Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 21:10:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/04_2023/6lum_0981_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/04_2023/6lum_0981.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/04_2023/6lum_0981_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/04_2023/6lum_0981_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/04_2023/6lum_0981_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/04_2023/6lum_0981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/04_2023/6lum_0981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/04_2023/6lum_0981_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/04_2023/6lum_0981_neut_updated.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.056 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: 6 Type Number sf(0) Gaussians Fe 33 7.16 5 P 24 5.49 5 S 192 5.16 5 C 16857 2.51 5 N 4407 2.21 5 O 4678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 22": "NH1" <-> "NH2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ASP 463": "OD1" <-> "OD2" Residue "A PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ASP 504": "OD1" <-> "OD2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A ARG 566": "NH1" <-> "NH2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B ASP 219": "OD1" <-> "OD2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 98": "OD1" <-> "OD2" Residue "G PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H GLU 86": "OE1" <-> "OE2" Residue "H ASP 152": "OD1" <-> "OD2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J GLU 59": "OE1" <-> "OE2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "J ASP 81": "OD1" <-> "OD2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J ASP 96": "OD1" <-> "OD2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 137": "OD1" <-> "OD2" Residue "J ASP 166": "OD1" <-> "OD2" Residue "J PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 208": "NH1" <-> "NH2" Residue "J TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 236": "OD1" <-> "OD2" Residue "J ASP 283": "OD1" <-> "OD2" Residue "J ARG 287": "NH1" <-> "NH2" Residue "J ARG 292": "NH1" <-> "NH2" Residue "J GLU 297": "OE1" <-> "OE2" Residue "J ASP 371": "OD1" <-> "OD2" Residue "J ASP 403": "OD1" <-> "OD2" Residue "J ARG 410": "NH1" <-> "NH2" Residue "J PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 429": "OE1" <-> "OE2" Residue "J ASP 441": "OD1" <-> "OD2" Residue "J GLU 449": "OE1" <-> "OE2" Residue "J ARG 450": "NH1" <-> "NH2" Residue "J ARG 488": "NH1" <-> "NH2" Residue "J ASP 496": "OD1" <-> "OD2" Residue "J GLU 519": "OE1" <-> "OE2" Residue "J GLU 530": "OE1" <-> "OE2" Residue "J ARG 537": "NH1" <-> "NH2" Residue "J ASP 544": "OD1" <-> "OD2" Residue "J ASP 564": "OD1" <-> "OD2" Residue "J ARG 566": "NH1" <-> "NH2" Residue "J TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 581": "OE1" <-> "OE2" Residue "K PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "K TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 126": "OE1" <-> "OE2" Residue "K ASP 128": "OD1" <-> "OD2" Residue "K TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 169": "OD1" <-> "OD2" Residue "M ARG 22": "NH1" <-> "NH2" Residue "M ASP 98": "OD1" <-> "OD2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 78": "NH1" <-> "NH2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N ASP 152": "OD1" <-> "OD2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 96": "OD1" <-> "OD2" Residue "P ASP 113": "OD1" <-> "OD2" Residue "P ASP 123": "OD1" <-> "OD2" Residue "P ASP 155": "OD1" <-> "OD2" Residue "P GLU 161": "OE1" <-> "OE2" Residue "P ASP 166": "OD1" <-> "OD2" Residue "P PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 208": "NH1" <-> "NH2" Residue "P GLU 235": "OE1" <-> "OE2" Residue "P GLU 269": "OE1" <-> "OE2" Residue "P ASP 288": "OD1" <-> "OD2" Residue "P ASP 371": "OD1" <-> "OD2" Residue "P GLU 384": "OE1" <-> "OE2" Residue "P PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 417": "OE1" <-> "OE2" Residue "P ASP 426": "OD1" <-> "OD2" Residue "P GLU 445": "OE1" <-> "OE2" Residue "P ARG 450": "NH1" <-> "NH2" Residue "P ASP 463": "OD1" <-> "OD2" Residue "P GLU 472": "OE1" <-> "OE2" Residue "P GLU 473": "OE1" <-> "OE2" Residue "P ASP 481": "OD1" <-> "OD2" Residue "P ARG 488": "NH1" <-> "NH2" Residue "P ASP 504": "OD1" <-> "OD2" Residue "P GLU 507": "OE1" <-> "OE2" Residue "P GLU 516": "OE1" <-> "OE2" Residue "P ARG 537": "NH1" <-> "NH2" Residue "P ASP 539": "OD1" <-> "OD2" Residue "P TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 560": "OD1" <-> "OD2" Residue "P GLU 581": "OE1" <-> "OE2" Residue "Q GLU 36": "OE1" <-> "OE2" Residue "Q ASP 39": "OD1" <-> "OD2" Residue "Q PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ASP 138": "OD1" <-> "OD2" Residue "Q PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 169": "OD1" <-> "OD2" Residue "Q ASP 219": "OD1" <-> "OD2" Residue "Q GLU 252": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 26191 Number of models: 1 Model: "" Number of chains: 28 Chain: "C" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 978 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1193 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 137} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "A" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4129 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 518} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1873 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 221} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 989 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 991 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "I" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "J" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4109 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 513} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1938 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 227} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 961 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain: "O" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "P" Number of atoms: 4025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4025 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 20, 'TRANS': 518} Chain breaks: 1 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 103 Chain: "Q" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1849 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 221} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'PEV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "D" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 262 Unusual residues: {'CDL': 1, 'HEM': 2, 'LPP': 1, 'MQ9': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'MQ9:plan-3': 2, 'MQ9:plan-2': 2, 'MQ9:plan-10': 2, 'MQ9:plan-6': 2, 'MQ9:plan-5': 2, 'MQ9:plan-4': 2, 'MQ9:plan-9': 2} Unresolved non-hydrogen planarities: 68 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'PIE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "H" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 285 Unusual residues: {'CDL': 1, 'HEM': 2, 'LPP': 1, 'MQ9': 1, 'PIE': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'MQ9:plan-3': 1, 'MQ9:plan-2': 1, 'MQ9:plan-10': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1, 'MQ9:plan-9': 1} Unresolved non-hydrogen planarities: 35 Chain: "J" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'F3S': 1, 'FES': 1, 'PEV': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'HEM': 1, 'PEV': 1, 'PIE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "N" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 241 Unusual residues: {'CDL': 1, 'HEM': 1, 'LPP': 1, 'MQ9': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'MQ9:plan-3': 3, 'MQ9:plan-2': 3, 'MQ9:plan-10': 3, 'MQ9:plan-6': 3, 'MQ9:plan-5': 3, 'MQ9:plan-4': 3, 'MQ9:plan-9': 3} Unresolved non-hydrogen planarities: 104 Chain: "P" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'F3S': 1, 'FES': 1, 'PEV': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7005 SG CYS B 77 99.408 67.715 51.220 1.00 5.32 S ATOM 7037 SG CYS B 82 95.374 66.168 51.476 1.00 9.75 S ATOM 7144 SG CYS B 97 101.425 66.489 56.040 1.00 24.51 S ATOM 7798 SG CYS B 180 87.869 68.988 65.143 1.00 6.28 S ATOM 7781 SG CYS B 177 92.574 67.789 60.331 1.00 5.72 S ATOM 8272 SG CYS B 240 93.389 73.414 63.714 1.00 12.32 S ATOM 7759 SG CYS B 174 87.337 72.421 59.239 1.00 6.05 S ATOM 7824 SG CYS B 184 84.918 66.640 72.367 1.00 24.51 S ATOM 8195 SG CYS B 230 83.610 72.361 74.706 1.00 3.96 S ATOM 8245 SG CYS B 236 88.744 71.671 70.970 1.00 5.76 S ATOM 15288 SG CYS K 77 36.575 41.113 50.382 1.00 9.71 S ATOM 15320 SG CYS K 82 37.190 44.673 50.407 1.00 5.96 S ATOM 15427 SG CYS K 97 34.151 39.513 55.057 1.00 8.82 S ATOM 16081 SG CYS K 180 41.776 50.609 64.475 1.00 3.48 S ATOM 16064 SG CYS K 177 38.921 46.880 59.644 1.00 4.26 S ATOM 16555 SG CYS K 240 43.353 43.719 63.322 1.00 6.63 S ATOM 16042 SG CYS K 174 45.492 49.404 58.761 1.00 5.82 S ATOM 16107 SG CYS K 184 40.538 54.607 71.422 1.00 5.33 S ATOM 16478 SG CYS K 230 45.955 53.196 74.269 1.00 4.91 S ATOM 16528 SG CYS K 236 43.429 48.873 70.473 1.00 6.30 S ATOM 23527 SG CYS Q 97 43.352 113.457 52.931 1.00 13.81 S ATOM 23393 SG CYS Q 77 43.717 110.192 48.516 1.00 19.64 S ATOM 23420 SG CYS Q 82 46.221 107.691 48.440 1.00 11.90 S ATOM 24166 SG CYS Q 180 48.029 100.925 62.877 1.00 6.58 S ATOM 24149 SG CYS Q 177 46.582 105.319 57.675 1.00 7.54 S ATOM 24636 SG CYS Q 240 41.447 103.593 61.300 1.00 10.36 S ATOM 24127 SG CYS Q 174 45.288 98.294 57.087 1.00 12.42 S ATOM 24192 SG CYS Q 184 51.758 99.915 70.042 1.00 6.03 S ATOM 24559 SG CYS Q 230 47.504 96.178 72.709 1.00 10.47 S ATOM 24609 SG CYS Q 236 45.363 100.750 68.765 1.00 12.97 S Time building chain proxies: 14.09, per 1000 atoms: 0.54 Number of scatterers: 26191 At special positions: 0 Unit cell: (136.94, 145.14, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 33 26.01 S 192 16.00 P 24 15.00 O 4678 8.00 N 4407 7.00 C 16857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=15, symmetry=0 Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.93 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 184 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 236 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 230 " pdb=" F3S K 303 " pdb="FE3 F3S K 303 " - pdb=" SG CYS K 230 " pdb="FE4 F3S K 303 " - pdb=" SG CYS K 236 " pdb="FE1 F3S K 303 " - pdb=" SG CYS K 184 " pdb=" F3S Q 303 " pdb="FE1 F3S Q 303 " - pdb=" SG CYS Q 184 " pdb="FE3 F3S Q 303 " - pdb=" SG CYS Q 230 " pdb="FE4 F3S Q 303 " - pdb=" SG CYS Q 236 " pdb=" FES B 301 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 97 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 82 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 77 " pdb=" FES K 301 " pdb="FE2 FES K 301 " - pdb=" SG CYS K 97 " pdb="FE1 FES K 301 " - pdb=" SG CYS K 82 " pdb="FE1 FES K 301 " - pdb=" SG CYS K 77 " pdb=" FES Q 301 " pdb="FE2 FES Q 301 " - pdb=" SG CYS Q 82 " pdb="FE1 FES Q 301 " - pdb=" SG CYS Q 97 " pdb="FE2 FES Q 301 " - pdb=" SG CYS Q 77 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 177 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 240 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 180 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 174 " pdb=" SF4 K 302 " pdb="FE1 SF4 K 302 " - pdb=" SG CYS K 180 " pdb="FE2 SF4 K 302 " - pdb=" SG CYS K 177 " pdb="FE3 SF4 K 302 " - pdb=" SG CYS K 240 " pdb="FE4 SF4 K 302 " - pdb=" SG CYS K 174 " pdb=" SF4 Q 302 " pdb="FE2 SF4 Q 302 " - pdb=" SG CYS Q 177 " pdb="FE3 SF4 Q 302 " - pdb=" SG CYS Q 240 " pdb="FE1 SF4 Q 302 " - pdb=" SG CYS Q 180 " pdb="FE4 SF4 Q 302 " - pdb=" SG CYS Q 174 " Number of angles added : 75 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 18 sheets defined 45.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'C' and resid 25 through 55 removed outlier: 4.664A pdb=" N VAL C 54 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'C' and resid 71 through 99 Processing helix chain 'C' and resid 103 through 106 No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 110 through 134 Processing helix chain 'D' and resid 26 through 29 Processing helix chain 'D' and resid 43 through 70 removed outlier: 4.224A pdb=" N PHE D 60 " --> pdb=" O ILE D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 78 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.540A pdb=" N ALA D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 119 Processing helix chain 'D' and resid 123 through 149 Processing helix chain 'E' and resid 2 through 28 Processing helix chain 'A' and resid 16 through 28 Proline residue: A 27 - end of helix Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 43 through 46 Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 80 through 100 removed outlier: 5.127A pdb=" N ASP A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 257 through 260 No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 399 through 421 Processing helix chain 'A' and resid 431 through 443 removed outlier: 4.164A pdb=" N MET A 434 " --> pdb=" O PRO A 431 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 439 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 465 Processing helix chain 'A' and resid 472 through 488 Processing helix chain 'A' and resid 503 through 527 removed outlier: 3.553A pdb=" N PHE A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.796A pdb=" N ALA B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 185 through 188 No H-bonds generated for 'chain 'B' and resid 185 through 188' Processing helix chain 'B' and resid 196 through 206 removed outlier: 4.176A pdb=" N PHE B 205 " --> pdb=" O ASN B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'G' and resid 25 through 55 removed outlier: 4.704A pdb=" N VAL G 54 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ARG G 55 " --> pdb=" O THR G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 67 Processing helix chain 'G' and resid 71 through 99 Processing helix chain 'G' and resid 104 through 136 removed outlier: 3.851A pdb=" N GLN G 107 " --> pdb=" O PRO G 104 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG G 108 " --> pdb=" O ARG G 105 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE G 121 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE G 129 " --> pdb=" O VAL G 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 70 removed outlier: 4.238A pdb=" N PHE H 60 " --> pdb=" O ILE H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 78 Processing helix chain 'H' and resid 81 through 87 Processing helix chain 'H' and resid 91 through 119 Processing helix chain 'H' and resid 123 through 150 Processing helix chain 'I' and resid 2 through 28 Processing helix chain 'J' and resid 16 through 24 Processing helix chain 'J' and resid 43 through 46 Processing helix chain 'J' and resid 63 through 73 Processing helix chain 'J' and resid 80 through 100 removed outlier: 4.353A pdb=" N ASP J 92 " --> pdb=" O LYS J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 153 Processing helix chain 'J' and resid 223 through 229 Processing helix chain 'J' and resid 274 through 277 No H-bonds generated for 'chain 'J' and resid 274 through 277' Processing helix chain 'J' and resid 287 through 298 Processing helix chain 'J' and resid 399 through 421 Processing helix chain 'J' and resid 433 through 443 Processing helix chain 'J' and resid 451 through 464 Processing helix chain 'J' and resid 472 through 488 Processing helix chain 'J' and resid 504 through 527 Processing helix chain 'K' and resid 56 through 65 Processing helix chain 'K' and resid 96 through 98 No H-bonds generated for 'chain 'K' and resid 96 through 98' Processing helix chain 'K' and resid 134 through 142 Processing helix chain 'K' and resid 162 through 165 No H-bonds generated for 'chain 'K' and resid 162 through 165' Processing helix chain 'K' and resid 181 through 183 No H-bonds generated for 'chain 'K' and resid 181 through 183' Processing helix chain 'K' and resid 185 through 188 No H-bonds generated for 'chain 'K' and resid 185 through 188' Processing helix chain 'K' and resid 196 through 206 removed outlier: 4.111A pdb=" N PHE K 205 " --> pdb=" O ASN K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 220 Processing helix chain 'K' and resid 227 through 229 No H-bonds generated for 'chain 'K' and resid 227 through 229' Processing helix chain 'K' and resid 235 through 239 Processing helix chain 'K' and resid 246 through 258 Processing helix chain 'M' and resid 25 through 54 removed outlier: 4.622A pdb=" N VAL M 54 " --> pdb=" O ASP M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 69 Processing helix chain 'M' and resid 71 through 99 Processing helix chain 'M' and resid 103 through 106 No H-bonds generated for 'chain 'M' and resid 103 through 106' Processing helix chain 'M' and resid 110 through 136 removed outlier: 3.857A pdb=" N ALA M 124 " --> pdb=" O VAL M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 70 removed outlier: 4.237A pdb=" N PHE N 60 " --> pdb=" O ILE N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 78 Processing helix chain 'N' and resid 81 through 87 Processing helix chain 'N' and resid 91 through 119 Processing helix chain 'N' and resid 123 through 150 Processing helix chain 'O' and resid 2 through 28 Processing helix chain 'P' and resid 16 through 25 Processing helix chain 'P' and resid 43 through 46 Processing helix chain 'P' and resid 63 through 73 Processing helix chain 'P' and resid 80 through 100 removed outlier: 4.121A pdb=" N ASP P 92 " --> pdb=" O LYS P 88 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 153 Processing helix chain 'P' and resid 223 through 230 removed outlier: 4.345A pdb=" N LYS P 230 " --> pdb=" O ILE P 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 274 through 277 No H-bonds generated for 'chain 'P' and resid 274 through 277' Processing helix chain 'P' and resid 287 through 300 Processing helix chain 'P' and resid 400 through 421 Processing helix chain 'P' and resid 433 through 443 Processing helix chain 'P' and resid 451 through 465 Processing helix chain 'P' and resid 472 through 490 removed outlier: 4.202A pdb=" N SER P 490 " --> pdb=" O LYS P 486 " (cutoff:3.500A) Processing helix chain 'P' and resid 504 through 527 removed outlier: 3.582A pdb=" N PHE P 513 " --> pdb=" O ILE P 509 " (cutoff:3.500A) Processing helix chain 'P' and resid 545 through 548 No H-bonds generated for 'chain 'P' and resid 545 through 548' Processing helix chain 'Q' and resid 56 through 65 Processing helix chain 'Q' and resid 96 through 98 No H-bonds generated for 'chain 'Q' and resid 96 through 98' Processing helix chain 'Q' and resid 105 through 107 No H-bonds generated for 'chain 'Q' and resid 105 through 107' Processing helix chain 'Q' and resid 134 through 142 Processing helix chain 'Q' and resid 162 through 165 No H-bonds generated for 'chain 'Q' and resid 162 through 165' Processing helix chain 'Q' and resid 181 through 183 No H-bonds generated for 'chain 'Q' and resid 181 through 183' Processing helix chain 'Q' and resid 185 through 188 No H-bonds generated for 'chain 'Q' and resid 185 through 188' Processing helix chain 'Q' and resid 196 through 206 removed outlier: 4.154A pdb=" N PHE Q 205 " --> pdb=" O ASN Q 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 221 Processing helix chain 'Q' and resid 227 through 229 No H-bonds generated for 'chain 'Q' and resid 227 through 229' Processing helix chain 'Q' and resid 235 through 239 Processing helix chain 'Q' and resid 246 through 258 Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.725A pdb=" N GLY A 180 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR A 184 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ALA A 164 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 198 through 201 removed outlier: 6.822A pdb=" N GLU A 157 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N THR A 35 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE A 159 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 169 through 172 Processing sheet with id= D, first strand: chain 'A' and resid 550 through 556 Processing sheet with id= E, first strand: chain 'A' and resid 240 through 243 removed outlier: 5.854A pdb=" N HIS A 243 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N CYS A 353 " --> pdb=" O HIS A 243 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 43 through 48 Processing sheet with id= G, first strand: chain 'J' and resid 4 through 6 removed outlier: 8.289A pdb=" N HIS J 5 " --> pdb=" O ILE J 191 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL J 193 " --> pdb=" O HIS J 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY J 180 " --> pdb=" O ALA J 168 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR J 184 " --> pdb=" O ALA J 164 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA J 164 " --> pdb=" O TYR J 184 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 199 through 201 removed outlier: 6.355A pdb=" N VAL J 10 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA J 32 " --> pdb=" O ILE J 11 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU J 157 " --> pdb=" O VAL J 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'J' and resid 169 through 172 Processing sheet with id= J, first strand: chain 'J' and resid 550 through 556 Processing sheet with id= K, first strand: chain 'J' and resid 240 through 243 removed outlier: 5.996A pdb=" N HIS J 243 " --> pdb=" O CYS J 353 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N CYS J 353 " --> pdb=" O HIS J 243 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 42 through 47 Processing sheet with id= M, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.808A pdb=" N GLY P 180 " --> pdb=" O ALA P 168 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP P 166 " --> pdb=" O ILE P 182 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR P 184 " --> pdb=" O ALA P 164 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA P 164 " --> pdb=" O TYR P 184 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'P' and resid 32 through 34 Processing sheet with id= O, first strand: chain 'P' and resid 169 through 172 Processing sheet with id= P, first strand: chain 'P' and resid 233 through 235 Processing sheet with id= Q, first strand: chain 'P' and resid 240 through 243 removed outlier: 3.628A pdb=" N TYR P 355 " --> pdb=" O GLN P 241 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS P 243 " --> pdb=" O CYS P 353 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS P 353 " --> pdb=" O HIS P 243 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Q' and resid 42 through 48 1102 hydrogen bonds defined for protein. 3156 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: 8.55 Time building geometry restraints manager: 11.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.78: 26521 1.78 - 2.38: 302 2.38 - 2.99: 0 2.99 - 3.60: 0 3.60 - 4.20: 9 Bond restraints: 26832 Sorted by residual: bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 4.205 -1.972 2.00e-02 2.50e+03 9.72e+03 bond pdb=" S4 F3S Q 303 " pdb="FE1 F3S Q 303 " ideal model delta sigma weight residual 2.233 4.203 -1.970 2.00e-02 2.50e+03 9.70e+03 bond pdb=" S4 F3S K 303 " pdb="FE1 F3S K 303 " ideal model delta sigma weight residual 2.233 4.181 -1.948 2.00e-02 2.50e+03 9.48e+03 bond pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.258 4.183 -1.925 2.00e-02 2.50e+03 9.26e+03 bond pdb=" S1 F3S Q 303 " pdb="FE4 F3S Q 303 " ideal model delta sigma weight residual 2.258 4.175 -1.917 2.00e-02 2.50e+03 9.19e+03 ... (remaining 26827 not shown) Histogram of bond angle deviations from ideal: 41.65 - 69.19: 18 69.19 - 96.73: 132 96.73 - 124.27: 35492 124.27 - 151.81: 782 151.81 - 179.35: 12 Bond angle restraints: 36436 Sorted by residual: angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 41.65 73.10 3.00e+00 1.11e-01 5.94e+02 angle pdb=" S1 F3S K 303 " pdb="FE4 F3S K 303 " pdb=" S3 F3S K 303 " ideal model delta sigma weight residual 114.75 41.82 72.93 3.00e+00 1.11e-01 5.91e+02 angle pdb=" S1 F3S Q 303 " pdb="FE4 F3S Q 303 " pdb=" S3 F3S Q 303 " ideal model delta sigma weight residual 114.75 41.84 72.91 3.00e+00 1.11e-01 5.91e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 42.45 70.14 3.00e+00 1.11e-01 5.47e+02 angle pdb=" S3 F3S Q 303 " pdb="FE1 F3S Q 303 " pdb=" S4 F3S Q 303 " ideal model delta sigma weight residual 112.59 43.09 69.50 3.00e+00 1.11e-01 5.37e+02 ... (remaining 36431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13667 17.98 - 35.97: 1444 35.97 - 53.95: 335 53.95 - 71.93: 81 71.93 - 89.91: 22 Dihedral angle restraints: 15549 sinusoidal: 6433 harmonic: 9116 Sorted by residual: dihedral pdb=" CA ASN K 37 " pdb=" C ASN K 37 " pdb=" N PRO K 38 " pdb=" CA PRO K 38 " ideal model delta harmonic sigma weight residual 180.00 149.08 30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA GLY K 80 " pdb=" C GLY K 80 " pdb=" N VAL K 81 " pdb=" CA VAL K 81 " ideal model delta harmonic sigma weight residual -180.00 -149.26 -30.74 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA GLY B 80 " pdb=" C GLY B 80 " pdb=" N VAL B 81 " pdb=" CA VAL B 81 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 15546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.335: 3927 1.335 - 2.669: 0 2.669 - 4.003: 0 4.003 - 5.338: 3 5.338 - 6.672: 3 Chirality restraints: 3933 Sorted by residual: chirality pdb=" S2 F3S Q 303 " pdb="FE1 F3S Q 303 " pdb="FE3 F3S Q 303 " pdb="FE4 F3S Q 303 " both_signs ideal model delta sigma weight residual False 10.77 4.10 6.67 2.00e-01 2.50e+01 1.11e+03 chirality pdb=" S2 F3S K 303 " pdb="FE1 F3S K 303 " pdb="FE3 F3S K 303 " pdb="FE4 F3S K 303 " both_signs ideal model delta sigma weight residual False 10.77 4.65 6.11 2.00e-01 2.50e+01 9.34e+02 chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 4.73 6.04 2.00e-01 2.50e+01 9.11e+02 ... (remaining 3930 not shown) Planarity restraints: 4540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 MQ9 N 203 " -0.367 2.00e-02 2.50e+03 5.12e-01 3.28e+03 pdb=" C11 MQ9 N 203 " -0.275 2.00e-02 2.50e+03 pdb=" C7 MQ9 N 203 " -0.572 2.00e-02 2.50e+03 pdb=" C8 MQ9 N 203 " 0.746 2.00e-02 2.50e+03 pdb=" C9 MQ9 N 203 " 0.467 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 MQ9 H 204 " -0.282 2.00e-02 2.50e+03 3.17e-01 1.26e+03 pdb=" C13 MQ9 H 204 " 0.578 2.00e-02 2.50e+03 pdb=" C14 MQ9 H 204 " -0.296 2.00e-02 2.50e+03 pdb=" C15 MQ9 H 204 " 0.022 2.00e-02 2.50e+03 pdb=" C16 MQ9 H 204 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 MQ9 D 205 " -0.280 2.00e-02 2.50e+03 3.16e-01 1.25e+03 pdb=" C13 MQ9 D 205 " 0.571 2.00e-02 2.50e+03 pdb=" C14 MQ9 D 205 " -0.303 2.00e-02 2.50e+03 pdb=" C15 MQ9 D 205 " -0.041 2.00e-02 2.50e+03 pdb=" C16 MQ9 D 205 " 0.053 2.00e-02 2.50e+03 ... (remaining 4537 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 347 2.63 - 3.20: 23547 3.20 - 3.76: 39054 3.76 - 4.33: 57763 4.33 - 4.90: 97387 Nonbonded interactions: 218098 Sorted by model distance: nonbonded pdb=" O THR K 233 " pdb=" S4 F3S K 303 " model vdw 2.061 3.400 nonbonded pdb=" O ILE D 68 " pdb=" NH2 ARG D 78 " model vdw 2.086 2.520 nonbonded pdb=" OH TYR P 501 " pdb=" OE1 GLU Q 126 " model vdw 2.087 2.440 nonbonded pdb=" O PHE H 50 " pdb=" OG SER H 54 " model vdw 2.087 2.440 nonbonded pdb=" O PHE N 50 " pdb=" OG SER N 54 " model vdw 2.088 2.440 ... (remaining 218093 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 2 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 108 or (resid 109 and (name \ N or name CA or name C or name O or name CB )) or resid 110 through 121 or (resi \ d 122 and (name N or name CA or name C or name O or name CB )) or resid 123 thro \ ugh 130 or (resid 131 through 132 and (name N or name CA or name C or name O or \ name CB )) or resid 133 through 137 or (resid 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 170 or (resid 171 and (name N or \ name CA or name C or name O or name CB )) or resid 172 through 255 or (resid 25 \ 6 through 257 and (name N or name CA or name C or name O or name CB )) or resid \ 258 through 260 or (resid 261 and (name N or name CA or name C or name O or name \ CB )) or resid 262 through 268 or (resid 269 and (name N or name CA or name C o \ r name O or name CB )) or resid 270 through 275 or (resid 276 through 278 and (n \ ame N or name CA or name C or name O or name CB )) or resid 279 through 280 or ( \ resid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 \ through 286 or (resid 287 and (name N or name CA or name C or name O or name CB \ )) or resid 288 through 296 or (resid 297 and (name N or name CA or name C or na \ me O or name CB )) or resid 298 through 300 or resid 347 through 426 or (resid 4 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 428 through \ 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) or r \ esid 431 through 440 or (resid 441 and (name N or name CA or name C or name O or \ name CB )) or resid 442 through 448 or (resid 449 and (name N or name CA or nam \ e C or name O or name CB )) or resid 450 through 468 or (resid 469 and (name N o \ r name CA or name C or name O or name CB )) or resid 470 through 531 or (resid 5 \ 32 and (name N or name CA or name C or name O or name CB )) or resid 533 through \ 569 or (resid 570 and (name N or name CA or name C or name O or name CB )) or r \ esid 571 through 577 or (resid 578 and (name N or name CA or name C or name O or \ name CB )) or resid 579 through 581 or resid 700)) selection = (chain 'J' and (resid 2 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 108 or (resid 109 and (name \ N or name CA or name C or name O or name CB )) or resid 110 through 121 or (resi \ d 122 and (name N or name CA or name C or name O or name CB )) or resid 123 thro \ ugh 125 or (resid 126 through 127 and (name N or name CA or name C or name O or \ name CB )) or resid 128 through 130 or (resid 131 through 132 and (name N or nam \ e CA or name C or name O or name CB )) or resid 133 through 137 or (resid 138 an \ d (name N or name CA or name C or name O or name CB )) or resid 139 through 156 \ or (resid 157 and (name N or name CA or name C or name O or name CB )) or resid \ 158 through 170 or (resid 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 260 or (resid 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 275 or (resid 276 through 278 and (n \ ame N or name CA or name C or name O or name CB )) or resid 279 through 280 or ( \ resid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 \ through 286 or (resid 287 and (name N or name CA or name C or name O or name CB \ )) or resid 288 through 296 or (resid 297 and (name N or name CA or name C or na \ me O or name CB )) or resid 298 through 426 or (resid 427 and (name N or name CA \ or name C or name O or name CB )) or resid 428 or (resid 429 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 and (name N or name CA or name C or name O or name CB )) or resid 434 \ through 440 or (resid 441 and (name N or name CA or name C or name O or name CB \ )) or resid 442 through 448 or (resid 449 and (name N or name CA or name C or na \ me O or name CB )) or resid 450 through 468 or (resid 469 and (name N or name CA \ or name C or name O or name CB )) or resid 470 through 531 or (resid 532 and (n \ ame N or name CA or name C or name O or name CB )) or resid 533 through 569 or ( \ resid 570 and (name N or name CA or name C or name O or name CB )) or resid 571 \ through 577 or (resid 578 and (name N or name CA or name C or name O or name CB \ )) or resid 579 through 581 or resid 700)) selection = (chain 'P' and (resid 2 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )) or resid 158 through 268 or (resid 269 and (name N or \ name CA or name C or name O or name CB )) or resid 270 through 300 or resid 347 \ through 432 or (resid 433 and (name N or name CA or name C or name O or name CB \ )) or resid 434 through 581 or resid 700)) } ncs_group { reference = (chain 'B' and (resid 23 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 111 or (resid 112 \ and (name N or name CA or name C or name O or name CB )) or resid 113 through 15 \ 6 or (resid 157 and (name N or name CA or name C or name O or name CB )) or resi \ d 158 through 159 or (resid 160 and (name N or name CA or name C or name O or na \ me CB )) or resid 161 through 211 or (resid 212 through 215 and (name N or name \ CA or name C or name O or name CB )) or resid 216 through 260 or resid 301 throu \ gh 303)) selection = (chain 'K' and (resid 23 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 111 or (resid 112 \ and (name N or name CA or name C or name O or name CB )) or resid 113 through 15 \ 6 or (resid 157 and (name N or name CA or name C or name O or name CB )) or resi \ d 158 through 159 or (resid 160 and (name N or name CA or name C or name O or na \ me CB )) or resid 161 through 211 or (resid 212 through 215 and (name N or name \ CA or name C or name O or name CB )) or resid 216 through 260 or resid 301 throu \ gh 303)) selection = (chain 'Q' and (resid 23 through 260 or resid 301 through 303)) } ncs_group { reference = (chain 'C' and (resid 16 through 136 or resid 202)) selection = (chain 'G' and (resid 16 through 136 or resid 201)) selection = (chain 'M' and (resid 16 through 136 or resid 203)) } ncs_group { reference = (chain 'E' and resid 1 through 31) selection = chain 'I' selection = chain 'O' } ncs_group { reference = (chain 'H' and (resid 41 through 156 or resid 202 or resid 204)) selection = (chain 'N' and (resid 41 through 156 or resid 202 or resid 204)) } 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 13.860 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 71.300 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.200 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: 0.010 Load rotamer database and sin/cos tables:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.038 1.972 26832 Z= 2.488 Angle : 1.828 73.100 36436 Z= 0.839 Chirality : 0.232 6.672 3933 Planarity : 0.016 0.512 4540 Dihedral : 15.908 89.914 9705 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.77 % Favored : 90.07 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.13), residues: 3142 helix: -0.95 (0.12), residues: 1515 sheet: -2.05 (0.30), residues: 231 loop : -3.92 (0.12), residues: 1396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 428 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 4 residues processed: 464 average time/residue: 1.4534 time to fit residues: 780.0820 Evaluate side-chains 350 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 346 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.2925 time to fit residues: 4.2609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 20.0000 chunk 235 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 282 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 87 HIS D 30 HIS A 57 ASN A 105 ASN A 114 GLN A 141 HIS A 195 HIS ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 421 ASN A 459 GLN A 465 ASN B 79 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN G 33 HIS G 47 HIS G 87 HIS G 109 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 459 GLN J 460 GLN J 464 ASN J 477 GLN J 557 GLN K 90 ASN K 132 ASN K 160 GLN K 245 GLN M 33 HIS M 87 HIS M 132 HIS N 123 ASN ** P 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 62 ASN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 241 GLN P 267 ASN P 405 ASN P 459 GLN P 465 ASN P 527 ASN P 557 GLN Q 132 ASN Q 245 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.157 26832 Z= 0.261 Angle : 1.180 89.330 36436 Z= 0.457 Chirality : 0.052 1.253 3933 Planarity : 0.005 0.071 4540 Dihedral : 12.166 85.558 4097 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3142 helix: 0.39 (0.13), residues: 1509 sheet: -1.47 (0.32), residues: 215 loop : -3.35 (0.13), residues: 1418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 374 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 32 residues processed: 421 average time/residue: 1.4218 time to fit residues: 696.4220 Evaluate side-chains 368 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 336 time to evaluate : 2.878 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 23 residues processed: 11 average time/residue: 0.3006 time to fit residues: 9.6134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 192 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 282 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 chunk 251 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 226 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 215 ASN J 423 ASN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.164 26832 Z= 0.235 Angle : 1.048 84.744 36436 Z= 0.411 Chirality : 0.063 2.321 3933 Planarity : 0.005 0.048 4540 Dihedral : 11.078 83.905 4097 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 3142 helix: 0.93 (0.13), residues: 1517 sheet: -0.96 (0.33), residues: 213 loop : -3.00 (0.14), residues: 1412 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 407 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 31 residues processed: 456 average time/residue: 1.3994 time to fit residues: 746.1244 Evaluate side-chains 391 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 360 time to evaluate : 2.902 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 7 average time/residue: 0.2564 time to fit residues: 7.2393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 7.9990 chunk 212 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 135 optimal weight: 0.0040 chunk 189 optimal weight: 0.9980 chunk 283 optimal weight: 20.0000 chunk 300 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 81 optimal weight: 0.3980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 423 ASN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN P 114 GLN ** P 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.103 26832 Z= 0.211 Angle : 1.042 83.270 36436 Z= 0.406 Chirality : 0.057 1.485 3933 Planarity : 0.004 0.048 4540 Dihedral : 10.566 80.891 4097 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3142 helix: 1.27 (0.13), residues: 1507 sheet: -0.67 (0.33), residues: 214 loop : -2.80 (0.15), residues: 1421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 373 time to evaluate : 3.028 Fit side-chains revert: symmetry clash outliers start: 80 outliers final: 41 residues processed: 427 average time/residue: 1.3421 time to fit residues: 673.3134 Evaluate side-chains 392 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 351 time to evaluate : 4.229 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 29 residues processed: 14 average time/residue: 0.4572 time to fit residues: 14.8826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 207 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 112 GLN J 48 GLN J 57 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 423 ASN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN P 57 ASN P 150 ASN P 354 HIS P 372 ASN ** P 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.152 26832 Z= 0.508 Angle : 1.155 84.953 36436 Z= 0.467 Chirality : 0.062 1.411 3933 Planarity : 0.005 0.052 4540 Dihedral : 11.215 77.741 4097 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer Outliers : 3.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 3142 helix: 0.80 (0.13), residues: 1498 sheet: -0.83 (0.33), residues: 223 loop : -2.80 (0.15), residues: 1421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 350 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 50 residues processed: 413 average time/residue: 1.3639 time to fit residues: 663.4185 Evaluate side-chains 395 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 345 time to evaluate : 2.922 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 37 residues processed: 15 average time/residue: 0.3828 time to fit residues: 13.1104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 176 optimal weight: 0.2980 chunk 74 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 423 ASN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 HIS ** P 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.103 26832 Z= 0.327 Angle : 1.098 84.547 36436 Z= 0.435 Chirality : 0.059 1.428 3933 Planarity : 0.005 0.050 4540 Dihedral : 10.776 76.952 4097 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer Outliers : 3.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.15), residues: 3142 helix: 0.93 (0.13), residues: 1500 sheet: -0.73 (0.33), residues: 223 loop : -2.72 (0.15), residues: 1419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 353 time to evaluate : 3.152 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 51 residues processed: 405 average time/residue: 1.4208 time to fit residues: 671.5559 Evaluate side-chains 384 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 333 time to evaluate : 2.919 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 37 residues processed: 16 average time/residue: 0.5535 time to fit residues: 16.3147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 219 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 253 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 79 HIS ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 GLN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 267 ASN ** P 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 26832 Z= 0.302 Angle : 1.087 84.799 36436 Z= 0.430 Chirality : 0.058 1.446 3933 Planarity : 0.005 0.052 4540 Dihedral : 10.406 75.500 4097 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3142 helix: 1.04 (0.13), residues: 1499 sheet: -0.65 (0.33), residues: 219 loop : -2.65 (0.15), residues: 1424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 346 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 48 residues processed: 401 average time/residue: 1.3825 time to fit residues: 654.3376 Evaluate side-chains 382 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 334 time to evaluate : 3.046 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 41 residues processed: 10 average time/residue: 0.6257 time to fit residues: 12.2933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 235 optimal weight: 20.0000 chunk 272 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN G 132 HIS ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 26832 Z= 0.263 Angle : 1.073 84.531 36436 Z= 0.422 Chirality : 0.058 1.460 3933 Planarity : 0.004 0.052 4540 Dihedral : 10.112 74.547 4097 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3142 helix: 1.18 (0.13), residues: 1502 sheet: -0.57 (0.33), residues: 219 loop : -2.60 (0.15), residues: 1421 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 343 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 48 residues processed: 402 average time/residue: 1.3269 time to fit residues: 628.7582 Evaluate side-chains 382 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 334 time to evaluate : 2.828 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 41 residues processed: 9 average time/residue: 0.3999 time to fit residues: 9.4373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 252 optimal weight: 9.9990 chunk 264 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.100 26832 Z= 0.302 Angle : 1.089 84.891 36436 Z= 0.431 Chirality : 0.058 1.453 3933 Planarity : 0.005 0.052 4540 Dihedral : 10.147 74.275 4097 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3142 helix: 1.14 (0.13), residues: 1506 sheet: -0.54 (0.34), residues: 219 loop : -2.58 (0.15), residues: 1417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 346 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 47 residues processed: 391 average time/residue: 1.3137 time to fit residues: 607.7378 Evaluate side-chains 391 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 344 time to evaluate : 2.865 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 42 residues processed: 8 average time/residue: 0.4489 time to fit residues: 9.5025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 0.0000 chunk 180 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 309 optimal weight: 0.3980 chunk 285 optimal weight: 7.9990 chunk 246 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 574 GLN Q 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 26832 Z= 0.230 Angle : 1.064 84.221 36436 Z= 0.417 Chirality : 0.057 1.446 3933 Planarity : 0.004 0.052 4540 Dihedral : 9.835 74.652 4097 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3142 helix: 1.30 (0.13), residues: 1515 sheet: -0.33 (0.34), residues: 215 loop : -2.51 (0.15), residues: 1412 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 353 time to evaluate : 2.848 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 41 residues processed: 396 average time/residue: 1.3394 time to fit residues: 626.5366 Evaluate side-chains 379 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 338 time to evaluate : 2.985 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 38 residues processed: 4 average time/residue: 0.3060 time to fit residues: 6.1304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 50.0000 chunk 75 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 253 optimal weight: 10.0000 chunk 31 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 574 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.170639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123267 restraints weight = 28280.495| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.00 r_work: 0.3192 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 26832 Z= 0.243 Angle : 1.069 84.498 36436 Z= 0.420 Chirality : 0.057 1.436 3933 Planarity : 0.004 0.052 4540 Dihedral : 9.741 73.441 4097 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 3142 helix: 1.33 (0.13), residues: 1509 sheet: -0.37 (0.34), residues: 218 loop : -2.49 (0.15), residues: 1415 =============================================================================== Job complete usr+sys time: 10125.43 seconds wall clock time: 180 minutes 28.42 seconds (10828.42 seconds total)