Starting phenix.real_space_refine on Sun Mar 17 14:46:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oce_12805/03_2024/7oce_12805_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oce_12805/03_2024/7oce_12805.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oce_12805/03_2024/7oce_12805_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oce_12805/03_2024/7oce_12805_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oce_12805/03_2024/7oce_12805_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oce_12805/03_2024/7oce_12805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oce_12805/03_2024/7oce_12805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oce_12805/03_2024/7oce_12805_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oce_12805/03_2024/7oce_12805_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12090 2.51 5 N 2800 2.21 5 O 3088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 389": "NH1" <-> "NH2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 515": "OD1" <-> "OD2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 624": "NH1" <-> "NH2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 519": "OD1" <-> "OD2" Residue "B TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B ASP 728": "OD1" <-> "OD2" Residue "B GLU 772": "OE1" <-> "OE2" Residue "B PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 59": "NH1" <-> "NH2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "D TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 519": "OD1" <-> "OD2" Residue "D TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "D ASP 728": "OD1" <-> "OD2" Residue "D GLU 772": "OE1" <-> "OE2" Residue "D PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 216": "OE1" <-> "OE2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 515": "OD1" <-> "OD2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "C PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 624": "NH1" <-> "NH2" Residue "C GLU 633": "OE1" <-> "OE2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 656": "NH1" <-> "NH2" Residue "C TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 809": "OE1" <-> "OE2" Residue "C PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18092 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3013 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 395} Chain breaks: 2 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 2975 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 16, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1248 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "I" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1284 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 2975 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 16, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "J" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1284 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3013 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 395} Chain breaks: 2 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1248 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 142 Unusual residues: {'E2Q': 1, 'PC1': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Unusual residues: {'E2Q': 1, 'PC1': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PC1:plan-2': 8, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'CLR': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'PC1': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Unusual residues: {'E2Q': 1, 'PC1': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PC1:plan-2': 8, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 35 Chain: "J" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'PC1': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 142 Unusual residues: {'E2Q': 1, 'PC1': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'CLR': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 9.49, per 1000 atoms: 0.52 Number of scatterers: 18092 At special positions: 0 Unit cell: (123.05, 110.21, 148.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 3088 8.00 N 2800 7.00 C 12090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.05 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.59 Conformation dependent library (CDL) restraints added in 3.3 seconds 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4276 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 14 sheets defined 54.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 413 through 416 removed outlier: 3.834A pdb=" N ARG A 416 " --> pdb=" O GLY A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 479 through 484 removed outlier: 4.080A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 592 through 625 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 661 through 669 Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 702 through 709 Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 789 through 819 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 523 through 546 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 625 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.627A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 756 Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 789 through 821 removed outlier: 5.587A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 39 removed outlier: 3.846A pdb=" N ALA G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 84 removed outlier: 4.499A pdb=" N VAL G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 88 through 107 Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 125 through 158 Processing helix chain 'I' and resid 17 through 40 Processing helix chain 'I' and resid 116 through 127 Processing helix chain 'I' and resid 129 through 148 Processing helix chain 'I' and resid 158 through 183 removed outlier: 3.596A pdb=" N GLY I 162 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 239 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 523 through 546 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 625 Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 665 through 676 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.627A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 756 Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 789 through 821 removed outlier: 5.587A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 40 Processing helix chain 'J' and resid 116 through 127 Processing helix chain 'J' and resid 129 through 148 Processing helix chain 'J' and resid 158 through 183 removed outlier: 3.597A pdb=" N GLY J 162 " --> pdb=" O ILE J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 239 Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 413 through 416 removed outlier: 3.834A pdb=" N ARG C 416 " --> pdb=" O GLY C 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 416' Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 459 through 464 Processing helix chain 'C' and resid 479 through 484 removed outlier: 4.080A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 540 Processing helix chain 'C' and resid 569 through 580 Processing helix chain 'C' and resid 592 through 625 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 661 through 669 Processing helix chain 'C' and resid 682 through 691 Processing helix chain 'C' and resid 702 through 709 Processing helix chain 'C' and resid 740 through 752 Processing helix chain 'C' and resid 754 through 763 Processing helix chain 'C' and resid 789 through 819 Processing helix chain 'E' and resid 5 through 39 removed outlier: 3.846A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 84 removed outlier: 4.499A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 88 through 107 Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 125 through 158 Processing sheet with id= A, first strand: chain 'A' and resid 391 through 393 Processing sheet with id= B, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.788A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 475 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA A 731 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA A 473 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 716 through 719 removed outlier: 3.865A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= E, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.844A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.003A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 45 through 49 removed outlier: 3.632A pdb=" N LEU I 45 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= I, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.844A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.004A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 45 through 49 removed outlier: 3.633A pdb=" N LEU J 45 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 391 through 393 Processing sheet with id= M, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.787A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU C 475 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA C 731 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ALA C 473 " --> pdb=" O ALA C 731 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 716 through 719 removed outlier: 3.866A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2934 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: 5.48 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2667 1.31 - 1.45: 5171 1.45 - 1.58: 10442 1.58 - 1.71: 8 1.71 - 1.84: 168 Bond restraints: 18456 Sorted by residual: bond pdb=" N15 E2Q D 901 " pdb=" O17 E2Q D 901 " ideal model delta sigma weight residual 1.401 1.187 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" N15 E2Q C2702 " pdb=" O17 E2Q C2702 " ideal model delta sigma weight residual 1.401 1.187 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" N15 E2Q A 901 " pdb=" O17 E2Q A 901 " ideal model delta sigma weight residual 1.401 1.187 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" N15 E2Q B2902 " pdb=" O17 E2Q B2902 " ideal model delta sigma weight residual 1.401 1.187 0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C09 E2Q D 901 " pdb=" S11 E2Q D 901 " ideal model delta sigma weight residual 1.820 1.691 0.129 2.00e-02 2.50e+03 4.15e+01 ... (remaining 18451 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.09: 307 106.09 - 113.09: 10287 113.09 - 120.09: 6067 120.09 - 127.09: 8017 127.09 - 134.09: 186 Bond angle restraints: 24864 Sorted by residual: angle pdb=" O12 E2Q B2902 " pdb=" S11 E2Q B2902 " pdb=" O13 E2Q B2902 " ideal model delta sigma weight residual 101.20 124.24 -23.04 3.00e+00 1.11e-01 5.90e+01 angle pdb=" O12 E2Q C2702 " pdb=" S11 E2Q C2702 " pdb=" O13 E2Q C2702 " ideal model delta sigma weight residual 101.20 124.23 -23.03 3.00e+00 1.11e-01 5.89e+01 angle pdb=" O12 E2Q D 901 " pdb=" S11 E2Q D 901 " pdb=" O13 E2Q D 901 " ideal model delta sigma weight residual 101.20 124.21 -23.01 3.00e+00 1.11e-01 5.88e+01 angle pdb=" O12 E2Q A 901 " pdb=" S11 E2Q A 901 " pdb=" O13 E2Q A 901 " ideal model delta sigma weight residual 101.20 124.20 -23.00 3.00e+00 1.11e-01 5.88e+01 angle pdb=" C10 E2Q D 901 " pdb=" C09 E2Q D 901 " pdb=" S11 E2Q D 901 " ideal model delta sigma weight residual 102.48 119.12 -16.64 3.00e+00 1.11e-01 3.07e+01 ... (remaining 24859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.04: 10140 23.04 - 46.08: 644 46.08 - 69.12: 82 69.12 - 92.16: 22 92.16 - 115.20: 4 Dihedral angle restraints: 10892 sinusoidal: 4198 harmonic: 6694 Sorted by residual: dihedral pdb=" CB CYS I 52 " pdb=" SG CYS I 52 " pdb=" SG CYS I 91 " pdb=" CB CYS I 91 " ideal model delta sinusoidal sigma weight residual -86.00 -163.21 77.21 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS J 52 " pdb=" SG CYS J 52 " pdb=" SG CYS J 91 " pdb=" CB CYS J 91 " ideal model delta sinusoidal sigma weight residual -86.00 -163.19 77.19 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual -86.00 -34.83 -51.17 1 1.00e+01 1.00e-02 3.58e+01 ... (remaining 10889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1527 0.027 - 0.053: 730 0.053 - 0.080: 351 0.080 - 0.107: 145 0.107 - 0.133: 45 Chirality restraints: 2798 Sorted by residual: chirality pdb=" CA ILE B 591 " pdb=" N ILE B 591 " pdb=" C ILE B 591 " pdb=" CB ILE B 591 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE D 591 " pdb=" N ILE D 591 " pdb=" C ILE D 591 " pdb=" CB ILE D 591 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE C 396 " pdb=" N ILE C 396 " pdb=" C ILE C 396 " pdb=" CB ILE C 396 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 2795 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 702 " -0.016 2.00e-02 2.50e+03 1.52e-02 4.62e+00 pdb=" CG TYR D 702 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR D 702 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR D 702 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 702 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 702 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 702 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 702 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 702 " 0.016 2.00e-02 2.50e+03 1.51e-02 4.57e+00 pdb=" CG TYR B 702 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 702 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 702 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 702 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 702 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 702 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 702 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 107 " 0.011 2.00e-02 2.50e+03 1.34e-02 2.68e+00 pdb=" CG HIS E 107 " -0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS E 107 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS E 107 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS E 107 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS E 107 " 0.005 2.00e-02 2.50e+03 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 189 2.64 - 3.21: 16884 3.21 - 3.77: 26800 3.77 - 4.34: 37424 4.34 - 4.90: 63100 Nonbonded interactions: 144397 Sorted by model distance: nonbonded pdb=" OG1 THR D 398 " pdb=" OE2 GLU D 466 " model vdw 2.080 2.440 nonbonded pdb=" N LYS B 716 " pdb=" OE1 GLU B 772 " model vdw 2.101 2.520 nonbonded pdb=" N LYS D 716 " pdb=" OE1 GLU D 772 " model vdw 2.101 2.520 nonbonded pdb=" OG SER D 635 " pdb=" OD1 ASP D 638 " model vdw 2.121 2.440 nonbonded pdb=" OG SER B 635 " pdb=" OD1 ASP B 638 " model vdw 2.121 2.440 ... (remaining 144392 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 393 through 394 or (resid 395 and (name N or name CA or na \ me C or name O or name CB )) or resid 396 or (resid 397 through 398 and (name N \ or name CA or name C or name O or name CB )) or resid 400 through 403 or resid 4 \ 05 through 407 or resid 412 through 414 or resid 416 through 420 or (resid 421 a \ nd (name N or name CA or name C or name O or name CB )) or resid 422 or resid 42 \ 4 through 431 or resid 433 or resid 436 or (resid 438 and (name N or name CA or \ name C or name O or name CB )) or resid 440 through 441 or resid 443 through 450 \ or (resid 452 through 454 and (name N or name CA or name C or name O or name CB \ )) or resid 456 through 466 or (resid 468 through 469 and (name N or name CA or \ name C or name O or name CB )) or resid 471 or resid 473 through 581 or resid 5 \ 83 through 629 or (resid 630 and (name N or name CA or name C or name O or name \ CB )) or resid 631 through 632 or (resid 633 and (name N or name CA or name C or \ name O or name CB )) or resid 634 through 635 or resid 637 or (resid 638 throug \ h 640 and (name N or name CA or name C or name O or name CB )) or resid 641 thro \ ugh 646 or resid 649 through 659 or (resid 660 through 661 and (name N or name C \ A or name C or name O or name CB )) or resid 662 through 663 or resid 665 throug \ h 670 or resid 672 through 682 or resid 684 through 685 or resid 688 through 708 \ or (resid 709 and (name N or name CA or name C or name O or name CB )) or resid \ 710 through 735 or (resid 736 and (name N or name CA or name C or name O or nam \ e CB )) or resid 738 or resid 741 through 756 or (resid 757 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or resid 758 through \ 759 or resid 761 through 765 or (resid 766 and (name N or name CA or name C or n \ ame O or name CB )) or resid 767 through 770 or resid 772 through 795 or resid 7 \ 97 through 815 or resid 817 or resid 819 or (resid 903 through 905 and (name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or \ name C2F or name C2G or name O21 or name O22)))) selection = (chain 'B' and (resid 397 through 402 or resid 404 through 407 or resid 409 thro \ ugh 411 or resid 416 through 418 or resid 420 through 421 or (resid 422 and (nam \ e N or name CA or name C or name O or name CB )) or resid 423 through 426 or res \ id 428 through 435 or resid 437 or resid 440 or resid 442 or resid 444 or (resid \ 445 and (name N or name CA or name C or name O or name CB )) or resid 447 throu \ gh 454 or resid 456 through 458 or resid 460 or (resid 461 and (name N or name C \ A or name C or name O or name CB )) or resid 462 through 470 or resid 472 throug \ h 473 or resid 475 or resid 477 through 489 or (resid 490 and (name N or name CA \ or name C or name O or name CB )) or resid 491 through 507 or (resid 508 throug \ h 511 and (name N or name CA or name C or name O or name CB )) or resid 512 thro \ ugh 546 or (resid 547 and (name N or name CA or name C or name O or name CB )) o \ r resid 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or resid 567 or resid 569 through 585 or resid 587 through 639 or resid 641 t \ hrough 650 or resid 653 through 655 or (resid 656 through 657 and (name N or nam \ e CA or name C or name O or name CB )) or resid 658 through 667 or resid 669 thr \ ough 671 or (resid 672 and (name N or name CA or name C or name O or name CB )) \ or resid 673 through 674 or resid 676 through 684 or (resid 685 and (name N or n \ ame CA or name C or name O or name CB )) or resid 686 or resid 688 through 689 o \ r resid 692 through 695 or (resid 696 through 697 and (name N or name CA or name \ C or name O or name CB )) or resid 698 through 727 or (resid 728 and (name N or \ name CA or name C or name O or name CB )) or resid 729 through 740 or resid 742 \ or resid 745 through 763 or resid 765 through 774 or resid 781 or (resid 783 th \ rough 784 and (name N or name CA or name C or name O or name CB )) or resid 785 \ through 799 or resid 801 through 819 or resid 821 or resid 823 or (resid 2904 th \ rough 2906 and (name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or \ name C2D or name C2E or name C2F or name C2G or name O21 or name O22)))) selection = (chain 'C' and (resid 393 through 394 or (resid 395 and (name N or name CA or na \ me C or name O or name CB )) or resid 396 or (resid 397 through 398 and (name N \ or name CA or name C or name O or name CB )) or resid 400 through 403 or resid 4 \ 05 through 407 or resid 412 through 414 or resid 416 through 420 or (resid 421 a \ nd (name N or name CA or name C or name O or name CB )) or resid 422 or resid 42 \ 4 through 431 or resid 433 or resid 436 or (resid 438 and (name N or name CA or \ name C or name O or name CB )) or resid 440 through 441 or resid 443 through 450 \ or (resid 452 through 454 and (name N or name CA or name C or name O or name CB \ )) or resid 456 through 466 or (resid 468 through 469 and (name N or name CA or \ name C or name O or name CB )) or resid 471 or resid 473 through 581 or resid 5 \ 83 through 629 or (resid 630 and (name N or name CA or name C or name O or name \ CB )) or resid 631 through 632 or (resid 633 and (name N or name CA or name C or \ name O or name CB )) or resid 634 through 635 or resid 637 or (resid 638 throug \ h 640 and (name N or name CA or name C or name O or name CB )) or resid 641 thro \ ugh 646 or resid 649 through 659 or (resid 660 through 661 and (name N or name C \ A or name C or name O or name CB )) or resid 662 through 663 or resid 665 throug \ h 670 or resid 672 through 682 or resid 684 through 685 or resid 688 through 708 \ or (resid 709 and (name N or name CA or name C or name O or name CB )) or resid \ 710 through 735 or (resid 736 and (name N or name CA or name C or name O or nam \ e CB )) or resid 738 or resid 741 through 756 or (resid 757 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or resid 758 through \ 759 or resid 761 through 765 or (resid 766 and (name N or name CA or name C or n \ ame O or name CB )) or resid 767 through 770 or resid 772 through 795 or resid 7 \ 97 through 815 or resid 817 or resid 819 or (resid 2703 through 2705 and (name C \ 21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or na \ me C28 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E o \ r name C2F or name C2G or name O21 or name O22)))) selection = (chain 'D' and (resid 397 through 402 or resid 404 through 407 or resid 409 thro \ ugh 411 or resid 416 through 418 or resid 420 through 421 or (resid 422 and (nam \ e N or name CA or name C or name O or name CB )) or resid 423 through 426 or res \ id 428 through 435 or resid 437 or resid 440 or resid 442 or resid 444 or (resid \ 445 and (name N or name CA or name C or name O or name CB )) or resid 447 throu \ gh 454 or resid 456 through 458 or resid 460 or (resid 461 and (name N or name C \ A or name C or name O or name CB )) or resid 462 through 470 or resid 472 throug \ h 473 or resid 475 or resid 477 through 489 or (resid 490 and (name N or name CA \ or name C or name O or name CB )) or resid 491 through 507 or (resid 508 throug \ h 511 and (name N or name CA or name C or name O or name CB )) or resid 512 thro \ ugh 546 or (resid 547 and (name N or name CA or name C or name O or name CB )) o \ r resid 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or resid 567 or resid 569 through 585 or resid 587 through 639 or resid 641 t \ hrough 650 or resid 653 through 655 or (resid 656 through 657 and (name N or nam \ e CA or name C or name O or name CB )) or resid 658 through 667 or resid 669 thr \ ough 671 or (resid 672 and (name N or name CA or name C or name O or name CB )) \ or resid 673 through 674 or resid 676 through 684 or (resid 685 and (name N or n \ ame CA or name C or name O or name CB )) or resid 686 or resid 688 through 689 o \ r resid 692 through 695 or (resid 696 through 697 and (name N or name CA or name \ C or name O or name CB )) or resid 698 through 727 or (resid 728 and (name N or \ name CA or name C or name O or name CB )) or resid 729 through 740 or resid 742 \ or resid 745 through 763 or resid 765 through 774 or resid 781 or (resid 783 th \ rough 784 and (name N or name CA or name C or name O or name CB )) or resid 785 \ through 799 or resid 801 through 819 or resid 821 or resid 823 or (resid 904 thr \ ough 906 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or na \ me C2D or name C2E or name C2F or name C2G or name O21 or name O22)))) } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 3101 through 3102 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or nam \ e C2F or name C2G or name O21 or name O22)) or resid 3103 through 3104)) selection = (chain 'G' and (resid 2 through 159 or (resid 3101 through 3102 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or nam \ e C2F or name C2G or name O21 or name O22)) or resid 3103 through 3104)) } ncs_group { reference = (chain 'I' and (resid 16 through 240 or resid 3001 through 3003 or (resid 3004 t \ hrough 3005 and (name C21 or name C22 or name C23 or name C24 or name C25 or nam \ e C26 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or \ name C2D or name C2E or name C2F or name C2G or name O21 or name O22)))) selection = (chain 'J' and (resid 16 through 240 or (resid 2501 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or nam \ e C2G or name O21 or name O22)) or resid 2502 through 2505)) } 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.600 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 47.640 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.140 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.009 0.214 18456 Z= 0.595 Angle : 1.069 23.041 24864 Z= 0.433 Chirality : 0.041 0.133 2798 Planarity : 0.003 0.036 2984 Dihedral : 15.044 115.199 6592 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.07 (0.18), residues: 2278 helix: 1.96 (0.14), residues: 1350 sheet: -0.70 (0.43), residues: 148 loop : -1.29 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 103 HIS 0.016 0.002 HIS E 107 PHE 0.022 0.002 PHE A 542 TYR 0.037 0.001 TYR D 702 ARG 0.006 0.001 ARG E 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.907 Fit side-chains REVERT: B 817 LYS cc_start: 0.5971 (tmmt) cc_final: 0.5592 (mttt) REVERT: D 817 LYS cc_start: 0.5964 (tmmt) cc_final: 0.5583 (mttt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2641 time to fit residues: 94.0584 Evaluate side-chains 184 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN B 756 GLN B 764 ASN D 726 ASN D 756 GLN D 764 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18456 Z= 0.215 Angle : 0.503 9.400 24864 Z= 0.256 Chirality : 0.039 0.157 2798 Planarity : 0.003 0.038 2984 Dihedral : 10.988 59.394 3354 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.07 % Allowed : 5.08 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.65 (0.18), residues: 2278 helix: 2.41 (0.14), residues: 1376 sheet: -0.61 (0.41), residues: 168 loop : -1.12 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 762 HIS 0.003 0.001 HIS J 83 PHE 0.012 0.001 PHE B 814 TYR 0.021 0.001 TYR B 702 ARG 0.002 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 211 time to evaluate : 2.039 Fit side-chains REVERT: A 482 GLU cc_start: 0.7419 (tp30) cc_final: 0.7159 (tp30) REVERT: A 807 LEU cc_start: 0.8161 (tp) cc_final: 0.7865 (tp) REVERT: B 407 MET cc_start: 0.7084 (mtm) cc_final: 0.6800 (mtm) REVERT: B 817 LYS cc_start: 0.6598 (tmmt) cc_final: 0.5825 (mttt) REVERT: D 407 MET cc_start: 0.7169 (mtm) cc_final: 0.6864 (mtm) REVERT: D 693 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8245 (t) REVERT: D 817 LYS cc_start: 0.6570 (tmmt) cc_final: 0.5817 (mttt) REVERT: C 482 GLU cc_start: 0.7418 (tp30) cc_final: 0.7153 (tp30) REVERT: C 807 LEU cc_start: 0.8041 (tp) cc_final: 0.7839 (tp) outliers start: 17 outliers final: 10 residues processed: 220 average time/residue: 0.2632 time to fit residues: 92.8872 Evaluate side-chains 201 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 190 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 631 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 140 optimal weight: 0.0170 chunk 57 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 184 optimal weight: 0.0270 chunk 205 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN D 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18456 Z= 0.133 Angle : 0.428 8.572 24864 Z= 0.222 Chirality : 0.037 0.141 2798 Planarity : 0.003 0.040 2984 Dihedral : 9.844 58.895 3354 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.00 % Allowed : 8.40 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.18), residues: 2278 helix: 2.73 (0.14), residues: 1380 sheet: -0.45 (0.41), residues: 166 loop : -0.95 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 762 HIS 0.003 0.001 HIS E 27 PHE 0.010 0.001 PHE A 663 TYR 0.019 0.001 TYR A 812 ARG 0.002 0.000 ARG B 545 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 1.954 Fit side-chains REVERT: A 704 MET cc_start: 0.8057 (tpt) cc_final: 0.7849 (tpt) REVERT: B 817 LYS cc_start: 0.6547 (tmmt) cc_final: 0.5760 (mttp) REVERT: D 693 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8132 (t) REVERT: D 817 LYS cc_start: 0.6535 (tmmt) cc_final: 0.5754 (mttp) REVERT: C 704 MET cc_start: 0.8058 (tpt) cc_final: 0.7854 (tpt) outliers start: 16 outliers final: 13 residues processed: 216 average time/residue: 0.2537 time to fit residues: 88.4864 Evaluate side-chains 199 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 0.0870 chunk 98 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 197 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN I 20 GLN J 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18456 Z= 0.209 Angle : 0.454 8.197 24864 Z= 0.235 Chirality : 0.038 0.162 2798 Planarity : 0.003 0.040 2984 Dihedral : 9.975 59.831 3354 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.94 % Allowed : 9.21 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.93 (0.18), residues: 2278 helix: 2.58 (0.14), residues: 1380 sheet: -0.52 (0.40), residues: 168 loop : -0.91 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 578 HIS 0.003 0.001 HIS I 83 PHE 0.010 0.001 PHE B 814 TYR 0.018 0.001 TYR A 812 ARG 0.002 0.000 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 201 time to evaluate : 1.929 Fit side-chains REVERT: B 817 LYS cc_start: 0.6617 (tmmt) cc_final: 0.5765 (mttp) REVERT: D 817 LYS cc_start: 0.6626 (tmmt) cc_final: 0.5768 (mttp) outliers start: 31 outliers final: 25 residues processed: 223 average time/residue: 0.2619 time to fit residues: 94.6850 Evaluate side-chains 212 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS B 714 GLN B 756 GLN B 764 ASN D 756 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18456 Z= 0.351 Angle : 0.532 8.770 24864 Z= 0.275 Chirality : 0.041 0.146 2798 Planarity : 0.004 0.041 2984 Dihedral : 10.913 59.622 3354 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.51 % Allowed : 9.46 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.50 (0.18), residues: 2278 helix: 2.16 (0.14), residues: 1380 sheet: -0.70 (0.40), residues: 170 loop : -0.86 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 578 HIS 0.006 0.001 HIS J 83 PHE 0.013 0.002 PHE B 531 TYR 0.019 0.002 TYR D 702 ARG 0.004 0.000 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 2.000 Fit side-chains REVERT: A 438 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 817 LYS cc_start: 0.6476 (tmmt) cc_final: 0.5691 (mttp) REVERT: D 817 LYS cc_start: 0.6485 (tmmt) cc_final: 0.5697 (mttp) REVERT: C 438 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8286 (mp) outliers start: 40 outliers final: 29 residues processed: 221 average time/residue: 0.2847 time to fit residues: 101.2474 Evaluate side-chains 219 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 183 optimal weight: 0.4980 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 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 752 GLN B 764 ASN D 764 ASN C 752 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18456 Z= 0.194 Angle : 0.453 8.722 24864 Z= 0.235 Chirality : 0.038 0.163 2798 Planarity : 0.003 0.041 2984 Dihedral : 10.105 59.817 3354 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.32 % Allowed : 10.59 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.75 (0.18), residues: 2278 helix: 2.40 (0.14), residues: 1382 sheet: -0.63 (0.40), residues: 170 loop : -0.88 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 578 HIS 0.004 0.001 HIS I 83 PHE 0.012 0.001 PHE B 546 TYR 0.015 0.001 TYR A 812 ARG 0.003 0.000 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 1.962 Fit side-chains REVERT: A 438 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8259 (mp) REVERT: C 438 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8365 (mp) outliers start: 37 outliers final: 31 residues processed: 219 average time/residue: 0.2573 time to fit residues: 89.9843 Evaluate side-chains 218 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain E residue 27 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN D 764 ASN C 431 HIS C 752 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18456 Z= 0.349 Angle : 0.529 8.806 24864 Z= 0.272 Chirality : 0.041 0.170 2798 Planarity : 0.004 0.041 2984 Dihedral : 10.634 58.388 3354 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.63 % Allowed : 11.09 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.47 (0.18), residues: 2278 helix: 2.12 (0.14), residues: 1380 sheet: -0.76 (0.39), residues: 170 loop : -0.82 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 578 HIS 0.005 0.001 HIS J 83 PHE 0.020 0.002 PHE B 546 TYR 0.016 0.002 TYR D 702 ARG 0.004 0.000 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 1.896 Fit side-chains REVERT: A 438 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 570 GLU cc_start: 0.5808 (OUTLIER) cc_final: 0.5419 (mm-30) REVERT: D 570 GLU cc_start: 0.5908 (OUTLIER) cc_final: 0.5528 (mm-30) REVERT: C 438 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8314 (mp) outliers start: 42 outliers final: 34 residues processed: 215 average time/residue: 0.2517 time to fit residues: 87.8538 Evaluate side-chains 219 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 181 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 27 HIS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain E residue 27 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 0.4980 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN C 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18456 Z= 0.235 Angle : 0.474 8.991 24864 Z= 0.245 Chirality : 0.039 0.156 2798 Planarity : 0.003 0.041 2984 Dihedral : 10.113 57.718 3354 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.38 % Allowed : 11.84 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.65 (0.18), residues: 2278 helix: 2.29 (0.14), residues: 1380 sheet: -0.75 (0.38), residues: 170 loop : -0.81 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 578 HIS 0.003 0.001 HIS E 75 PHE 0.014 0.001 PHE B 546 TYR 0.015 0.001 TYR A 812 ARG 0.003 0.000 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 1.869 Fit side-chains REVERT: A 438 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8218 (mp) REVERT: D 570 GLU cc_start: 0.5854 (OUTLIER) cc_final: 0.5541 (mm-30) REVERT: C 438 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8258 (mp) outliers start: 38 outliers final: 32 residues processed: 215 average time/residue: 0.2564 time to fit residues: 90.4800 Evaluate side-chains 221 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 27 HIS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain E residue 27 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 8.9990 chunk 210 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 89 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 62 optimal weight: 0.0010 chunk 185 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN C 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18456 Z= 0.152 Angle : 0.435 8.837 24864 Z= 0.224 Chirality : 0.037 0.166 2798 Planarity : 0.003 0.042 2984 Dihedral : 9.154 59.998 3354 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.88 % Allowed : 12.53 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.92 (0.18), residues: 2278 helix: 2.57 (0.14), residues: 1380 sheet: -0.68 (0.38), residues: 170 loop : -0.84 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 203 HIS 0.002 0.001 HIS G 27 PHE 0.015 0.001 PHE D 546 TYR 0.015 0.001 TYR A 812 ARG 0.003 0.000 ARG C 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 204 time to evaluate : 1.966 Fit side-chains REVERT: A 438 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8258 (mp) REVERT: C 438 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8214 (mp) outliers start: 30 outliers final: 28 residues processed: 221 average time/residue: 0.2549 time to fit residues: 91.9671 Evaluate side-chains 218 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain G residue 27 HIS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain E residue 27 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 150 optimal weight: 0.0170 chunk 227 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN B 764 ASN C 752 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18456 Z= 0.295 Angle : 0.506 9.018 24864 Z= 0.259 Chirality : 0.040 0.175 2798 Planarity : 0.003 0.040 2984 Dihedral : 9.979 58.444 3354 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.01 % Allowed : 12.66 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.64 (0.18), residues: 2278 helix: 2.28 (0.14), residues: 1382 sheet: -0.70 (0.38), residues: 170 loop : -0.84 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 578 HIS 0.005 0.001 HIS I 83 PHE 0.016 0.002 PHE D 546 TYR 0.015 0.001 TYR D 702 ARG 0.004 0.000 ARG C 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 2.079 Fit side-chains REVERT: A 438 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8265 (mp) REVERT: B 570 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.5520 (mm-30) REVERT: C 438 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8254 (mp) outliers start: 32 outliers final: 28 residues processed: 209 average time/residue: 0.2525 time to fit residues: 85.6365 Evaluate side-chains 217 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 27 HIS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain E residue 27 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 50 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN C 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.158376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.106111 restraints weight = 21352.289| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.03 r_work: 0.2953 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18456 Z= 0.152 Angle : 0.440 8.978 24864 Z= 0.226 Chirality : 0.038 0.168 2798 Planarity : 0.003 0.042 2984 Dihedral : 9.185 59.906 3354 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.82 % Allowed : 12.84 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.93 (0.18), residues: 2278 helix: 2.55 (0.14), residues: 1384 sheet: -0.68 (0.38), residues: 170 loop : -0.81 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 203 HIS 0.003 0.001 HIS G 27 PHE 0.015 0.001 PHE B 546 TYR 0.015 0.001 TYR A 812 ARG 0.003 0.000 ARG C 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3654.81 seconds wall clock time: 66 minutes 35.81 seconds (3995.81 seconds total)