Starting phenix.real_space_refine on Sat Feb 17 10:14:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1r_16381/02_2024/8c1r_16381_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1r_16381/02_2024/8c1r_16381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1r_16381/02_2024/8c1r_16381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1r_16381/02_2024/8c1r_16381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1r_16381/02_2024/8c1r_16381_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1r_16381/02_2024/8c1r_16381_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 S 124 5.16 5 C 12024 2.51 5 N 2880 2.21 5 O 3284 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 427": "OD1" <-> "OD2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 490": "OD1" <-> "OD2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 644": "OE1" <-> "OE2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 668": "OD1" <-> "OD2" Residue "A TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 710": "OE1" <-> "OE2" Residue "A ASP 728": "OD1" <-> "OD2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 490": "OD1" <-> "OD2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 713": "OE1" <-> "OE2" Residue "B ASP 719": "OD1" <-> "OD2" Residue "B GLU 782": "OE1" <-> "OE2" Residue "C TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 454": "OD1" <-> "OD2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 590": "OD1" <-> "OD2" Residue "C PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 627": "OE1" <-> "OE2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "C GLU 637": "OE1" <-> "OE2" Residue "C GLU 644": "OE1" <-> "OE2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 657": "OE1" <-> "OE2" Residue "C PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 627": "OE1" <-> "OE2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 760": "OD1" <-> "OD2" Residue "D TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 5": "OD1" <-> "OD2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18333 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 405, 3083 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Conformer: "B" Number of residues, atoms: 405, 3083 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 bond proxies already assigned to first conformer: 3127 Chain: "B" Number of atoms: 3068 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3057 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 64 Conformer: "B" Number of residues, atoms: 406, 3057 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 64 bond proxies already assigned to first conformer: 3114 Chain: "C" Number of atoms: 3063 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 405, 3052 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 Conformer: "B" Number of residues, atoms: 405, 3052 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 bond proxies already assigned to first conformer: 3109 Chain: "D" Number of atoms: 3076 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3065 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 60 Conformer: "B" Number of residues, atoms: 406, 3065 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 60 bond proxies already assigned to first conformer: 3122 Chain: "E" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1366 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1381 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1367 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'OLC': 1, 'PLM': 2, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'OLC': 1, 'PLM': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'PLM': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N APHE A 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 574 " occ=0.50 residue: pdb=" N APHE A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE C 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 623 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 15.26, per 1000 atoms: 0.83 Number of scatterers: 18333 At special positions: 0 Unit cell: (118.944, 116.466, 137.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 9 15.00 F 12 9.00 O 3284 8.00 N 2880 7.00 C 12024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.01 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.01 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.04 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.01 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.06 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.04 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: 8.17 Conformation dependent library (CDL) restraints added in 5.5 seconds 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 21 sheets defined 53.5% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 488 removed outlier: 4.184A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 523 through 543 Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 628 Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 743 through 756 Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 793 through 820 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 483 through 488 removed outlier: 3.501A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 483 through 488' 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 545 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 625 Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.961A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 676 removed outlier: 4.147A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 741 through 756 Proline residue: B 745 - end of helix removed outlier: 3.626A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 793 through 822 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 418 through 420 No H-bonds generated for 'chain 'C' and resid 418 through 420' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 523 through 545 Processing helix chain 'C' and resid 548 through 550 No H-bonds generated for 'chain 'C' and resid 548 through 550' Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 628 Processing helix chain 'C' and resid 637 through 640 No H-bonds generated for 'chain 'C' and resid 637 through 640' Processing helix chain 'C' and resid 654 through 660 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 793 through 820 Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 463 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 545 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 625 Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.600A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 793 through 822 Processing helix chain 'E' and resid 8 through 29 Processing helix chain 'E' and resid 93 through 103 Processing helix chain 'E' and resid 106 through 125 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.759A pdb=" N VAL E 143 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 145 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 209 Processing helix chain 'F' and resid 6 through 29 Processing helix chain 'F' and resid 93 through 104 removed outlier: 3.653A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 126 removed outlier: 3.891A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 159 Processing helix chain 'F' and resid 178 through 208 Processing helix chain 'G' and resid 8 through 29 Processing helix chain 'G' and resid 93 through 103 Processing helix chain 'G' and resid 106 through 126 removed outlier: 4.098A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 161 removed outlier: 3.569A pdb=" N SER G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 209 Processing helix chain 'H' and resid 6 through 29 removed outlier: 4.058A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 106 through 127 removed outlier: 4.271A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 160 removed outlier: 3.525A pdb=" N ASN H 160 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 208 Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= C, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.770A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 720 through 722 removed outlier: 4.956A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 396 through 399 removed outlier: 6.202A pdb=" N LYS B 441 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR B 399 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 443 " --> pdb=" O THR B 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 451 through 453 Processing sheet with id= G, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.757A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.021A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= J, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= K, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.772A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 720 through 722 removed outlier: 4.727A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 395 through 397 Processing sheet with id= N, first strand: chain 'D' and resid 451 through 454 removed outlier: 3.554A pdb=" N ILE D 459 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= P, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.768A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.173A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 34 through 38 removed outlier: 3.554A pdb=" N LEU E 34 " --> pdb=" O SER E 61 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 65 through 67 Processing sheet with id= T, first strand: chain 'H' and resid 36 through 38 Processing sheet with id= U, first strand: chain 'H' and resid 65 through 67 965 hydrogen bonds defined for protein. 2728 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: 5.32 Time building geometry restraints manager: 8.53 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: 2850 1.31 - 1.45: 5429 1.45 - 1.58: 10240 1.58 - 1.72: 13 1.72 - 1.85: 201 Bond restraints: 18733 Sorted by residual: bond pdb=" CAO ZK1 A 901 " pdb=" PBA ZK1 A 901 " ideal model delta sigma weight residual 1.896 1.785 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" CAO ZK1 B 901 " pdb=" PBA ZK1 B 901 " ideal model delta sigma weight residual 1.896 1.797 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CAO ZK1 C 901 " pdb=" PBA ZK1 C 901 " ideal model delta sigma weight residual 1.896 1.799 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C LEU C 581 " pdb=" N GLY C 582 " ideal model delta sigma weight residual 1.335 1.273 0.061 1.26e-02 6.30e+03 2.35e+01 bond pdb=" CG MET B 585 " pdb=" SD MET B 585 " ideal model delta sigma weight residual 1.803 1.686 0.117 2.50e-02 1.60e+03 2.18e+01 ... (remaining 18728 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.92: 276 104.92 - 112.34: 8934 112.34 - 119.77: 7307 119.77 - 127.19: 8614 127.19 - 134.62: 181 Bond angle restraints: 25312 Sorted by residual: angle pdb=" N ASP A 590 " pdb=" CA ASP A 590 " pdb=" C ASP A 590 " ideal model delta sigma weight residual 113.23 107.12 6.11 1.24e+00 6.50e-01 2.42e+01 angle pdb=" N LEU C 639 " pdb=" CA LEU C 639 " pdb=" C LEU C 639 " ideal model delta sigma weight residual 112.23 106.07 6.16 1.26e+00 6.30e-01 2.39e+01 angle pdb=" O11 POV G1103 " pdb=" P POV G1103 " pdb=" O12 POV G1103 " ideal model delta sigma weight residual 97.67 110.96 -13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" CA TYR C 673 " pdb=" CB TYR C 673 " pdb=" CG TYR C 673 " ideal model delta sigma weight residual 113.90 121.77 -7.87 1.80e+00 3.09e-01 1.91e+01 angle pdb=" N GLY D 653 " pdb=" CA GLY D 653 " pdb=" C GLY D 653 " ideal model delta sigma weight residual 110.56 117.75 -7.19 1.66e+00 3.63e-01 1.88e+01 ... (remaining 25307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.07: 10404 29.07 - 58.13: 480 58.13 - 87.20: 65 87.20 - 116.26: 14 116.26 - 145.33: 5 Dihedral angle restraints: 10968 sinusoidal: 4283 harmonic: 6685 Sorted by residual: dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 6.09 86.91 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 6.74 86.26 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual -86.00 -12.88 -73.12 1 1.00e+01 1.00e-02 6.81e+01 ... (remaining 10965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1865 0.069 - 0.137: 780 0.137 - 0.206: 150 0.206 - 0.274: 24 0.274 - 0.343: 6 Chirality restraints: 2825 Sorted by residual: chirality pdb=" CB VAL A 604 " pdb=" CA VAL A 604 " pdb=" CG1 VAL A 604 " pdb=" CG2 VAL A 604 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA SER D 615 " pdb=" N SER D 615 " pdb=" C SER D 615 " pdb=" CB SER D 615 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CB ILE A 612 " pdb=" CA ILE A 612 " pdb=" CG1 ILE A 612 " pdb=" CG2 ILE A 612 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 2822 not shown) Planarity restraints: 3073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 571 " 0.064 2.00e-02 2.50e+03 4.10e-02 2.94e+01 pdb=" CG PHE A 571 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 571 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 571 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE A 571 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 571 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 571 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " 0.052 2.00e-02 2.50e+03 3.20e-02 2.56e+01 pdb=" CG TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " 0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " -0.050 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 176 " -0.053 2.00e-02 2.50e+03 2.91e-02 1.69e+01 pdb=" CG TYR H 176 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR H 176 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR H 176 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR H 176 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR H 176 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 176 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR H 176 " -0.029 2.00e-02 2.50e+03 ... (remaining 3070 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 228 2.63 - 3.20: 17601 3.20 - 3.77: 28316 3.77 - 4.33: 39761 4.33 - 4.90: 65636 Nonbonded interactions: 151542 Sorted by model distance: nonbonded pdb=" OG SER C 547 " pdb=" OE2 GLU C 550 " model vdw 2.068 2.440 nonbonded pdb=" O VAL B 681 " pdb=" OH TYR B 700 " model vdw 2.120 2.440 nonbonded pdb=" OD1 ASP A 651 " pdb=" N SER A 652 " model vdw 2.226 2.520 nonbonded pdb=" O GLU H 70 " pdb=" OE1 GLU H 70 " model vdw 2.226 3.040 nonbonded pdb=" NH2 ARG B 715 " pdb=" O LYS B 770 " model vdw 2.262 2.520 ... (remaining 151537 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 394 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB )) or resid 435 through 440 or (resid 441 and (name N \ or name CA or name C or name O or name CB )) or resid 442 through 453 or (resid \ 454 through 456 and (name N or name CA or name C or name O or name CB )) or resi \ d 457 or (resid 458 and (name N or name CA or name C or name O or name CB )) or \ resid 459 through 507 or (resid 508 through 509 and (name N or name CA or name C \ or name O or name CB )) or resid 510 through 573 or resid 575 through 593 or (r \ esid 594 and (name N or name CA or name C or name O or name CB )) or resid 595 t \ hrough 622 or resid 624 through 626 or (resid 627 and (name N or name CA or name \ C or name O or name CB )) or resid 628 through 633 or (resid 634 and (name N or \ name CA or name C or name O or name CB )) or resid 635 through 637 or (resid 63 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 639 through \ 642 or (resid 643 through 644 and (name N or name CA or name C or name O or name \ CB )) or resid 645 through 650 or (resid 651 through 652 and (name N or name CA \ or name C or name O or name CB )) or resid 653 through 674 or (resid 675 and (n \ ame N or name CA or name C or name O or name CB )) or resid 676 through 687 or ( \ resid 688 and (name N or name CA or name C or name O or name CB )) or resid 689 \ through 715 or (resid 716 and (name N or name CA or name C or name O or name CB \ )) or resid 717 through 737 or (resid 738 and (name N or name CA or name C or na \ me O or name CB )) or resid 739 through 751 or (resid 752 and (name N or name CA \ or name C or name O or name CB )) or resid 753 through 754 or (resid 755 throug \ h 756 and (name N or name CA or name C or name O or name CB )) or resid 757 thro \ ugh 759 or (resid 760 through 761 and (name N or name CA or name C or name O or \ name CB )) or resid 762 through 764 or (resid 765 and (name N or name CA or name \ C or name O or name CB )) or resid 766 through 768 or (resid 769 and (name N or \ name CA or name C or name O or name CB )) or resid 770 through 774 or resid 784 \ through 812 or (resid 813 and (name N or name CA or name C or name O or name CB \ )) or resid 814 through 816 or (resid 817 and (name N or name CA or name C or n \ ame O or name CB )) or resid 818 or (resid 819 through 823 and (name N or name C \ A or name C or name O or name CB )) or resid 901)) selection = (chain 'B' and (resid 394 through 448 or (resid 449 and (name N or name CA or na \ me C or name O or name CB )) or resid 450 through 457 or (resid 458 and (name N \ or name CA or name C or name O or name CB )) or resid 459 through 507 or (resid \ 508 through 509 and (name N or name CA or name C or name O or name CB )) or resi \ d 510 or (resid 511 and (name N or name CA or name C or name O or name CB )) or \ resid 512 through 551 or (resid 569 and (name N or name CA or name C or name O o \ r name CB )) or resid 570 through 573 or resid 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 through 593 or (resid 594 \ and (name N or name CA or name C or name O or name CB )) or resid 595 through 6 \ 22 or resid 624 through 637 or (resid 638 and (name N or name CA or name C or na \ me O or name CB )) or resid 639 through 650 or (resid 651 through 652 and (name \ N or name CA or name C or name O or name CB )) or resid 653 through 662 or (resi \ d 663 and (name N or name CA or name C or name O or name CB )) or resid 664 thro \ ugh 674 or (resid 675 and (name N or name CA or name C or name O or name CB )) o \ r resid 676 through 687 or (resid 688 and (name N or name CA or name C or name O \ or name CB )) or resid 689 through 694 or (resid 695 and (name N or name CA or \ name C or name O or name CB )) or resid 696 or (resid 697 and (name N or name CA \ or name C or name O or name CB )) or resid 698 through 755 or (resid 756 and (n \ ame N or name CA or name C or name O or name CB )) or resid 757 through 759 or ( \ resid 760 through 761 and (name N or name CA or name C or name O or name CB )) o \ r resid 762 through 771 or (resid 772 and (name N or name CA or name C or name O \ or name CB )) or resid 773 through 774 or (resid 784 and (name N or name CA or \ name C or name O or name CB )) or resid 785 through 816 or (resid 817 and (name \ N or name CA or name C or name O or name CB )) or resid 818 through 823 or resid \ 901)) selection = (chain 'C' and (resid 394 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB )) or resid 435 through 448 or (resid 449 and (name N \ or name CA or name C or name O or name CB )) or resid 450 through 453 or (resid \ 454 through 456 and (name N or name CA or name C or name O or name CB )) or resi \ d 457 through 573 or resid 575 or (resid 576 and (name N or name CA or name C or \ name O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resi \ d 627 and (name N or name CA or name C or name O or name CB )) or resid 628 thro \ ugh 633 or (resid 634 and (name N or name CA or name C or name O or name CB )) o \ r resid 635 through 642 or (resid 643 through 644 and (name N or name CA or name \ C or name O or name CB )) or resid 645 through 674 or (resid 675 and (name N or \ name CA or name C or name O or name CB )) or resid 676 through 715 or (resid 71 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 717 through \ 751 or (resid 752 and (name N or name CA or name C or name O or name CB )) or re \ sid 753 through 754 or (resid 755 through 756 and (name N or name CA or name C o \ r name O or name CB )) or resid 757 through 760 or (resid 761 and (name N or nam \ e CA or name C or name O or name CB )) or resid 762 through 764 or (resid 765 an \ d (name N or name CA or name C or name O or name CB )) or resid 766 through 768 \ or (resid 769 and (name N or name CA or name C or name O or name CB )) or resid \ 770 through 774 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 816 or (resid 817 and (name \ N or name CA or name C or name O or name CB )) or resid 818 or (resid 819 throu \ gh 823 and (name N or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'D' and (resid 394 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB )) or resid 435 through 448 or (resid 449 and (name N \ or name CA or name C or name O or name CB )) or resid 450 through 507 or (resid \ 508 through 509 and (name N or name CA or name C or name O or name CB )) or resi \ d 510 or (resid 511 and (name N or name CA or name C or name O or name CB )) or \ resid 512 through 551 or (resid 569 and (name N or name CA or name C or name O o \ r name CB )) or resid 570 through 573 or resid 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 through 593 or (resid 594 \ and (name N or name CA or name C or name O or name CB )) or resid 595 through 6 \ 22 or resid 624 through 626 or (resid 627 and (name N or name CA or name C or na \ me O or name CB )) or resid 628 through 637 or (resid 638 and (name N or name CA \ or name C or name O or name CB )) or resid 639 through 650 or (resid 651 throug \ h 652 and (name N or name CA or name C or name O or name CB )) or resid 653 thro \ ugh 660 or (resid 661 and (name N or name CA or name C or name O or name CB )) o \ r resid 662 or (resid 663 and (name N or name CA or name C or name O or name CB \ )) or resid 664 through 687 or (resid 688 and (name N or name CA or name C or na \ me O or name CB )) or resid 689 through 694 or (resid 695 and (name N or name CA \ or name C or name O or name CB )) or resid 696 or (resid 697 and (name N or nam \ e CA or name C or name O or name CB )) or resid 698 through 737 or (resid 738 an \ d (name N or name CA or name C or name O or name CB )) or resid 739 through 754 \ or (resid 755 through 756 and (name N or name CA or name C or name O or name CB \ )) or resid 757 through 759 or (resid 760 through 761 and (name N or name CA or \ name C or name O or name CB )) or resid 762 through 764 or (resid 765 and (name \ N or name CA or name C or name O or name CB )) or resid 766 through 771 or (resi \ d 772 and (name N or name CA or name C or name O or name CB )) or resid 773 thro \ ugh 774 or (resid 784 and (name N or name CA or name C or name O or name CB )) o \ r resid 785 through 823 or resid 901)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 42 or resid 55 through 84 or resid 93 through 21 \ 0)) selection = (chain 'G' and (resid 5 or (resid 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 84 or resid 93 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 210)) } 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=0.50 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: 1.770 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: 0.020 Extract box with map and model: 7.960 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 58.640 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.110 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.011 0.117 18733 Z= 0.702 Angle : 1.149 13.289 25312 Z= 0.704 Chirality : 0.075 0.343 2825 Planarity : 0.009 0.082 3073 Dihedral : 17.108 145.329 6668 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 3.23 % Allowed : 3.94 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2290 helix: 1.64 (0.14), residues: 1334 sheet: -1.27 (0.41), residues: 168 loop : -2.37 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.010 TRP A 606 HIS 0.012 0.004 HIS G 60 PHE 0.068 0.010 PHE A 571 TYR 0.059 0.008 TYR D 616 ARG 0.025 0.003 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 328 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 768 TYR cc_start: 0.7836 (m-10) cc_final: 0.7229 (m-10) REVERT: B 422 GLU cc_start: 0.6327 (pt0) cc_final: 0.6089 (pm20) REVERT: B 473 ASP cc_start: 0.7455 (m-30) cc_final: 0.7202 (m-30) REVERT: B 590 ASP cc_start: 0.8378 (m-30) cc_final: 0.8065 (t0) REVERT: B 766 TRP cc_start: 0.7168 (m100) cc_final: 0.6960 (m100) REVERT: B 816 TYR cc_start: 0.7173 (t80) cc_final: 0.6917 (t80) REVERT: C 756 GLN cc_start: 0.6906 (mm110) cc_final: 0.6671 (mm110) REVERT: D 651 ASP cc_start: 0.8125 (t0) cc_final: 0.7795 (p0) REVERT: D 682 PHE cc_start: 0.7658 (m-80) cc_final: 0.7422 (m-80) REVERT: E 24 MET cc_start: 0.8255 (tpt) cc_final: 0.7767 (tpt) REVERT: E 40 CYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7026 (m) REVERT: E 131 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5781 (mmm160) REVERT: F 6 ARG cc_start: 0.6797 (tmt170) cc_final: 0.6475 (ttm-80) REVERT: G 41 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.6050 (ptmm) REVERT: G 65 ARG cc_start: 0.7089 (mtm110) cc_final: 0.6798 (mtm-85) REVERT: G 130 THR cc_start: 0.7703 (OUTLIER) cc_final: 0.7470 (t) REVERT: G 132 HIS cc_start: 0.6875 (OUTLIER) cc_final: 0.6346 (m90) REVERT: H 10 MET cc_start: 0.8295 (tpp) cc_final: 0.8002 (tpp) REVERT: H 65 ARG cc_start: 0.7077 (ptt180) cc_final: 0.6842 (ptt-90) REVERT: H 129 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7757 (mtpp) outliers start: 59 outliers final: 21 residues processed: 364 average time/residue: 0.3328 time to fit residues: 176.9014 Evaluate side-chains 301 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 274 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 690 VAL Chi-restraints excluded: chain D residue 782 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 129 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 chunk 133 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN D 569 ASN E 133 ASN F 132 HIS F 205 HIS G 132 HIS G 205 HIS ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18733 Z= 0.158 Angle : 0.498 6.490 25312 Z= 0.263 Chirality : 0.039 0.202 2825 Planarity : 0.004 0.041 3073 Dihedral : 11.622 103.082 2979 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.31 % Allowed : 9.57 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2290 helix: 2.54 (0.14), residues: 1341 sheet: -1.07 (0.42), residues: 166 loop : -1.90 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 460 HIS 0.004 0.001 HIS G 60 PHE 0.013 0.001 PHE D 438 TYR 0.013 0.001 TYR B 673 ARG 0.009 0.000 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 312 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 647 TYR cc_start: 0.8039 (p90) cc_final: 0.7727 (p90) REVERT: B 422 GLU cc_start: 0.6331 (pt0) cc_final: 0.6069 (pm20) REVERT: B 473 ASP cc_start: 0.7221 (m-30) cc_final: 0.6897 (m-30) REVERT: C 505 LYS cc_start: 0.7287 (tptp) cc_final: 0.6943 (mtpp) REVERT: C 642 GLN cc_start: 0.7079 (pp30) cc_final: 0.6791 (pp30) REVERT: C 721 MET cc_start: 0.7889 (ttp) cc_final: 0.7605 (ttp) REVERT: C 756 GLN cc_start: 0.7090 (mm110) cc_final: 0.6880 (mm110) REVERT: D 407 MET cc_start: 0.5982 (mtm) cc_final: 0.5749 (mtm) REVERT: D 651 ASP cc_start: 0.7937 (t0) cc_final: 0.7431 (p0) REVERT: D 674 MET cc_start: 0.7221 (mtp) cc_final: 0.6977 (mtp) REVERT: D 714 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: D 766 TRP cc_start: 0.7678 (m100) cc_final: 0.6964 (m100) REVERT: D 807 MET cc_start: 0.8818 (mtm) cc_final: 0.8603 (mtp) REVERT: E 24 MET cc_start: 0.8129 (tpt) cc_final: 0.7867 (tpt) REVERT: E 31 ASP cc_start: 0.7718 (m-30) cc_final: 0.7509 (m-30) REVERT: E 98 LEU cc_start: 0.7652 (tt) cc_final: 0.7428 (tp) REVERT: E 131 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5747 (mmm160) REVERT: F 74 LYS cc_start: 0.7255 (mttp) cc_final: 0.6959 (mmtm) REVERT: F 99 ARG cc_start: 0.7411 (mmm-85) cc_final: 0.7142 (mtp180) REVERT: G 41 LYS cc_start: 0.6569 (tptp) cc_final: 0.6225 (pttm) outliers start: 24 outliers final: 11 residues processed: 326 average time/residue: 0.3180 time to fit residues: 153.9465 Evaluate side-chains 287 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 274 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 68 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN E 199 HIS G 205 HIS ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18733 Z= 0.323 Angle : 0.548 9.218 25312 Z= 0.288 Chirality : 0.042 0.206 2825 Planarity : 0.004 0.043 3073 Dihedral : 11.261 105.206 2936 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.19 % Allowed : 11.11 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2290 helix: 2.18 (0.14), residues: 1342 sheet: -1.12 (0.40), residues: 168 loop : -1.84 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 460 HIS 0.005 0.001 HIS E 199 PHE 0.012 0.002 PHE A 571 TYR 0.018 0.001 TYR C 673 ARG 0.009 0.001 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 283 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.4415 (mtm) cc_final: 0.3849 (mtm) REVERT: B 473 ASP cc_start: 0.7177 (m-30) cc_final: 0.6774 (m-30) REVERT: D 651 ASP cc_start: 0.7937 (t0) cc_final: 0.7404 (p0) REVERT: D 674 MET cc_start: 0.7242 (mtp) cc_final: 0.7011 (mtp) REVERT: D 766 TRP cc_start: 0.7759 (m100) cc_final: 0.7246 (m100) REVERT: E 24 MET cc_start: 0.8087 (tpt) cc_final: 0.7803 (tpt) REVERT: E 31 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: E 95 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7600 (pt0) REVERT: E 131 ARG cc_start: 0.6177 (OUTLIER) cc_final: 0.5635 (mmm160) REVERT: F 74 LYS cc_start: 0.7115 (mttp) cc_final: 0.6755 (mmtm) REVERT: F 99 ARG cc_start: 0.7376 (mmm-85) cc_final: 0.7112 (mtp180) REVERT: G 41 LYS cc_start: 0.6711 (tptp) cc_final: 0.6056 (pttm) REVERT: H 10 MET cc_start: 0.8346 (tpp) cc_final: 0.8101 (tpp) outliers start: 40 outliers final: 28 residues processed: 307 average time/residue: 0.3120 time to fit residues: 144.1489 Evaluate side-chains 302 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 272 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN C 764 ASN D 569 ASN G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18733 Z= 0.194 Angle : 0.487 14.140 25312 Z= 0.256 Chirality : 0.039 0.240 2825 Planarity : 0.004 0.042 3073 Dihedral : 10.566 107.631 2935 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.97 % Allowed : 12.25 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2290 helix: 2.38 (0.14), residues: 1344 sheet: -1.04 (0.42), residues: 146 loop : -1.77 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 460 HIS 0.007 0.001 HIS E 60 PHE 0.010 0.001 PHE G 107 TYR 0.019 0.001 TYR C 673 ARG 0.011 0.000 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 296 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 407 MET cc_start: 0.4449 (mtm) cc_final: 0.4170 (mtm) REVERT: B 473 ASP cc_start: 0.7186 (m-30) cc_final: 0.6794 (m-30) REVERT: C 431 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8055 (tm-30) REVERT: C 721 MET cc_start: 0.7946 (ttp) cc_final: 0.7589 (ttp) REVERT: D 407 MET cc_start: 0.5958 (mtm) cc_final: 0.5698 (mtm) REVERT: D 443 THR cc_start: 0.7160 (t) cc_final: 0.6686 (p) REVERT: D 551 TRP cc_start: 0.6593 (m100) cc_final: 0.6381 (m100) REVERT: D 651 ASP cc_start: 0.7921 (t0) cc_final: 0.7384 (p0) REVERT: D 766 TRP cc_start: 0.7717 (m100) cc_final: 0.7208 (m100) REVERT: E 24 MET cc_start: 0.8105 (tpt) cc_final: 0.7870 (tpt) REVERT: E 31 ASP cc_start: 0.7667 (m-30) cc_final: 0.7282 (m-30) REVERT: E 95 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7577 (pt0) REVERT: F 74 LYS cc_start: 0.7253 (mttp) cc_final: 0.6942 (mmtp) REVERT: F 99 ARG cc_start: 0.7354 (mmm-85) cc_final: 0.7096 (mtp180) REVERT: G 41 LYS cc_start: 0.6638 (tptp) cc_final: 0.5922 (pttm) REVERT: H 10 MET cc_start: 0.8292 (tpp) cc_final: 0.8075 (tpp) outliers start: 36 outliers final: 27 residues processed: 318 average time/residue: 0.3383 time to fit residues: 162.5527 Evaluate side-chains 316 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 289 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 68 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN D 569 ASN G 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 18733 Z= 0.372 Angle : 0.566 8.840 25312 Z= 0.297 Chirality : 0.043 0.246 2825 Planarity : 0.004 0.045 3073 Dihedral : 10.972 106.481 2931 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.84 % Allowed : 12.69 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 2290 helix: 2.10 (0.14), residues: 1341 sheet: -1.17 (0.42), residues: 148 loop : -1.83 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 460 HIS 0.004 0.001 HIS A 412 PHE 0.014 0.002 PHE A 495 TYR 0.014 0.002 TYR C 673 ARG 0.010 0.001 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 278 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 473 ASP cc_start: 0.7177 (m-30) cc_final: 0.6778 (m-30) REVERT: C 395 VAL cc_start: 0.8180 (t) cc_final: 0.7968 (m) REVERT: C 570 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: D 629 MET cc_start: 0.7590 (mmm) cc_final: 0.7360 (mtt) REVERT: D 651 ASP cc_start: 0.7928 (t0) cc_final: 0.7380 (p0) REVERT: D 766 TRP cc_start: 0.7778 (m100) cc_final: 0.7364 (m100) REVERT: E 24 MET cc_start: 0.8089 (tpt) cc_final: 0.7600 (tpt) REVERT: E 31 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: E 95 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7580 (pt0) REVERT: E 131 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.5638 (mmm160) REVERT: F 74 LYS cc_start: 0.7019 (mttp) cc_final: 0.6791 (mttp) REVERT: F 99 ARG cc_start: 0.7359 (mmm-85) cc_final: 0.7096 (mtp180) REVERT: G 41 LYS cc_start: 0.6613 (tptp) cc_final: 0.5898 (pttm) outliers start: 52 outliers final: 42 residues processed: 313 average time/residue: 0.3038 time to fit residues: 142.0578 Evaluate side-chains 318 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 273 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 115 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN D 569 ASN G 205 HIS H 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 18733 Z= 0.160 Angle : 0.465 8.251 25312 Z= 0.244 Chirality : 0.038 0.240 2825 Planarity : 0.004 0.046 3073 Dihedral : 9.949 106.491 2931 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.24 % Allowed : 13.46 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2290 helix: 2.41 (0.15), residues: 1342 sheet: -1.02 (0.42), residues: 146 loop : -1.71 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 460 HIS 0.004 0.001 HIS H 205 PHE 0.010 0.001 PHE G 201 TYR 0.020 0.001 TYR C 673 ARG 0.011 0.001 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 296 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 473 ASP cc_start: 0.7222 (m-30) cc_final: 0.6848 (m-30) REVERT: C 395 VAL cc_start: 0.8002 (t) cc_final: 0.7768 (m) REVERT: C 431 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 721 MET cc_start: 0.8016 (ttp) cc_final: 0.7788 (ttp) REVERT: C 770 LYS cc_start: 0.7955 (mptt) cc_final: 0.7744 (mptt) REVERT: D 651 ASP cc_start: 0.7897 (t0) cc_final: 0.7349 (p0) REVERT: E 31 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: E 95 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7557 (pt0) REVERT: E 131 ARG cc_start: 0.6347 (mmm-85) cc_final: 0.5689 (mmm160) REVERT: F 99 ARG cc_start: 0.7348 (mmm-85) cc_final: 0.7092 (mtp180) REVERT: G 41 LYS cc_start: 0.6648 (tptp) cc_final: 0.5950 (pttm) outliers start: 41 outliers final: 32 residues processed: 324 average time/residue: 0.3174 time to fit residues: 153.9070 Evaluate side-chains 317 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 284 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 726 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN D 569 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS H 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 18733 Z= 0.501 Angle : 0.637 9.548 25312 Z= 0.333 Chirality : 0.046 0.261 2825 Planarity : 0.005 0.059 3073 Dihedral : 11.210 102.444 2931 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.06 % Allowed : 13.13 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2290 helix: 1.85 (0.14), residues: 1341 sheet: -1.17 (0.42), residues: 148 loop : -1.89 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 460 HIS 0.009 0.001 HIS H 205 PHE 0.017 0.002 PHE A 495 TYR 0.016 0.002 TYR A 549 ARG 0.011 0.001 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 269 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 644 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6206 (pt0) REVERT: B 473 ASP cc_start: 0.7160 (m-30) cc_final: 0.6739 (m-30) REVERT: C 395 VAL cc_start: 0.8252 (t) cc_final: 0.8038 (m) REVERT: D 651 ASP cc_start: 0.7953 (t0) cc_final: 0.7408 (p0) REVERT: D 766 TRP cc_start: 0.7757 (m100) cc_final: 0.7381 (m100) REVERT: E 31 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: E 95 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7579 (pt0) REVERT: E 131 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5598 (mmm160) REVERT: F 99 ARG cc_start: 0.7355 (mmm-85) cc_final: 0.7137 (mtp180) REVERT: G 41 LYS cc_start: 0.6682 (tptp) cc_final: 0.5938 (pttm) REVERT: H 10 MET cc_start: 0.8290 (tpp) cc_final: 0.8069 (tpp) outliers start: 56 outliers final: 47 residues processed: 315 average time/residue: 0.3121 time to fit residues: 148.0510 Evaluate side-chains 313 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 264 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN D 569 ASN F 132 HIS G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18733 Z= 0.170 Angle : 0.489 12.225 25312 Z= 0.254 Chirality : 0.039 0.209 2825 Planarity : 0.004 0.053 3073 Dihedral : 10.137 104.699 2931 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.13 % Allowed : 14.28 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.18), residues: 2290 helix: 2.28 (0.14), residues: 1343 sheet: -1.04 (0.42), residues: 146 loop : -1.72 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP D 460 HIS 0.006 0.001 HIS H 205 PHE 0.009 0.001 PHE H 201 TYR 0.024 0.001 TYR C 673 ARG 0.013 0.001 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 283 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 GLU cc_start: 0.6422 (mm-30) cc_final: 0.6194 (pt0) REVERT: B 473 ASP cc_start: 0.7223 (m-30) cc_final: 0.6924 (m-30) REVERT: C 395 VAL cc_start: 0.8120 (t) cc_final: 0.7909 (m) REVERT: C 431 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8049 (tm-30) REVERT: C 721 MET cc_start: 0.7920 (ttp) cc_final: 0.7668 (ttp) REVERT: C 770 LYS cc_start: 0.7958 (mptt) cc_final: 0.7752 (mptt) REVERT: D 651 ASP cc_start: 0.7887 (t0) cc_final: 0.7325 (p0) REVERT: E 31 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: E 95 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7564 (pt0) REVERT: F 74 LYS cc_start: 0.7361 (mmtp) cc_final: 0.7121 (mmtp) REVERT: F 99 ARG cc_start: 0.7335 (mmm-85) cc_final: 0.7073 (mtp180) REVERT: G 41 LYS cc_start: 0.6626 (tptp) cc_final: 0.5884 (pttm) REVERT: H 10 MET cc_start: 0.8302 (tpp) cc_final: 0.8056 (tpp) outliers start: 39 outliers final: 33 residues processed: 309 average time/residue: 0.3208 time to fit residues: 148.3823 Evaluate side-chains 311 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 277 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS 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: 0.8980 chunk 192 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 747 ASN C 764 ASN G 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18733 Z= 0.352 Angle : 0.570 11.687 25312 Z= 0.297 Chirality : 0.042 0.232 2825 Planarity : 0.004 0.051 3073 Dihedral : 10.574 102.774 2931 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.41 % Allowed : 14.33 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2290 helix: 2.08 (0.14), residues: 1341 sheet: -1.13 (0.42), residues: 148 loop : -1.79 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 460 HIS 0.004 0.001 HIS A 412 PHE 0.014 0.002 PHE A 495 TYR 0.023 0.001 TYR D 549 ARG 0.013 0.001 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 269 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8325 (tp) REVERT: A 644 GLU cc_start: 0.6410 (mm-30) cc_final: 0.6189 (pt0) REVERT: B 473 ASP cc_start: 0.7136 (m-30) cc_final: 0.6736 (m-30) REVERT: C 395 VAL cc_start: 0.8127 (t) cc_final: 0.7917 (m) REVERT: C 721 MET cc_start: 0.7940 (ttp) cc_final: 0.7664 (ttp) REVERT: D 651 ASP cc_start: 0.7945 (t0) cc_final: 0.7423 (p0) REVERT: E 31 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: E 95 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7568 (pt0) REVERT: E 131 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5664 (mmm160) REVERT: F 74 LYS cc_start: 0.7291 (mmtp) cc_final: 0.7085 (mmtt) REVERT: F 99 ARG cc_start: 0.7353 (mmm-85) cc_final: 0.7085 (mtp180) REVERT: G 41 LYS cc_start: 0.6682 (tptp) cc_final: 0.5947 (pttm) REVERT: H 10 MET cc_start: 0.8255 (tpp) cc_final: 0.8032 (tpp) outliers start: 44 outliers final: 36 residues processed: 301 average time/residue: 0.3029 time to fit residues: 137.6072 Evaluate side-chains 307 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 268 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 150 optimal weight: 0.0470 chunk 227 optimal weight: 0.6980 chunk 209 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 764 ASN D 569 ASN G 205 HIS H 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 18733 Z= 0.150 Angle : 0.494 12.564 25312 Z= 0.256 Chirality : 0.038 0.215 2825 Planarity : 0.004 0.056 3073 Dihedral : 9.834 103.454 2931 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.08 % Allowed : 14.82 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.18), residues: 2290 helix: 2.38 (0.15), residues: 1339 sheet: -1.04 (0.42), residues: 146 loop : -1.67 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 460 HIS 0.004 0.001 HIS H 205 PHE 0.009 0.001 PHE A 571 TYR 0.025 0.001 TYR C 673 ARG 0.014 0.001 ARG D 661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 284 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 GLU cc_start: 0.6384 (mm-30) cc_final: 0.6172 (pt0) REVERT: A 647 TYR cc_start: 0.7705 (p90) cc_final: 0.7491 (p90) REVERT: B 473 ASP cc_start: 0.7215 (m-30) cc_final: 0.6912 (m-30) REVERT: C 395 VAL cc_start: 0.8076 (t) cc_final: 0.7857 (m) REVERT: C 721 MET cc_start: 0.7857 (ttp) cc_final: 0.7600 (ttp) REVERT: C 770 LYS cc_start: 0.7966 (mptt) cc_final: 0.7756 (mptt) REVERT: D 651 ASP cc_start: 0.7902 (t0) cc_final: 0.7349 (p0) REVERT: E 31 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: E 67 CYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6759 (t) REVERT: E 95 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7643 (pt0) REVERT: E 131 ARG cc_start: 0.6388 (mmm-85) cc_final: 0.5719 (mmm160) REVERT: F 99 ARG cc_start: 0.7309 (mmm-85) cc_final: 0.7046 (mtp180) REVERT: G 41 LYS cc_start: 0.6594 (tptp) cc_final: 0.5773 (pttm) outliers start: 38 outliers final: 32 residues processed: 309 average time/residue: 0.3204 time to fit residues: 148.1116 Evaluate side-chains 314 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 280 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 784 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 132 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 764 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.095773 restraints weight = 61112.919| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.75 r_work: 0.2669 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 18733 Z= 0.393 Angle : 0.594 12.053 25312 Z= 0.308 Chirality : 0.043 0.226 2825 Planarity : 0.004 0.047 3073 Dihedral : 10.572 100.701 2931 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.30 % Allowed : 15.04 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2290 helix: 2.05 (0.14), residues: 1340 sheet: -1.11 (0.43), residues: 148 loop : -1.78 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 460 HIS 0.005 0.001 HIS H 205 PHE 0.016 0.002 PHE C 495 TYR 0.016 0.002 TYR C 673 ARG 0.011 0.001 ARG D 661 =============================================================================== Job complete usr+sys time: 4121.99 seconds wall clock time: 75 minutes 28.22 seconds (4528.22 seconds total)