and resid 321 through 325 removed outlier: 6.295A pdb=" N ILE M 503 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N MET M 324 " --> pdb=" O ILE M 503 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA M 505 " --> pdb=" O MET M 324 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'M' and resid 337 through 339 Processing sheet with id= L, first strand: chain 'N' and resid 78 through 82 Processing sheet with id= M, first strand: chain 'N' and resid 297 through 301 removed outlier: 6.508A pdb=" N MET N 484 " --> pdb=" O PHE N 298 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ARG N 300 " --> pdb=" O MET N 484 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER N 486 " --> pdb=" O ARG N 300 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE N 381 " --> pdb=" O PHE N 313 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'O' and resid 27 through 29 Processing sheet with id= O, first strand: chain 'P' and resid 134 through 137 removed outlier: 3.768A pdb=" N PHE P 146 " --> pdb=" O ASP P 137 " (cutoff:3.500A) 1595 hydrogen bonds defined for protein. 4509 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: 10.72 Time building geometry restraints manager: 15.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 10525 1.36 - 1.53: 20243 1.53 - 1.69: 2710 1.69 - 1.85: 228 1.85 - 2.02: 24 Bond restraints: 33730 Sorted by residual: bond pdb=" C2D HEC P 501 " pdb=" C3D HEC P 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C2D HEC D 501 " pdb=" C3D HEC D 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAC HEC P 501 " pdb=" CBC HEC P 501 " ideal model delta sigma weight residual 1.544 1.361 0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" CAC HEC D 501 " pdb=" CBC HEC D 501 " ideal model delta sigma weight residual 1.544 1.362 0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" CAB HEC D 501 " pdb=" CBB HEC D 501 " ideal model delta sigma weight residual 1.544 1.402 0.142 2.00e-02 2.50e+03 5.01e+01 ... (remaining 33725 not shown) Histogram of bond angle deviations from ideal: 87.86 - 106.12: 1045 106.12 - 124.39: 43696 124.39 - 142.65: 915 142.65 - 160.91: 0 160.91 - 179.17: 12 Bond angle restraints: 45668 Sorted by residual: angle pdb=" N GLY B 107 " pdb=" CA GLY B 107 " pdb=" C GLY B 107 " ideal model delta sigma weight residual 110.29 117.62 -7.33 1.28e+00 6.10e-01 3.28e+01 angle pdb=" CG MET D 225 " pdb=" SD MET D 225 " pdb=" CE MET D 225 " ideal model delta sigma weight residual 100.90 92.70 8.20 2.20e+00 2.07e-01 1.39e+01 angle pdb=" CB LYS B 472 " pdb=" CG LYS B 472 " pdb=" CD LYS B 472 " ideal model delta sigma weight residual 111.30 119.84 -8.54 2.30e+00 1.89e-01 1.38e+01 angle pdb=" C ARG Q 119 " pdb=" N PHE Q 120 " pdb=" CA PHE Q 120 " ideal model delta sigma weight residual 121.14 114.84 6.30 1.75e+00 3.27e-01 1.30e+01 angle pdb=" C ALA N 370 " pdb=" N PHE N 371 " pdb=" CA PHE N 371 " ideal model delta sigma weight residual 122.82 128.79 -5.97 1.68e+00 3.54e-01 1.26e+01 ... (remaining 45663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.55: 19056 26.55 - 53.09: 1164 53.09 - 79.64: 186 79.64 - 106.18: 33 106.18 - 132.73: 6 Dihedral angle restraints: 20445 sinusoidal: 8870 harmonic: 11575 Sorted by residual: dihedral pdb=" C2C HEM O 403 " pdb=" C3C HEM O 403 " pdb=" CAC HEM O 403 " pdb=" CBC HEM O 403 " ideal model delta sinusoidal sigma weight residual -180.00 -104.81 -75.19 2 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" C2C HEM O 404 " pdb=" C3C HEM O 404 " pdb=" CAC HEM O 404 " pdb=" CBC HEM O 404 " ideal model delta sinusoidal sigma weight residual 0.00 -56.66 56.66 2 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" C2C HEM C 402 " pdb=" C3C HEM C 402 " pdb=" CAC HEM C 402 " pdb=" CBC HEM C 402 " ideal model delta sinusoidal sigma weight residual -0.00 56.04 -56.04 2 1.00e+01 1.00e-02 3.30e+01 ... (remaining 20442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4272 0.069 - 0.139: 565 0.139 - 0.208: 32 0.208 - 0.277: 4 0.277 - 0.347: 2 Chirality restraints: 4875 Sorted by residual: chirality pdb=" CA4 CDL P 502 " pdb=" CA3 CDL P 502 " pdb=" CA6 CDL P 502 " pdb=" OA6 CDL P 502 " both_signs ideal model delta sigma weight residual False -2.57 -2.23 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C2 3PE F 201 " pdb=" C1 3PE F 201 " pdb=" C3 3PE F 201 " pdb=" O21 3PE F 201 " both_signs ideal model delta sigma weight residual False -2.53 -2.23 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA4 CDL M 603 " pdb=" CA3 CDL M 603 " pdb=" CA6 CDL M 603 " pdb=" OA6 CDL M 603 " both_signs ideal model delta sigma weight residual False -2.57 -2.31 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4872 not shown) Planarity restraints: 5715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 190 " -0.015 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR C 190 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 190 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR C 190 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR C 190 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 190 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 190 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 190 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 246 " 0.025 2.00e-02 2.50e+03 2.49e-02 1.08e+01 pdb=" CG PHE O 246 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE O 246 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE O 246 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE O 246 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE O 246 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE O 246 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 190 " 0.013 2.00e-02 2.50e+03 2.25e-02 1.02e+01 pdb=" CG TYR O 190 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR O 190 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR O 190 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR O 190 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR O 190 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR O 190 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR O 190 " -0.002 2.00e-02 2.50e+03 ... (remaining 5712 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 353 2.62 - 3.19: 29689 3.19 - 3.76: 50579 3.76 - 4.33: 71606 4.33 - 4.90: 119673 Nonbonded interactions: 271900 Sorted by model distance: nonbonded pdb=" NE2 HIS O 88 " pdb="FE HEM O 403 " model vdw 2.045 3.080 nonbonded pdb=" NE2 HIS C 88 " pdb="FE HEM C 402 " model vdw 2.053 3.080 nonbonded pdb=" NE2 HIS O 102 " pdb="FE HEM O 404 " model vdw 2.062 3.080 nonbonded pdb=" NE2 HIS C 203 " pdb="FE HEM C 403 " model vdw 2.079 3.080 nonbonded pdb=" O SER C 316 " pdb=" OH TYR F 43 " model vdw 2.111 2.440 ... (remaining 271895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 527 or resid 601 or (resid 603 and (name CB2 or \ name OB2 or name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C51 or name C52 or name C53 or name C54 or name C55 or name C56 or name \ C71 or name C72 or name C73 or name C74 or name C75 or name C76 or name CA2 or \ name CA3 or name CA4 or name CA5 or name CA6 or name CA7 or name CB4 or name CB5 \ or name CB6 or name CB7 or name O1 or name OA2 or name OA3 or name OA4 or name \ OA5 or name OA6 or name OA7 or name OA8 or name OA9 or name OB4 or name OB5 or n \ ame OB6 or name OB7 or name OB8 or name OB9 or name PA1 or name PB2)))) selection = (chain 'M' and (resid 41 through 527 or resid 601 or (resid 603 and (name CB2 or \ name OB2 or name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C51 or name C52 or name C53 or name C54 or name C55 or name C56 or name \ C71 or name C72 or name C73 or name C74 or name C75 or name C76 or name CA2 or \ name CA3 or name CA4 or name CA5 or name CA6 or name CA7 or name CB4 or name CB5 \ or name CB6 or name CB7 or name O1 or name OA2 or name OA3 or name OA4 or name \ OA5 or name OA6 or name OA7 or name OA8 or name OA9 or name OB4 or name OB5 or n \ ame OB6 or name OB7 or name OB8 or name OB9 or name PA1 or name PB2)))) } ncs_group { reference = (chain 'B' and resid 50 through 504) selection = chain 'N' } ncs_group { reference = (chain 'C' and (resid 2 through 389 or resid 403 or (resid 405 and (name N or na \ me C1 or name C11 or name C12 or name C2 or name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or \ (resid 407 and (name N or name C1 or name C11 or name C12 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name O11 or name O12 or name O13 or name O14 \ or name O21 or name O22 or name O31 or name O32 or name P )) or resid 408 throug \ h 409)) selection = (chain 'O' and (resid 2 through 389 or resid 403 or (resid 405 and (name N or na \ me C1 or name C11 or name C12 or name C2 or name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or \ (resid 407 and (name N or name C1 or name C11 or name C12 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name O11 or name O12 or name O13 or name O14 \ or name O21 or name O22 or name O31 or name O32 or name P )) or (resid 408 and ( \ name N or name C1 or name C11 or name C12 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or \ (resid 409 and (name N or name C1 or name C11 or name C12 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C3A or name C3B or name C3C or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) } ncs_group { reference = (chain 'D' and (resid 63 through 306 or resid 501 or (resid 502 and (name CB2 or \ name OB2 or name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C31 or name C32 or name C33 or name C34 or name C51 or name C52 or \ name C53 or name C54 or name C55 or name C71 or name C72 or name C73 or name C74 \ or name C75 or name C76 or name CA2 or name CA3 or name CA4 or name CA5 or name \ CA6 or name CA7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or n \ ame OA2 or name OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 \ or name OA9 or name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name \ OB9 or name PA1 or name PB2)))) selection = (chain 'P' and (resid 63 through 306 or resid 501 or (resid 502 and (name CB2 or \ name OB2 or name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C31 or name C32 or name C33 or name C34 or name C51 or name C52 or \ name C53 or name C54 or name C55 or name C71 or name C72 or name C73 or name C74 \ or name C75 or name C76 or name CA2 or name CA3 or name CA4 or name CA5 or name \ CA6 or name CA7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or n \ ame OA2 or name OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 \ or name OA9 or name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name \ OB9 or name PA1 or name PB2)))) } ncs_group { reference = (chain 'E' and resid 75 through 148) selection = chain 'Q' } ncs_group { reference = (chain 'F' and resid 8 through 122) selection = chain 'R' } ncs_group { reference = (chain 'G' and resid 3 through 72) selection = (chain 'S' and resid 3 through 72) } ncs_group { reference = (chain 'H' and resid 6 through 69) selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 11 through 69) selection = chain 'V' } ncs_group { reference = chain 'K' selection = (chain 'W' and resid 16 through 46) } 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 individual isotropic 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: 9.080 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: 0.030 Extract box with map and model: 29.390 Check model and map are aligned: 0.510 Set scattering table: 0.320 Process input model: 89.480 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.220 33730 Z= 0.486 Angle : 0.784 11.609 45668 Z= 0.392 Chirality : 0.047 0.347 4875 Planarity : 0.005 0.065 5715 Dihedral : 16.914 132.727 12998 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.10 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3943 helix: 1.33 (0.11), residues: 2197 sheet: -0.99 (0.27), residues: 361 loop : -1.38 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 273 HIS 0.009 0.001 HIS C 203 PHE 0.057 0.002 PHE O 246 TYR 0.058 0.002 TYR C 190 ARG 0.019 0.001 ARG M 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 333 time to evaluate : 3.670 Fit side-chains revert: symmetry clash REVERT: B 335 MET cc_start: 0.8444 (mmm) cc_final: 0.7993 (mmm) REVERT: H 7 VAL cc_start: 0.7111 (p) cc_final: 0.6883 (t) REVERT: H 8 ASP cc_start: 0.8015 (m-30) cc_final: 0.7676 (m-30) REVERT: H 14 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7818 (tm-30) REVERT: H 15 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7684 (mm-30) REVERT: H 51 ASP cc_start: 0.8297 (m-30) cc_final: 0.8047 (m-30) REVERT: N 335 MET cc_start: 0.7990 (tpp) cc_final: 0.7750 (mmm) outliers start: 3 outliers final: 2 residues processed: 335 average time/residue: 0.4808 time to fit residues: 256.9607 Evaluate side-chains 269 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 267 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 306 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 328 optimal weight: 0.9990 chunk 294 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 198 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 185 optimal weight: 0.6980 chunk 226 optimal weight: 0.8980 chunk 353 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 301 HIS ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 HIS ** T 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33730 Z= 0.181 Angle : 0.597 15.531 45668 Z= 0.286 Chirality : 0.042 0.273 4875 Planarity : 0.005 0.062 5715 Dihedral : 15.434 136.884 5628 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.51 % Allowed : 5.49 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3943 helix: 1.56 (0.11), residues: 2188 sheet: -0.71 (0.28), residues: 350 loop : -1.25 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 273 HIS 0.008 0.001 HIS N 301 PHE 0.036 0.001 PHE Q 120 TYR 0.015 0.001 TYR A 404 ARG 0.007 0.000 ARG M 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 299 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 THR cc_start: 0.8009 (m) cc_final: 0.7803 (m) REVERT: C 315 LYS cc_start: 0.7521 (mmtt) cc_final: 0.6961 (mmtt) REVERT: G 64 GLU cc_start: 0.8178 (tp30) cc_final: 0.7805 (tp30) REVERT: H 7 VAL cc_start: 0.7176 (p) cc_final: 0.6858 (t) REVERT: H 8 ASP cc_start: 0.7972 (m-30) cc_final: 0.7728 (m-30) REVERT: H 14 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7842 (tm-30) REVERT: H 51 ASP cc_start: 0.8401 (m-30) cc_final: 0.8015 (m-30) REVERT: S 61 ASN cc_start: 0.7862 (t0) cc_final: 0.7616 (t0) REVERT: S 67 LYS cc_start: 0.8404 (ttpp) cc_final: 0.8190 (ttpt) outliers start: 17 outliers final: 15 residues processed: 311 average time/residue: 0.5022 time to fit residues: 253.0759 Evaluate side-chains 288 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 273 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 196 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 294 optimal weight: 0.0040 chunk 240 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 353 optimal weight: 3.9990 chunk 382 optimal weight: 4.9990 chunk 315 optimal weight: 8.9990 chunk 350 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33730 Z= 0.203 Angle : 0.566 11.440 45668 Z= 0.274 Chirality : 0.041 0.249 4875 Planarity : 0.004 0.060 5715 Dihedral : 14.768 137.131 5626 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.84 % Allowed : 7.64 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3943 helix: 1.68 (0.11), residues: 2179 sheet: -0.78 (0.28), residues: 356 loop : -1.17 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 273 HIS 0.010 0.001 HIS V 47 PHE 0.034 0.001 PHE Q 120 TYR 0.014 0.001 TYR P 199 ARG 0.005 0.000 ARG B 501 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 291 time to evaluate : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.9247 (mmm) cc_final: 0.8942 (mmp) REVERT: C 315 LYS cc_start: 0.7515 (mmtt) cc_final: 0.7283 (mmtt) REVERT: G 64 GLU cc_start: 0.8234 (tp30) cc_final: 0.7854 (tp30) REVERT: H 7 VAL cc_start: 0.7164 (p) cc_final: 0.6876 (t) REVERT: H 8 ASP cc_start: 0.8015 (m-30) cc_final: 0.7758 (m-30) REVERT: H 14 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7664 (tm-30) REVERT: H 51 ASP cc_start: 0.8391 (m-30) cc_final: 0.8012 (m-30) REVERT: S 61 ASN cc_start: 0.7865 (t0) cc_final: 0.7638 (t0) outliers start: 28 outliers final: 20 residues processed: 309 average time/residue: 0.4714 time to fit residues: 238.6351 Evaluate side-chains 294 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 274 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 349 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 355 optimal weight: 0.7980 chunk 376 optimal weight: 3.9990 chunk 185 optimal weight: 0.0670 chunk 336 optimal weight: 0.0670 chunk 101 optimal weight: 0.5980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 HIS C 179 ASN C 259 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 33730 Z= 0.156 Angle : 0.535 11.556 45668 Z= 0.260 Chirality : 0.040 0.248 4875 Planarity : 0.004 0.057 5715 Dihedral : 14.043 140.770 5626 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.15 % Favored : 94.83 % Rotamer: Outliers : 1.07 % Allowed : 8.96 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3943 helix: 1.87 (0.11), residues: 2165 sheet: -0.62 (0.28), residues: 350 loop : -1.12 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 273 HIS 0.005 0.001 HIS V 47 PHE 0.033 0.001 PHE Q 120 TYR 0.015 0.001 TYR T 52 ARG 0.004 0.000 ARG M 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 293 time to evaluate : 4.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 315 LYS cc_start: 0.7404 (mmtt) cc_final: 0.7151 (mmtt) REVERT: G 28 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7780 (tttt) REVERT: G 64 GLU cc_start: 0.8207 (tp30) cc_final: 0.7854 (tp30) REVERT: H 7 VAL cc_start: 0.7173 (p) cc_final: 0.6867 (t) REVERT: H 8 ASP cc_start: 0.7976 (m-30) cc_final: 0.7720 (m-30) REVERT: H 14 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7768 (tm-30) REVERT: H 15 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7386 (mm-30) REVERT: H 51 ASP cc_start: 0.8346 (m-30) cc_final: 0.7998 (m-30) REVERT: K 35 LEU cc_start: 0.8607 (tp) cc_final: 0.8361 (tp) outliers start: 36 outliers final: 22 residues processed: 315 average time/residue: 0.4762 time to fit residues: 243.9427 Evaluate side-chains 294 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 272 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 21 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 40 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 313 optimal weight: 7.9990 chunk 213 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 279 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 320 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 chunk 337 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33730 Z= 0.181 Angle : 0.540 11.011 45668 Z= 0.260 Chirality : 0.040 0.231 4875 Planarity : 0.004 0.057 5715 Dihedral : 13.764 143.652 5626 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.10 % Allowed : 9.88 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3943 helix: 1.91 (0.11), residues: 2161 sheet: -0.58 (0.28), residues: 354 loop : -1.06 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 273 HIS 0.005 0.001 HIS T 44 PHE 0.032 0.001 PHE Q 120 TYR 0.015 0.001 TYR N 384 ARG 0.005 0.000 ARG N 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 284 time to evaluate : 4.077 Fit side-chains revert: symmetry clash REVERT: C 315 LYS cc_start: 0.7514 (mmtt) cc_final: 0.7254 (mmtt) REVERT: G 28 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7738 (tttt) REVERT: G 64 GLU cc_start: 0.8205 (tp30) cc_final: 0.7818 (tp30) REVERT: H 7 VAL cc_start: 0.7153 (p) cc_final: 0.6874 (t) REVERT: H 8 ASP cc_start: 0.8008 (m-30) cc_final: 0.7602 (m-30) REVERT: H 14 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7672 (tm-30) REVERT: H 15 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7353 (mm-30) REVERT: H 51 ASP cc_start: 0.8320 (m-30) cc_final: 0.7985 (m-30) REVERT: S 72 TYR cc_start: 0.6543 (m-10) cc_final: 0.6285 (m-80) outliers start: 37 outliers final: 22 residues processed: 313 average time/residue: 0.4695 time to fit residues: 239.9484 Evaluate side-chains 290 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 268 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 64 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 126 optimal weight: 0.9990 chunk 338 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 chunk 312 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 197 optimal weight: 0.5980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33730 Z= 0.174 Angle : 0.542 12.054 45668 Z= 0.261 Chirality : 0.040 0.243 4875 Planarity : 0.004 0.056 5715 Dihedral : 13.528 146.679 5625 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.07 % Allowed : 10.54 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3943 helix: 1.95 (0.11), residues: 2160 sheet: -0.47 (0.28), residues: 348 loop : -1.06 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 273 HIS 0.003 0.001 HIS C 203 PHE 0.032 0.001 PHE Q 120 TYR 0.025 0.001 TYR N 384 ARG 0.003 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 281 time to evaluate : 3.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 315 LYS cc_start: 0.7439 (mmtt) cc_final: 0.7121 (mmtt) REVERT: G 28 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7701 (tttt) REVERT: G 64 GLU cc_start: 0.8197 (tp30) cc_final: 0.7820 (tp30) REVERT: H 7 VAL cc_start: 0.7169 (p) cc_final: 0.6884 (t) REVERT: H 8 ASP cc_start: 0.8031 (m-30) cc_final: 0.7648 (m-30) REVERT: H 14 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7632 (tm-30) REVERT: H 15 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7372 (mm-30) REVERT: H 51 ASP cc_start: 0.8288 (m-30) cc_final: 0.7958 (m-30) REVERT: S 72 TYR cc_start: 0.6639 (m-10) cc_final: 0.6378 (m-80) outliers start: 36 outliers final: 26 residues processed: 306 average time/residue: 0.4583 time to fit residues: 227.8767 Evaluate side-chains 296 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 270 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 144 PHE Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 158 MET Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 362 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 374 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 33730 Z= 0.213 Angle : 0.563 14.011 45668 Z= 0.268 Chirality : 0.041 0.254 4875 Planarity : 0.004 0.057 5715 Dihedral : 13.392 149.125 5625 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.10 % Allowed : 10.99 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3943 helix: 1.95 (0.11), residues: 2159 sheet: -0.51 (0.28), residues: 354 loop : -1.05 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 273 HIS 0.005 0.001 HIS C 203 PHE 0.032 0.001 PHE Q 120 TYR 0.025 0.001 TYR N 384 ARG 0.004 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 280 time to evaluate : 3.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 315 LYS cc_start: 0.7507 (mmtt) cc_final: 0.6979 (mmtt) REVERT: G 64 GLU cc_start: 0.8208 (tp30) cc_final: 0.7816 (tp30) REVERT: H 7 VAL cc_start: 0.7207 (p) cc_final: 0.6936 (t) REVERT: H 8 ASP cc_start: 0.8051 (m-30) cc_final: 0.7686 (m-30) REVERT: H 14 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7686 (tm-30) REVERT: H 15 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7447 (mm-30) REVERT: H 51 ASP cc_start: 0.8306 (m-30) cc_final: 0.7978 (m-30) REVERT: S 72 TYR cc_start: 0.6750 (m-10) cc_final: 0.6442 (m-80) outliers start: 37 outliers final: 31 residues processed: 305 average time/residue: 0.4659 time to fit residues: 232.4794 Evaluate side-chains 301 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 270 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 158 MET Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 21 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 231 optimal weight: 0.0870 chunk 149 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 255 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 294 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33730 Z= 0.168 Angle : 0.545 12.948 45668 Z= 0.260 Chirality : 0.040 0.231 4875 Planarity : 0.004 0.057 5715 Dihedral : 13.093 152.217 5625 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.90 % Allowed : 11.53 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3943 helix: 2.02 (0.11), residues: 2147 sheet: -0.40 (0.28), residues: 348 loop : -1.01 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 273 HIS 0.003 0.001 HIS C 203 PHE 0.032 0.001 PHE Q 120 TYR 0.022 0.001 TYR N 384 ARG 0.005 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 280 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 315 LYS cc_start: 0.7412 (mmtt) cc_final: 0.7042 (mmtt) REVERT: G 64 GLU cc_start: 0.8166 (tp30) cc_final: 0.7763 (tp30) REVERT: H 7 VAL cc_start: 0.7210 (p) cc_final: 0.6939 (t) REVERT: H 8 ASP cc_start: 0.8061 (m-30) cc_final: 0.7631 (m-30) REVERT: H 11 ARG cc_start: 0.7586 (ptt180) cc_final: 0.7343 (ptt180) REVERT: H 14 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7624 (tm-30) REVERT: H 15 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7463 (mm-30) REVERT: H 51 ASP cc_start: 0.8232 (m-30) cc_final: 0.7854 (m-30) REVERT: O 145 MET cc_start: 0.8204 (tpp) cc_final: 0.7741 (mpp) REVERT: S 72 TYR cc_start: 0.6745 (m-10) cc_final: 0.6428 (m-80) outliers start: 30 outliers final: 23 residues processed: 303 average time/residue: 0.4551 time to fit residues: 224.1349 Evaluate side-chains 294 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 271 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 341 optimal weight: 0.2980 chunk 359 optimal weight: 4.9990 chunk 327 optimal weight: 7.9990 chunk 349 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 274 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 chunk 348 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33730 Z= 0.235 Angle : 0.579 12.365 45668 Z= 0.275 Chirality : 0.041 0.232 4875 Planarity : 0.004 0.058 5715 Dihedral : 13.125 152.630 5625 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.93 % Allowed : 11.82 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3943 helix: 1.94 (0.11), residues: 2158 sheet: -0.45 (0.28), residues: 354 loop : -1.01 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 273 HIS 0.005 0.001 HIS C 203 PHE 0.031 0.001 PHE Q 120 TYR 0.018 0.001 TYR T 52 ARG 0.004 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 272 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 64 GLU cc_start: 0.8208 (tp30) cc_final: 0.7816 (tp30) REVERT: H 7 VAL cc_start: 0.7220 (p) cc_final: 0.6959 (t) REVERT: H 8 ASP cc_start: 0.8095 (m-30) cc_final: 0.7710 (m-30) REVERT: H 11 ARG cc_start: 0.7575 (ptt180) cc_final: 0.7333 (ptt180) REVERT: H 14 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7591 (tm-30) REVERT: H 15 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7457 (mm-30) REVERT: H 51 ASP cc_start: 0.8273 (m-30) cc_final: 0.7937 (m-30) REVERT: S 72 TYR cc_start: 0.6746 (m-10) cc_final: 0.6463 (m-80) outliers start: 31 outliers final: 25 residues processed: 292 average time/residue: 0.4612 time to fit residues: 218.7937 Evaluate side-chains 291 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 266 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 158 MET Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 21 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 229 optimal weight: 3.9990 chunk 369 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 256 optimal weight: 5.9990 chunk 387 optimal weight: 9.9990 chunk 356 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 238 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33730 Z= 0.208 Angle : 0.573 12.219 45668 Z= 0.272 Chirality : 0.041 0.244 4875 Planarity : 0.004 0.057 5715 Dihedral : 13.067 153.581 5625 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.81 % Allowed : 12.09 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.14), residues: 3943 helix: 1.96 (0.11), residues: 2148 sheet: -0.38 (0.28), residues: 348 loop : -0.99 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 273 HIS 0.004 0.001 HIS C 203 PHE 0.031 0.001 PHE Q 120 TYR 0.019 0.001 TYR T 52 ARG 0.006 0.000 ARG D 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7886 Ramachandran restraints generated. 3943 Oldfield, 0 Emsley, 3943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 271 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 315 LYS cc_start: 0.7556 (mmtt) cc_final: 0.7005 (mttt) REVERT: G 64 GLU cc_start: 0.8173 (tp30) cc_final: 0.7785 (tp30) REVERT: H 7 VAL cc_start: 0.7237 (p) cc_final: 0.6972 (t) REVERT: H 8 ASP cc_start: 0.8085 (m-30) cc_final: 0.7714 (m-30) REVERT: H 11 ARG cc_start: 0.7573 (ptt180) cc_final: 0.7339 (ptt180) REVERT: H 14 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7591 (tm-30) REVERT: H 15 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7451 (mm-30) REVERT: H 51 ASP cc_start: 0.8271 (m-30) cc_final: 0.7932 (m-30) REVERT: O 145 MET cc_start: 0.8214 (tpp) cc_final: 0.7803 (mpp) REVERT: S 72 TYR cc_start: 0.6785 (m-10) cc_final: 0.6495 (m-80) outliers start: 27 outliers final: 26 residues processed: 289 average time/residue: 0.4763 time to fit residues: 223.9988 Evaluate side-chains 291 residues out of total 3349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 265 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 70 HIS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 322 VAL Chi-restraints excluded: chain M residue 383 GLU Chi-restraints excluded: chain N residue 158 MET Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain T residue 55 CYS Chi-restraints excluded: chain V residue 21 MET Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain W residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 245 optimal weight: 0.1980 chunk 328 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 284 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 309 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 475 GLN ** S 20 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 = 0.3338 r_free = 0.3338 target = 0.082410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.065051 restraints weight = 77787.976| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.19 r_work: 0.2865 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33730 Z= 0.181 Angle : 0.558 12.178 45668 Z= 0.265 Chirality : 0.040 0.227 4875 Planarity : 0.004 0.057 5715 Dihedral : 12.902 154.796 5625 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.81 % Allowed : 12.09 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3943 helix: 2.00 (0.11), residues: 2145 sheet: -0.36 (0.28), residues: 348 loop : -0.96 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 273 HIS 0.003 0.001 HIS C 203 PHE 0.031 0.001 PHE Q 120 TYR 0.021 0.001 TYR T 52 ARG 0.006 0.000 ARG D 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6973.09 seconds wall clock time: 128 minutes 27.25 seconds (7707.25 seconds total)