Starting phenix.real_space_refine on Sun Feb 18 12:31:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uai_26426/02_2024/7uai_26426.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uai_26426/02_2024/7uai_26426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uai_26426/02_2024/7uai_26426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uai_26426/02_2024/7uai_26426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uai_26426/02_2024/7uai_26426.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uai_26426/02_2024/7uai_26426.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.053 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 Ca 8 9.91 5 Zn 4 6.06 5 S 111 5.16 5 C 13848 2.51 5 N 3637 2.21 5 O 4328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 74": "NH1" <-> "NH2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 251": "OE1" <-> "OE2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E ARG 255": "NH1" <-> "NH2" Residue "E ARG 284": "NH1" <-> "NH2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E GLU 331": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 364": "NH1" <-> "NH2" Residue "E ARG 439": "NH1" <-> "NH2" Residue "E ARG 458": "NH1" <-> "NH2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E ARG 504": "NH1" <-> "NH2" Residue "E GLU 514": "OE1" <-> "OE2" Residue "E PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 546": "NH1" <-> "NH2" Residue "E ARG 578": "NH1" <-> "NH2" Residue "E GLU 594": "OE1" <-> "OE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B ARG 546": "NH1" <-> "NH2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C GLU 514": "OE1" <-> "OE2" Residue "C ARG 546": "NH1" <-> "NH2" Residue "C ARG 549": "NH1" <-> "NH2" Residue "C ARG 578": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "D GLU 272": "OE1" <-> "OE2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 364": "NH1" <-> "NH2" Residue "D PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D GLU 514": "OE1" <-> "OE2" Residue "D ARG 546": "NH1" <-> "NH2" Residue "D ARG 578": "NH1" <-> "NH2" Residue "D GLU 594": "OE1" <-> "OE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H GLU 173": "OE1" <-> "OE2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H GLU 208": "OE1" <-> "OE2" Residue "H GLU 213": "OE1" <-> "OE2" Residue "H GLU 337": "OE1" <-> "OE2" Residue "H GLU 347": "OE1" <-> "OE2" Residue "H GLU 350": "OE1" <-> "OE2" Residue "H GLU 351": "OE1" <-> "OE2" Residue "H GLU 367": "OE1" <-> "OE2" 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: 21936 Number of models: 1 Model: "" Number of chains: 26 Chain: "E" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4280 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2004 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 254} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 4296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4296 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 4250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4250 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 509} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4300 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2192 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 262} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.93, per 1000 atoms: 0.54 Number of scatterers: 21936 At special positions: 0 Unit cell: (125.786, 149.813, 161.12, 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) Zn 4 29.99 Ca 8 19.99 S 111 16.00 O 4328 8.00 N 3637 7.00 C 13848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS E 107 " - pdb=" SG CYS E 259 " distance=2.02 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 147 " distance=2.01 Simple disulfide: pdb=" SG CYS E 269 " - pdb=" SG CYS E 277 " distance=2.02 Simple disulfide: pdb=" SG CYS E 343 " - pdb=" SG CYS E 431 " distance=2.03 Simple disulfide: pdb=" SG CYS E 557 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 368 " distance=2.06 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 104 " distance=2.07 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 137 " distance=2.05 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 254 " distance=2.06 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 259 " distance=2.02 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 147 " distance=1.99 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 277 " distance=2.02 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS D 308 " distance=2.02 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 431 " distance=2.02 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS B 559 " distance=2.04 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 259 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 147 " distance=1.99 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 277 " distance=2.02 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 431 " distance=2.02 Simple disulfide: pdb=" SG CYS C 557 " - pdb=" SG CYS C 559 " distance=2.04 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 259 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 147 " distance=1.99 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 277 " distance=2.00 Simple disulfide: pdb=" SG CYS D 343 " - pdb=" SG CYS D 431 " distance=2.00 Simple disulfide: pdb=" SG CYS D 557 " - pdb=" SG CYS D 559 " distance=2.04 Simple disulfide: pdb=" SG CYS H 36 " - pdb=" SG CYS H 368 " distance=2.06 Simple disulfide: pdb=" SG CYS H 93 " - pdb=" SG CYS H 104 " distance=2.06 Simple disulfide: pdb=" SG CYS H 117 " - pdb=" SG CYS H 137 " distance=2.04 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 154 " distance=2.03 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS H 254 " distance=2.06 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " NAG R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG I 1 " - " FUC I 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 4 " " NAG Q 1 " - " FUC Q 4 " " NAG T 1 " - " FUC T 4 " NAG-ASN " NAG B 704 " - " ASN B 440 " " NAG C 704 " - " ASN C 440 " " NAG D 703 " - " ASN D 440 " " NAG E 704 " - " ASN E 440 " " NAG F 1 " - " ASN E 258 " " NAG G 1 " - " ASN E 222 " " NAG I 1 " - " ASN E 414 " " NAG J 1 " - " ASN E 140 " " NAG K 1 " - " ASN B 140 " " NAG L 1 " - " ASN B 258 " " NAG M 1 " - " ASN B 222 " " NAG N 1 " - " ASN B 414 " " NAG O 1 " - " ASN C 140 " " NAG P 1 " - " ASN C 222 " " NAG Q 1 " - " ASN C 414 " " NAG R 1 " - " ASN D 258 " " NAG S 1 " - " ASN D 222 " " NAG T 1 " - " ASN D 414 " " NAG U 1 " - " ASN D 140 " Time building additional restraints: 9.28 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS D 165 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS D 155 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS D 159 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 165 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 155 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 159 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 165 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 159 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 155 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 165 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 155 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 159 " 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5038 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 48 sheets defined 23.1% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 88 through 106 Processing helix chain 'E' and resid 149 through 162 Processing helix chain 'E' and resid 165 through 169 Processing helix chain 'E' and resid 171 through 174 Processing helix chain 'E' and resid 180 through 183 Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 232 through 238 Processing helix chain 'E' and resid 246 through 258 Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 411 through 415 Processing helix chain 'E' and resid 440 through 448 Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 516 through 520 Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'E' and resid 546 through 551 Processing helix chain 'E' and resid 573 through 577 Processing helix chain 'E' and resid 597 through 600 Processing helix chain 'A' and resid 38 through 56 removed outlier: 3.799A pdb=" N GLY A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 108 through 111 Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 164 through 182 Processing helix chain 'A' and resid 342 through 345 removed outlier: 3.629A pdb=" N PHE A 345 " --> pdb=" O SER A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU A 380 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 88 through 106 Processing helix chain 'B' and resid 149 through 161 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 180 through 183 Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 440 through 448 Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 546 through 551 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 578 through 581 removed outlier: 4.028A pdb=" N PHE B 581 " --> pdb=" O ARG B 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 578 through 581' Processing helix chain 'B' and resid 597 through 600 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 88 through 106 Processing helix chain 'C' and resid 149 through 162 Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 171 through 174 Processing helix chain 'C' and resid 180 through 183 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 234 through 239 removed outlier: 4.241A pdb=" N ILE C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 440 through 448 Processing helix chain 'C' and resid 493 through 497 Processing helix chain 'C' and resid 546 through 551 Processing helix chain 'C' and resid 573 through 577 Processing helix chain 'C' and resid 597 through 600 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 149 through 161 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 171 through 174 Processing helix chain 'D' and resid 180 through 183 Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 232 through 238 Processing helix chain 'D' and resid 246 through 258 Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 440 through 448 Processing helix chain 'D' and resid 493 through 497 Processing helix chain 'D' and resid 535 through 539 Processing helix chain 'D' and resid 546 through 551 Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 597 through 600 Processing helix chain 'H' and resid 38 through 56 removed outlier: 3.574A pdb=" N ALA H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 98 No H-bonds generated for 'chain 'H' and resid 96 through 98' Processing helix chain 'H' and resid 100 through 104 Processing helix chain 'H' and resid 108 through 111 Processing helix chain 'H' and resid 143 through 151 Processing helix chain 'H' and resid 164 through 182 Processing helix chain 'H' and resid 342 through 345 Processing helix chain 'H' and resid 360 through 364 Processing sheet with id=AA1, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'E' and resid 110 through 112 removed outlier: 7.996A pdb=" N PHE E 122 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 82 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 176 through 178 Processing sheet with id=AA4, first strand: chain 'E' and resid 265 through 269 removed outlier: 6.191A pdb=" N ASP E 423 " --> pdb=" O TYR E 313 " (cutoff:3.500A) removed outlier: 12.047A pdb=" N TYR E 313 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 265 through 269 removed outlier: 5.700A pdb=" N LEU E 421 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS E 349 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP E 423 " --> pdb=" O PHE E 347 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE E 347 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 280 through 281 removed outlier: 6.285A pdb=" N VAL E 362 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LYS E 376 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG E 364 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU E 374 " --> pdb=" O ARG E 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 434 through 438 Processing sheet with id=AA8, first strand: chain 'E' and resid 454 through 455 Processing sheet with id=AA9, first strand: chain 'E' and resid 454 through 455 removed outlier: 6.204A pdb=" N LEU E 482 " --> pdb=" O GLY E 569 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 552 through 554 Processing sheet with id=AB2, first strand: chain 'A' and resid 32 through 33 removed outlier: 5.595A pdb=" N CYS A 93 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG A 63 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 91 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN A 65 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU A 89 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL A 67 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASP A 87 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL A 113 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 122 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU A 132 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASN A 124 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU A 130 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 156 through 157 removed outlier: 6.549A pdb=" N LEU A 210 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL A 192 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU A 208 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG A 194 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N PHE A 206 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER A 196 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER A 204 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 235 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 156 through 157 removed outlier: 6.549A pdb=" N LEU A 210 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL A 192 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU A 208 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG A 194 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N PHE A 206 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER A 196 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER A 204 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 235 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 337 through 340 Processing sheet with id=AB6, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AB7, first strand: chain 'B' and resid 110 through 112 Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 269 Processing sheet with id=AC1, first strand: chain 'B' and resid 265 through 269 removed outlier: 5.763A pdb=" N LEU B 421 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS B 349 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASP B 423 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE B 347 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 280 through 281 removed outlier: 5.914A pdb=" N VAL B 362 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS B 376 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG B 364 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU B 374 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 434 through 439 Processing sheet with id=AC4, first strand: chain 'B' and resid 454 through 455 Processing sheet with id=AC5, first strand: chain 'B' and resid 454 through 455 removed outlier: 6.189A pdb=" N LEU B 482 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 569 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 552 through 554 Processing sheet with id=AC7, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AC8, first strand: chain 'C' and resid 110 through 112 removed outlier: 7.881A pdb=" N PHE C 122 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 82 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AD1, first strand: chain 'C' and resid 265 through 269 Processing sheet with id=AD2, first strand: chain 'C' and resid 265 through 269 removed outlier: 5.602A pdb=" N LEU C 421 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LYS C 349 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP C 423 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE C 347 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 280 through 281 removed outlier: 6.479A pdb=" N LEU C 358 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR C 379 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 360 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 434 through 438 Processing sheet with id=AD5, first strand: chain 'C' and resid 454 through 455 Processing sheet with id=AD6, first strand: chain 'C' and resid 454 through 455 removed outlier: 4.129A pdb=" N ILE C 571 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU C 484 " --> pdb=" O GLY C 569 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY C 569 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N PHE C 486 " --> pdb=" O TRP C 567 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TRP C 567 " --> pdb=" O PHE C 486 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL C 488 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N LEU C 565 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 534 through 535 removed outlier: 3.683A pdb=" N THR C 541 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 552 through 554 Processing sheet with id=AD9, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AE1, first strand: chain 'D' and resid 110 through 112 removed outlier: 8.056A pdb=" N PHE D 122 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 82 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 176 through 178 Processing sheet with id=AE3, first strand: chain 'D' and resid 265 through 269 removed outlier: 5.983A pdb=" N ASP D 423 " --> pdb=" O TYR D 313 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N TYR D 313 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 265 through 269 removed outlier: 5.708A pdb=" N LEU D 421 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS D 349 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP D 423 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE D 347 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 280 through 281 removed outlier: 6.093A pdb=" N VAL D 362 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS D 376 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU D 374 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 434 through 438 Processing sheet with id=AE7, first strand: chain 'D' and resid 454 through 455 Processing sheet with id=AE8, first strand: chain 'D' and resid 454 through 455 removed outlier: 3.666A pdb=" N ILE D 571 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU D 484 " --> pdb=" O GLY D 569 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLY D 569 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE D 486 " --> pdb=" O TRP D 567 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TRP D 567 " --> pdb=" O PHE D 486 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL D 488 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N LEU D 565 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 552 through 554 Processing sheet with id=AF1, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.017A pdb=" N ALA H 70 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N CYS H 93 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ARG H 63 " --> pdb=" O THR H 91 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR H 91 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASN H 65 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU H 89 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL H 67 " --> pdb=" O ASP H 87 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASP H 87 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL H 113 " --> pdb=" O GLU H 90 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR H 122 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU H 132 " --> pdb=" O TYR H 122 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN H 124 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU H 130 " --> pdb=" O ASN H 124 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG H 301 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 156 through 157 removed outlier: 3.928A pdb=" N GLN H 186 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU H 210 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL H 192 " --> pdb=" O GLU H 208 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU H 208 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ARG H 194 " --> pdb=" O PHE H 206 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE H 206 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER H 196 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER H 204 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 211 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY H 235 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 337 through 340 836 hydrogen bonds defined for protein. 2013 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.89 Time building geometry restraints manager: 9.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3814 1.31 - 1.44: 6064 1.44 - 1.57: 12422 1.57 - 1.70: 0 1.70 - 1.83: 154 Bond restraints: 22454 Sorted by residual: bond pdb=" C VAL E 300 " pdb=" N ASP E 301 " ideal model delta sigma weight residual 1.330 1.220 0.110 1.38e-02 5.25e+03 6.32e+01 bond pdb=" C VAL B 550 " pdb=" N GLY B 551 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.20e-02 6.94e+03 3.38e+01 bond pdb=" CA PRO A 381 " pdb=" C PRO A 381 " ideal model delta sigma weight residual 1.514 1.546 -0.032 5.50e-03 3.31e+04 3.36e+01 bond pdb=" C ARG B 549 " pdb=" N VAL B 550 " ideal model delta sigma weight residual 1.332 1.255 0.077 1.36e-02 5.41e+03 3.19e+01 bond pdb=" C ASP E 301 " pdb=" N HIS E 302 " ideal model delta sigma weight residual 1.333 1.271 0.062 1.50e-02 4.44e+03 1.71e+01 ... (remaining 22449 not shown) Histogram of bond angle deviations from ideal: 95.17 - 103.15: 177 103.15 - 111.13: 7694 111.13 - 119.11: 10430 119.11 - 127.10: 11928 127.10 - 135.08: 271 Bond angle restraints: 30500 Sorted by residual: angle pdb=" C VAL B 550 " pdb=" N GLY B 551 " pdb=" CA GLY B 551 " ideal model delta sigma weight residual 122.30 114.84 7.46 1.03e+00 9.43e-01 5.24e+01 angle pdb=" CA ASP D 564 " pdb=" CB ASP D 564 " pdb=" CG ASP D 564 " ideal model delta sigma weight residual 112.60 119.59 -6.99 1.00e+00 1.00e+00 4.89e+01 angle pdb=" CA PHE B 590 " pdb=" CB PHE B 590 " pdb=" CG PHE B 590 " ideal model delta sigma weight residual 113.80 120.62 -6.82 1.00e+00 1.00e+00 4.65e+01 angle pdb=" CA ASP B 174 " pdb=" CB ASP B 174 " pdb=" CG ASP B 174 " ideal model delta sigma weight residual 112.60 118.62 -6.02 1.00e+00 1.00e+00 3.63e+01 angle pdb=" N ASP D 512 " pdb=" CA ASP D 512 " pdb=" C ASP D 512 " ideal model delta sigma weight residual 108.96 99.55 9.41 1.59e+00 3.96e-01 3.50e+01 ... (remaining 30495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.92: 12985 20.92 - 41.83: 676 41.83 - 62.74: 125 62.74 - 83.66: 55 83.66 - 104.57: 26 Dihedral angle restraints: 13867 sinusoidal: 6037 harmonic: 7830 Sorted by residual: dihedral pdb=" CB CYS D 557 " pdb=" SG CYS D 557 " pdb=" SG CYS D 559 " pdb=" CB CYS D 559 " ideal model delta sinusoidal sigma weight residual -86.00 -151.03 65.03 1 1.00e+01 1.00e-02 5.55e+01 dihedral pdb=" CB CYS C 128 " pdb=" SG CYS C 128 " pdb=" SG CYS C 147 " pdb=" CB CYS C 147 " ideal model delta sinusoidal sigma weight residual 93.00 157.36 -64.36 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS C 557 " pdb=" SG CYS C 557 " pdb=" SG CYS C 559 " pdb=" CB CYS C 559 " ideal model delta sinusoidal sigma weight residual -86.00 -147.38 61.38 1 1.00e+01 1.00e-02 5.00e+01 ... (remaining 13864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2208 0.099 - 0.198: 1024 0.198 - 0.297: 178 0.297 - 0.395: 23 0.395 - 0.494: 6 Chirality restraints: 3439 Sorted by residual: chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.14e+02 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.37e+01 ... (remaining 3436 not shown) Planarity restraints: 3923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 199 " -0.158 2.00e-02 2.50e+03 8.23e-02 1.69e+02 pdb=" CG TRP H 199 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP H 199 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TRP H 199 " 0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP H 199 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP H 199 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP H 199 " 0.092 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 199 " -0.113 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 199 " 0.064 2.00e-02 2.50e+03 pdb=" CH2 TRP H 199 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 199 " 0.153 2.00e-02 2.50e+03 7.99e-02 1.60e+02 pdb=" CG TRP A 199 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 199 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 TRP A 199 " -0.062 2.00e-02 2.50e+03 pdb=" NE1 TRP A 199 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 199 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 199 " -0.104 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 199 " 0.098 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 199 " -0.045 2.00e-02 2.50e+03 pdb=" CH2 TRP A 199 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 436 " 0.123 2.00e-02 2.50e+03 6.80e-02 1.16e+02 pdb=" CG TRP B 436 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 436 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 436 " -0.075 2.00e-02 2.50e+03 pdb=" NE1 TRP B 436 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TRP B 436 " -0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP B 436 " -0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 436 " 0.067 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 436 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 436 " 0.085 2.00e-02 2.50e+03 ... (remaining 3920 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 23 2.36 - 2.99: 11861 2.99 - 3.63: 32582 3.63 - 4.26: 56311 4.26 - 4.90: 90232 Nonbonded interactions: 191009 Sorted by model distance: nonbonded pdb=" OD2 ASP A 153 " pdb="ZN ZN A 401 " model vdw 1.724 2.230 nonbonded pdb=" OD1 ASP B 285 " pdb="CA CA B 701 " model vdw 2.158 2.510 nonbonded pdb=" OD1 ASP C 288 " pdb="CA CA C 701 " model vdw 2.262 2.510 nonbonded pdb=" CG ASP A 153 " pdb="ZN ZN A 401 " model vdw 2.267 2.460 nonbonded pdb=" OD1 ASP B 288 " pdb="CA CA B 701 " model vdw 2.269 2.510 ... (remaining 191004 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 31 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 152 or (resid 153 and \ (name N or name CA or name C or name O or name CB )) or resid 154 through 382)) \ selection = (chain 'H' and (resid 31 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 56 or (resid 57 and (name N or nam \ e CA or name C or name O or name CB )) or resid 58 through 65 or (resid 66 and ( \ name N or name CA or name C or name O or name CB )) or resid 67 through 74 or re \ sid 79 through 127 or (resid 128 and (name N or name CA or name C or name O or n \ ame CB )) or resid 129 through 242 or (resid 243 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 244 through 310 or (res \ id 324 through 335 and (name N or name CA or name C or name O or name CB )) or r \ esid 336 or (resid 337 through 361 and (name N or name CA or name C or name O or \ name CB )) or resid 366 through 382)) } ncs_group { reference = (chain 'B' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 171 or (resid 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 241 or (resid 242 \ and (name N or name CA or name C or name O or name CB )) or resid 243 through 27 \ 1 or (resid 272 and (name N or name CA or name C or name O or name CB )) or resi \ d 273 through 295 or resid 299 through 324 or (resid 325 and (name N or name CA \ or name C or name O or name CB )) or resid 326 through 332 or (resid 333 and (na \ me N or name CA or name C or name O or name CB )) or resid 334 through 407 or (r \ esid 408 and (name N or name CA or name C or name O or name CB )) or resid 409 t \ hrough 533 or (resid 534 and (name N or name CA or name C or name O or name CB ) \ ) or resid 535 through 536 or resid 540 through 548 or (resid 549 and (name N or \ name CA or name C or name O or name CB )) or resid 550 through 560 or (resid 56 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 562 through \ 600 or resid 701)) selection = (chain 'C' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 171 or (resid 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 271 or (resid 272 \ and (name N or name CA or name C or name O or name CB )) or resid 273 through 28 \ 3 or (resid 284 and (name N or name CA or name C or name O or name CB )) or resi \ d 285 through 407 or (resid 408 and (name N or name CA or name C or name O or na \ me CB )) or resid 409 through 476 or (resid 477 and (name N or name CA or name C \ or name O or name CB )) or resid 478 through 548 or (resid 549 and (name N or n \ ame CA or name C or name O or name CB )) or resid 550 through 560 or (resid 561 \ and (name N or name CA or name C or name O or name CB )) or resid 562 through 60 \ 0 or resid 701)) selection = (chain 'D' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 171 or (resid 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 241 or (resid 242 \ and (name N or name CA or name C or name O or name CB )) or resid 243 through 27 \ 1 or (resid 272 and (name N or name CA or name C or name O or name CB )) or resi \ d 273 through 283 or (resid 284 and (name N or name CA or name C or name O or na \ me CB )) or resid 285 through 295 or resid 299 through 324 or (resid 325 and (na \ me N or name CA or name C or name O or name CB )) or resid 326 through 332 or (r \ esid 333 and (name N or name CA or name C or name O or name CB )) or resid 334 t \ hrough 407 or (resid 408 and (name N or name CA or name C or name O or name CB ) \ ) or resid 409 through 476 or (resid 477 and (name N or name CA or name C or nam \ e O or name CB )) or resid 478 through 533 or (resid 534 and (name N or name CA \ or name C or name O or name CB )) or resid 535 through 536 or resid 540 through \ 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or re \ sid 550 through 600 or resid 701)) selection = (chain 'E' and (resid 66 through 241 or (resid 242 and (name N or name CA or nam \ e C or name O or name CB )) or resid 243 through 283 or (resid 284 and (name N o \ r name CA or name C or name O or name CB )) or resid 285 through 295 or resid 29 \ 9 through 324 or (resid 325 and (name N or name CA or name C or name O or name C \ B )) or resid 326 through 332 or (resid 333 and (name N or name CA or name C or \ name O or name CB )) or resid 334 through 476 or (resid 477 and (name N or name \ CA or name C or name O or name CB )) or resid 478 through 533 or (resid 534 and \ (name N or name CA or name C or name O or name CB )) or resid 535 through 536 or \ resid 540 through 600 or resid 701)) } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'Q' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 3.480 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 65.890 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 : 0.013 0.110 22454 Z= 0.863 Angle : 1.784 9.410 30500 Z= 1.206 Chirality : 0.107 0.494 3439 Planarity : 0.013 0.114 3904 Dihedral : 14.624 104.573 8736 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 1.03 % Allowed : 4.86 % Favored : 94.11 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 8.77 % 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: -0.93 (0.15), residues: 2658 helix: -0.98 (0.24), residues: 355 sheet: -0.42 (0.20), residues: 636 loop : -0.56 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.158 0.023 TRP H 199 HIS 0.016 0.004 HIS B 165 PHE 0.100 0.013 PHE A 206 TYR 0.113 0.017 TYR A 148 ARG 0.010 0.001 ARG C 549 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 667 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 LEU cc_start: 0.8787 (tp) cc_final: 0.8488 (tp) REVERT: E 116 GLU cc_start: 0.7778 (mp0) cc_final: 0.7185 (mp0) REVERT: E 122 PHE cc_start: 0.9276 (m-80) cc_final: 0.9074 (m-80) REVERT: E 124 GLN cc_start: 0.7885 (tt0) cc_final: 0.7627 (tp40) REVERT: E 136 HIS cc_start: 0.7916 (m-70) cc_final: 0.7648 (m-70) REVERT: E 141 ILE cc_start: 0.9042 (mt) cc_final: 0.8837 (mp) REVERT: E 143 ILE cc_start: 0.8254 (mt) cc_final: 0.8034 (mm) REVERT: E 201 ASP cc_start: 0.8670 (p0) cc_final: 0.8456 (m-30) REVERT: E 207 ASP cc_start: 0.7842 (t0) cc_final: 0.7318 (t0) REVERT: E 210 SER cc_start: 0.9123 (t) cc_final: 0.8571 (t) REVERT: E 263 HIS cc_start: 0.7625 (m-70) cc_final: 0.6981 (m-70) REVERT: E 338 LYS cc_start: 0.9149 (mttm) cc_final: 0.8913 (mtpm) REVERT: E 389 LYS cc_start: 0.8835 (mttp) cc_final: 0.8472 (mttm) REVERT: E 409 LYS cc_start: 0.8679 (mttt) cc_final: 0.8431 (mtmt) REVERT: E 423 ASP cc_start: 0.7934 (m-30) cc_final: 0.7526 (m-30) REVERT: E 428 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7103 (mt-10) REVERT: E 443 GLN cc_start: 0.8433 (tt0) cc_final: 0.7690 (tt0) REVERT: E 447 ASN cc_start: 0.8901 (m-40) cc_final: 0.8578 (m110) REVERT: E 453 LYS cc_start: 0.8710 (pttt) cc_final: 0.8407 (ptmt) REVERT: E 514 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7619 (mp0) REVERT: E 518 ARG cc_start: 0.8664 (mtm110) cc_final: 0.8284 (mtm-85) REVERT: E 525 MET cc_start: 0.7900 (mmm) cc_final: 0.7160 (mtp) REVERT: E 538 ILE cc_start: 0.7554 (pt) cc_final: 0.7204 (pt) REVERT: E 567 TRP cc_start: 0.7123 (m-90) cc_final: 0.5805 (m-90) REVERT: E 577 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8805 (mtpp) REVERT: A 60 TYR cc_start: 0.8392 (m-80) cc_final: 0.8168 (m-10) REVERT: A 85 THR cc_start: 0.8209 (m) cc_final: 0.7992 (p) REVERT: A 89 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9173 (pp) REVERT: A 106 MET cc_start: 0.8043 (mpt) cc_final: 0.7752 (mpm) REVERT: A 111 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8015 (tm-30) REVERT: A 132 LEU cc_start: 0.8752 (tp) cc_final: 0.8003 (mt) REVERT: A 140 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7476 (mtm-85) REVERT: A 168 LEU cc_start: 0.9089 (tp) cc_final: 0.8879 (tm) REVERT: A 173 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8412 (mm-30) REVERT: A 374 ASN cc_start: 0.9112 (t0) cc_final: 0.8513 (p0) REVERT: B 154 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8209 (mt-10) REVERT: B 215 GLN cc_start: 0.8242 (pt0) cc_final: 0.7812 (pp30) REVERT: B 235 PHE cc_start: 0.8929 (m-80) cc_final: 0.8267 (m-80) REVERT: B 245 PHE cc_start: 0.9073 (m-80) cc_final: 0.8769 (m-10) REVERT: B 266 LEU cc_start: 0.9212 (tp) cc_final: 0.8884 (tt) REVERT: B 502 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7090 (mt-10) REVERT: B 521 MET cc_start: 0.8568 (mtp) cc_final: 0.8142 (mtp) REVERT: C 131 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: C 149 TYR cc_start: 0.8426 (m-10) cc_final: 0.8153 (m-80) REVERT: C 187 TYR cc_start: 0.8586 (m-80) cc_final: 0.8255 (m-80) REVERT: C 195 ASP cc_start: 0.7264 (p0) cc_final: 0.6858 (p0) REVERT: C 197 SER cc_start: 0.9289 (t) cc_final: 0.8975 (p) REVERT: C 212 MET cc_start: 0.8830 (mmm) cc_final: 0.8332 (mmt) REVERT: C 245 PHE cc_start: 0.8802 (m-80) cc_final: 0.8102 (m-10) REVERT: C 263 HIS cc_start: 0.8025 (m-70) cc_final: 0.7487 (m170) REVERT: C 331 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7176 (mt-10) REVERT: C 525 MET cc_start: 0.7931 (mmm) cc_final: 0.7280 (mmm) REVERT: C 543 ILE cc_start: 0.8857 (mt) cc_final: 0.8649 (tt) REVERT: C 584 ASN cc_start: 0.8602 (t0) cc_final: 0.7973 (t0) REVERT: D 212 MET cc_start: 0.9409 (mmm) cc_final: 0.9091 (mmm) REVERT: D 238 ILE cc_start: 0.8927 (mt) cc_final: 0.8653 (mm) REVERT: D 251 GLU cc_start: 0.7559 (tt0) cc_final: 0.7316 (tt0) REVERT: D 253 LEU cc_start: 0.9194 (tp) cc_final: 0.8953 (tt) REVERT: D 315 MET cc_start: 0.8837 (mmm) cc_final: 0.8580 (mmt) REVERT: D 396 LYS cc_start: 0.8675 (mttt) cc_final: 0.8470 (mtmp) REVERT: D 517 VAL cc_start: 0.9243 (t) cc_final: 0.9025 (m) REVERT: H 41 VAL cc_start: 0.5990 (t) cc_final: 0.5691 (m) REVERT: H 74 ARG cc_start: 0.8853 (mtt180) cc_final: 0.8480 (tpp-160) REVERT: H 128 ARG cc_start: 0.8529 (mtt180) cc_final: 0.8044 (mmm160) REVERT: H 135 TYR cc_start: 0.8148 (p90) cc_final: 0.7645 (p90) REVERT: H 149 MET cc_start: 0.8232 (mmm) cc_final: 0.7959 (mtm) REVERT: H 199 TRP cc_start: 0.7863 (t-100) cc_final: 0.7603 (t60) REVERT: H 205 TYR cc_start: 0.8883 (m-80) cc_final: 0.8519 (m-80) REVERT: H 212 LYS cc_start: 0.8716 (pttt) cc_final: 0.8285 (mtmm) REVERT: H 307 LEU cc_start: 0.8866 (mt) cc_final: 0.8620 (pt) outliers start: 24 outliers final: 5 residues processed: 685 average time/residue: 1.1843 time to fit residues: 936.4846 Evaluate side-chains 424 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 417 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain H residue 122 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 241 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 ASN E 341 GLN E 381 GLN E 386 HIS E 474 ASN E 573 HIS E 584 ASN B 190 ASN B 341 GLN B 513 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN C 386 HIS C 455 GLN C 505 GLN C 513 GLN C 558 ASN C 584 ASN D 72 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 341 GLN D 370 ASN D 455 GLN D 503 ASN D 513 GLN D 573 HIS ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22454 Z= 0.231 Angle : 0.723 9.726 30500 Z= 0.378 Chirality : 0.046 0.169 3439 Planarity : 0.004 0.050 3904 Dihedral : 8.971 65.886 3842 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.23 % Allowed : 15.44 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.19 (0.16), residues: 2658 helix: 0.55 (0.26), residues: 359 sheet: -0.34 (0.19), residues: 723 loop : -0.07 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 361 HIS 0.011 0.001 HIS B 189 PHE 0.032 0.002 PHE A 121 TYR 0.033 0.002 TYR A 131 ARG 0.009 0.001 ARG E 578 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 456 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.6496 (m-30) REVERT: E 141 ILE cc_start: 0.8810 (mt) cc_final: 0.8591 (mp) REVERT: E 143 ILE cc_start: 0.8099 (mt) cc_final: 0.7682 (mm) REVERT: E 175 TYR cc_start: 0.8407 (m-80) cc_final: 0.7759 (m-80) REVERT: E 207 ASP cc_start: 0.7469 (t0) cc_final: 0.7267 (t0) REVERT: E 210 SER cc_start: 0.9116 (t) cc_final: 0.8882 (t) REVERT: E 215 GLN cc_start: 0.8089 (tt0) cc_final: 0.7702 (tm-30) REVERT: E 256 MET cc_start: 0.8662 (ttp) cc_final: 0.8257 (ttt) REVERT: E 340 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7994 (mmmt) REVERT: E 423 ASP cc_start: 0.7908 (m-30) cc_final: 0.7597 (m-30) REVERT: E 443 GLN cc_start: 0.8338 (tt0) cc_final: 0.7591 (pt0) REVERT: E 447 ASN cc_start: 0.8934 (m-40) cc_final: 0.8615 (p0) REVERT: E 453 LYS cc_start: 0.8877 (pttt) cc_final: 0.8637 (ptmm) REVERT: E 471 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7829 (tm) REVERT: E 514 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7353 (mp0) REVERT: E 521 MET cc_start: 0.6723 (mtp) cc_final: 0.5851 (mtp) REVERT: E 525 MET cc_start: 0.7568 (mmm) cc_final: 0.7334 (mtp) REVERT: E 538 ILE cc_start: 0.7426 (pt) cc_final: 0.6813 (tp) REVERT: E 574 GLN cc_start: 0.8759 (pt0) cc_final: 0.8363 (pm20) REVERT: A 89 LEU cc_start: 0.9410 (mp) cc_final: 0.9180 (pt) REVERT: A 97 ARG cc_start: 0.7516 (tpm170) cc_final: 0.7276 (tpm170) REVERT: A 111 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8229 (tm-30) REVERT: A 118 LYS cc_start: 0.6485 (OUTLIER) cc_final: 0.5828 (mtmm) REVERT: A 140 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7322 (mpp80) REVERT: A 167 VAL cc_start: 0.8880 (t) cc_final: 0.8652 (p) REVERT: A 169 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 173 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8361 (mm-30) REVERT: A 178 TYR cc_start: 0.9379 (t80) cc_final: 0.9152 (t80) REVERT: A 255 ASP cc_start: 0.7793 (p0) cc_final: 0.7349 (p0) REVERT: A 374 ASN cc_start: 0.8920 (t0) cc_final: 0.8231 (p0) REVERT: B 132 VAL cc_start: 0.8946 (t) cc_final: 0.8710 (m) REVERT: B 154 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 214 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: B 215 GLN cc_start: 0.8367 (pt0) cc_final: 0.7857 (pp30) REVERT: B 235 PHE cc_start: 0.8871 (m-80) cc_final: 0.8257 (m-80) REVERT: B 251 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7921 (mm-30) REVERT: B 266 LEU cc_start: 0.9146 (tp) cc_final: 0.8662 (tp) REVERT: B 503 ASN cc_start: 0.8743 (m-40) cc_final: 0.8450 (m110) REVERT: B 521 MET cc_start: 0.8667 (mtp) cc_final: 0.8336 (mtm) REVERT: B 579 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7869 (tpm-80) REVERT: B 586 ASP cc_start: 0.7279 (m-30) cc_final: 0.6640 (m-30) REVERT: C 195 ASP cc_start: 0.7437 (p0) cc_final: 0.6963 (p0) REVERT: C 212 MET cc_start: 0.8933 (mmm) cc_final: 0.8254 (mmt) REVERT: C 245 PHE cc_start: 0.8842 (m-80) cc_final: 0.8531 (m-10) REVERT: C 356 ASP cc_start: 0.7383 (m-30) cc_final: 0.7082 (m-30) REVERT: C 521 MET cc_start: 0.8687 (mtm) cc_final: 0.8412 (mtm) REVERT: D 121 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8454 (tp) REVERT: D 212 MET cc_start: 0.9376 (mmm) cc_final: 0.9171 (mmm) REVERT: D 215 GLN cc_start: 0.8594 (tt0) cc_final: 0.8222 (tm-30) REVERT: D 249 ASP cc_start: 0.8074 (m-30) cc_final: 0.7783 (m-30) REVERT: D 315 MET cc_start: 0.8696 (mmm) cc_final: 0.8487 (mmt) REVERT: D 498 GLU cc_start: 0.7705 (pt0) cc_final: 0.7494 (pt0) REVERT: D 531 LYS cc_start: 0.8739 (ptpp) cc_final: 0.8506 (mtpp) REVERT: H 32 LEU cc_start: 0.8772 (tp) cc_final: 0.8501 (tt) REVERT: H 41 VAL cc_start: 0.6058 (t) cc_final: 0.5790 (m) REVERT: H 60 TYR cc_start: 0.7887 (m-80) cc_final: 0.7484 (m-80) REVERT: H 128 ARG cc_start: 0.8616 (mtt180) cc_final: 0.8177 (mmm160) REVERT: H 187 TYR cc_start: 0.9048 (m-80) cc_final: 0.8350 (m-10) REVERT: H 238 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7371 (mppt) REVERT: H 243 ARG cc_start: 0.8273 (ttm110) cc_final: 0.7890 (ttm-80) REVERT: H 307 LEU cc_start: 0.8773 (mt) cc_final: 0.8560 (pp) outliers start: 75 outliers final: 17 residues processed: 493 average time/residue: 1.1164 time to fit residues: 641.5075 Evaluate side-chains 396 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 371 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 238 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 215 optimal weight: 0.9980 chunk 239 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 ASN E 513 GLN E 573 HIS E 584 ASN A 37 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 558 ASN C 584 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 307 GLN D 392 HIS ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22454 Z= 0.406 Angle : 0.715 10.995 30500 Z= 0.375 Chirality : 0.046 0.163 3439 Planarity : 0.005 0.061 3904 Dihedral : 7.388 58.050 3832 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.04 % Allowed : 17.38 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.34 (0.16), residues: 2658 helix: 0.37 (0.25), residues: 377 sheet: -0.63 (0.18), residues: 764 loop : -0.03 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 199 HIS 0.014 0.002 HIS D 189 PHE 0.027 0.003 PHE A 110 TYR 0.026 0.002 TYR H 135 ARG 0.011 0.001 ARG E 578 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 373 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 129 TRP cc_start: 0.7836 (p-90) cc_final: 0.7369 (p-90) REVERT: E 141 ILE cc_start: 0.8823 (mt) cc_final: 0.8589 (mp) REVERT: E 201 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7865 (t0) REVERT: E 210 SER cc_start: 0.9152 (t) cc_final: 0.8519 (t) REVERT: E 215 GLN cc_start: 0.8005 (tt0) cc_final: 0.7493 (tm-30) REVERT: E 242 ARG cc_start: 0.8547 (mmt90) cc_final: 0.8136 (mmt90) REVERT: E 256 MET cc_start: 0.8797 (ttp) cc_final: 0.8527 (ttt) REVERT: E 423 ASP cc_start: 0.7954 (m-30) cc_final: 0.7613 (m-30) REVERT: E 443 GLN cc_start: 0.8329 (tt0) cc_final: 0.7647 (pt0) REVERT: E 447 ASN cc_start: 0.8965 (m-40) cc_final: 0.8628 (p0) REVERT: E 453 LYS cc_start: 0.8956 (pttt) cc_final: 0.8610 (ptmm) REVERT: E 525 MET cc_start: 0.7748 (mmm) cc_final: 0.7429 (mtp) REVERT: E 574 GLN cc_start: 0.8732 (pt0) cc_final: 0.8302 (pm20) REVERT: E 579 ARG cc_start: 0.7542 (mmm160) cc_final: 0.7052 (ttt90) REVERT: E 586 ASP cc_start: 0.7951 (p0) cc_final: 0.7606 (p0) REVERT: A 55 ASP cc_start: 0.8967 (t0) cc_final: 0.8765 (m-30) REVERT: A 63 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.7459 (mtt180) REVERT: A 89 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9191 (pt) REVERT: A 106 MET cc_start: 0.7274 (mpt) cc_final: 0.6983 (mmt) REVERT: A 111 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8277 (tm-30) REVERT: A 140 ARG cc_start: 0.7764 (mtt90) cc_final: 0.7115 (mpp80) REVERT: A 169 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 173 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8398 (mm-30) REVERT: A 247 GLU cc_start: 0.6489 (pm20) cc_final: 0.6188 (pm20) REVERT: A 249 PHE cc_start: 0.6996 (m-80) cc_final: 0.6275 (m-80) REVERT: A 255 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7154 (p0) REVERT: A 374 ASN cc_start: 0.8932 (t0) cc_final: 0.8165 (p0) REVERT: A 380 LEU cc_start: 0.8968 (tp) cc_final: 0.8429 (mt) REVERT: B 132 VAL cc_start: 0.9074 (t) cc_final: 0.8801 (m) REVERT: B 154 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 214 TYR cc_start: 0.8494 (m-10) cc_final: 0.8128 (m-80) REVERT: B 215 GLN cc_start: 0.8340 (pt0) cc_final: 0.7791 (pp30) REVERT: B 235 PHE cc_start: 0.8930 (m-80) cc_final: 0.8295 (m-80) REVERT: B 251 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: B 266 LEU cc_start: 0.9016 (tp) cc_final: 0.8763 (tp) REVERT: B 428 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: B 575 MET cc_start: 0.8775 (tpp) cc_final: 0.8565 (tpp) REVERT: C 195 ASP cc_start: 0.7489 (p0) cc_final: 0.7095 (p0) REVERT: C 212 MET cc_start: 0.8838 (mmm) cc_final: 0.8092 (mmt) REVERT: C 245 PHE cc_start: 0.8671 (m-80) cc_final: 0.8404 (m-10) REVERT: C 356 ASP cc_start: 0.7752 (m-30) cc_final: 0.7404 (m-30) REVERT: C 521 MET cc_start: 0.8581 (mtm) cc_final: 0.8370 (ttp) REVERT: D 109 ASP cc_start: 0.8188 (t0) cc_final: 0.7975 (t0) REVERT: D 212 MET cc_start: 0.9378 (mmm) cc_final: 0.9071 (mmm) REVERT: D 214 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.6749 (m-10) REVERT: D 215 GLN cc_start: 0.8563 (tt0) cc_final: 0.8182 (tm-30) REVERT: D 340 LYS cc_start: 0.8913 (mptt) cc_final: 0.8691 (mptt) REVERT: D 463 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: D 504 ARG cc_start: 0.8562 (mmt-90) cc_final: 0.8303 (mmt-90) REVERT: H 41 VAL cc_start: 0.6156 (t) cc_final: 0.5863 (m) REVERT: H 60 TYR cc_start: 0.7832 (m-80) cc_final: 0.7396 (m-80) REVERT: H 145 LYS cc_start: 0.9370 (tmmt) cc_final: 0.8959 (tmmt) REVERT: H 199 TRP cc_start: 0.7896 (t-100) cc_final: 0.7433 (t60) REVERT: H 238 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7208 (mppt) outliers start: 94 outliers final: 41 residues processed: 430 average time/residue: 1.1064 time to fit residues: 554.5491 Evaluate side-chains 392 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 343 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 242 optimal weight: 8.9990 chunk 257 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 189 HIS E 455 GLN E 474 ASN E 584 ASN A 37 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 392 HIS ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 22454 Z= 0.384 Angle : 0.683 9.564 30500 Z= 0.356 Chirality : 0.045 0.155 3439 Planarity : 0.004 0.055 3904 Dihedral : 6.519 57.475 3832 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.39 % Allowed : 18.24 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.40 (0.16), residues: 2658 helix: 0.22 (0.25), residues: 383 sheet: -0.65 (0.19), residues: 742 loop : -0.06 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 199 HIS 0.012 0.002 HIS B 189 PHE 0.022 0.002 PHE D 441 TYR 0.030 0.002 TYR H 209 ARG 0.008 0.001 ARG E 578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 361 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 129 TRP cc_start: 0.7946 (p-90) cc_final: 0.7478 (p-90) REVERT: E 210 SER cc_start: 0.8982 (t) cc_final: 0.8725 (t) REVERT: E 215 GLN cc_start: 0.8037 (tt0) cc_final: 0.7378 (tm-30) REVERT: E 256 MET cc_start: 0.8791 (ttp) cc_final: 0.8499 (ttt) REVERT: E 293 ASP cc_start: 0.8477 (t0) cc_final: 0.8214 (p0) REVERT: E 423 ASP cc_start: 0.7949 (m-30) cc_final: 0.7607 (m-30) REVERT: E 443 GLN cc_start: 0.8323 (tt0) cc_final: 0.7736 (pt0) REVERT: E 447 ASN cc_start: 0.8967 (m-40) cc_final: 0.8661 (p0) REVERT: E 453 LYS cc_start: 0.8936 (pttt) cc_final: 0.8724 (ptmm) REVERT: E 471 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7988 (tt) REVERT: E 525 MET cc_start: 0.7602 (mmm) cc_final: 0.6898 (mtp) REVERT: E 567 TRP cc_start: 0.6881 (m-90) cc_final: 0.5444 (m-90) REVERT: E 579 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7103 (ttt90) REVERT: E 586 ASP cc_start: 0.8170 (p0) cc_final: 0.7832 (p0) REVERT: A 63 ARG cc_start: 0.8316 (mtp-110) cc_final: 0.7148 (mtt180) REVERT: A 72 GLU cc_start: 0.6416 (tp30) cc_final: 0.6075 (mm-30) REVERT: A 89 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8939 (pp) REVERT: A 97 ARG cc_start: 0.7498 (tpm170) cc_final: 0.7159 (tpp-160) REVERT: A 106 MET cc_start: 0.7095 (mpt) cc_final: 0.6879 (mmt) REVERT: A 111 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8288 (tm-30) REVERT: A 140 ARG cc_start: 0.7705 (mtt90) cc_final: 0.6967 (mpp80) REVERT: A 169 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7687 (mm-30) REVERT: A 173 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8397 (mm-30) REVERT: A 301 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7586 (mmm160) REVERT: A 374 ASN cc_start: 0.8933 (t0) cc_final: 0.8169 (p0) REVERT: A 380 LEU cc_start: 0.8994 (tp) cc_final: 0.8528 (mt) REVERT: B 154 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8371 (mt-10) REVERT: B 214 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: B 215 GLN cc_start: 0.8301 (pt0) cc_final: 0.7696 (pp30) REVERT: B 235 PHE cc_start: 0.8912 (m-80) cc_final: 0.8289 (m-80) REVERT: B 251 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: B 266 LEU cc_start: 0.8993 (tp) cc_final: 0.8745 (tp) REVERT: B 351 THR cc_start: 0.8595 (p) cc_final: 0.8351 (p) REVERT: B 428 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: B 438 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8427 (m) REVERT: B 453 LYS cc_start: 0.8245 (ptmm) cc_final: 0.7561 (tttp) REVERT: B 484 LEU cc_start: 0.8757 (mt) cc_final: 0.8441 (mp) REVERT: C 195 ASP cc_start: 0.7620 (p0) cc_final: 0.7206 (p0) REVERT: C 212 MET cc_start: 0.8817 (mmm) cc_final: 0.8129 (mmt) REVERT: C 245 PHE cc_start: 0.8610 (m-80) cc_final: 0.8409 (m-10) REVERT: C 356 ASP cc_start: 0.7719 (m-30) cc_final: 0.7432 (m-30) REVERT: C 525 MET cc_start: 0.8130 (mtp) cc_final: 0.7748 (mmm) REVERT: C 584 ASN cc_start: 0.8533 (t0) cc_final: 0.7679 (t0) REVERT: D 77 PHE cc_start: 0.8715 (m-10) cc_final: 0.8479 (m-10) REVERT: D 109 ASP cc_start: 0.8233 (t0) cc_final: 0.8027 (t0) REVERT: D 214 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.6740 (m-10) REVERT: D 215 GLN cc_start: 0.8541 (tt0) cc_final: 0.8161 (tm-30) REVERT: D 272 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: D 340 LYS cc_start: 0.8832 (mptt) cc_final: 0.8606 (mptt) REVERT: D 463 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: D 504 ARG cc_start: 0.8396 (mmt-90) cc_final: 0.7952 (mmt90) REVERT: D 531 LYS cc_start: 0.8614 (ptpp) cc_final: 0.8335 (ptpp) REVERT: H 41 VAL cc_start: 0.6172 (t) cc_final: 0.5884 (m) REVERT: H 60 TYR cc_start: 0.7859 (m-80) cc_final: 0.7364 (m-80) REVERT: H 69 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6590 (t70) REVERT: H 145 LYS cc_start: 0.9369 (tmmt) cc_final: 0.9054 (ttpp) REVERT: H 199 TRP cc_start: 0.8031 (t-100) cc_final: 0.7619 (t60) REVERT: H 238 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7670 (mppt) outliers start: 102 outliers final: 51 residues processed: 429 average time/residue: 1.0831 time to fit residues: 543.5615 Evaluate side-chains 404 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 342 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 496 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 190 PHE Chi-restraints excluded: chain H residue 238 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 ASN ** E 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN A 37 ASN A 53 ASN A 68 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 307 GLN ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22454 Z= 0.213 Angle : 0.626 12.595 30500 Z= 0.323 Chirality : 0.043 0.205 3439 Planarity : 0.004 0.053 3904 Dihedral : 5.843 54.954 3832 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.23 % Allowed : 20.47 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.37 (0.16), residues: 2658 helix: 0.37 (0.26), residues: 383 sheet: -0.67 (0.18), residues: 811 loop : -0.00 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 199 HIS 0.013 0.001 HIS B 189 PHE 0.027 0.002 PHE A 256 TYR 0.030 0.002 TYR H 135 ARG 0.009 0.001 ARG H 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 381 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 PHE cc_start: 0.8793 (m-10) cc_final: 0.8228 (m-80) REVERT: E 129 TRP cc_start: 0.7933 (p-90) cc_final: 0.7428 (p-90) REVERT: E 210 SER cc_start: 0.8926 (t) cc_final: 0.8682 (t) REVERT: E 215 GLN cc_start: 0.8055 (tt0) cc_final: 0.7375 (tm-30) REVERT: E 293 ASP cc_start: 0.8357 (t0) cc_final: 0.8119 (p0) REVERT: E 443 GLN cc_start: 0.8419 (tt0) cc_final: 0.7969 (pt0) REVERT: E 453 LYS cc_start: 0.9027 (pttt) cc_final: 0.8735 (ptmm) REVERT: E 525 MET cc_start: 0.7541 (mmm) cc_final: 0.6841 (mtp) REVERT: E 567 TRP cc_start: 0.6802 (m-90) cc_final: 0.5426 (m-90) REVERT: E 579 ARG cc_start: 0.7645 (mmm160) cc_final: 0.7277 (ttt90) REVERT: E 586 ASP cc_start: 0.7997 (p0) cc_final: 0.7633 (p0) REVERT: A 63 ARG cc_start: 0.8101 (mtp-110) cc_final: 0.6931 (mtt90) REVERT: A 72 GLU cc_start: 0.6518 (tp30) cc_final: 0.6200 (mm-30) REVERT: A 89 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8863 (pp) REVERT: A 97 ARG cc_start: 0.7484 (tpm170) cc_final: 0.6670 (tpp-160) REVERT: A 106 MET cc_start: 0.7031 (mpt) cc_final: 0.6790 (mmt) REVERT: A 111 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8323 (tm-30) REVERT: A 123 MET cc_start: 0.8997 (tmm) cc_final: 0.8767 (tpp) REVERT: A 140 ARG cc_start: 0.7733 (mtt90) cc_final: 0.6955 (mpp80) REVERT: A 169 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 173 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8376 (mm-30) REVERT: A 178 TYR cc_start: 0.9344 (t80) cc_final: 0.9005 (t80) REVERT: A 257 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: A 374 ASN cc_start: 0.8909 (t0) cc_final: 0.8154 (p0) REVERT: A 380 LEU cc_start: 0.8948 (tp) cc_final: 0.8482 (mt) REVERT: B 154 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8136 (mt-10) REVERT: B 214 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: B 215 GLN cc_start: 0.8232 (pt0) cc_final: 0.7629 (pp30) REVERT: B 235 PHE cc_start: 0.8862 (m-80) cc_final: 0.8570 (m-80) REVERT: B 251 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: B 351 THR cc_start: 0.8528 (p) cc_final: 0.8301 (p) REVERT: B 438 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8120 (m) REVERT: B 453 LYS cc_start: 0.8199 (ptmm) cc_final: 0.7734 (tttp) REVERT: B 484 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8440 (mp) REVERT: C 157 ILE cc_start: 0.8804 (mt) cc_final: 0.8589 (mt) REVERT: C 195 ASP cc_start: 0.7634 (p0) cc_final: 0.7187 (p0) REVERT: C 212 MET cc_start: 0.8870 (mmm) cc_final: 0.8068 (mmt) REVERT: C 245 PHE cc_start: 0.8575 (m-80) cc_final: 0.8336 (m-10) REVERT: C 584 ASN cc_start: 0.8454 (t0) cc_final: 0.7618 (t0) REVERT: D 214 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.6711 (m-10) REVERT: D 215 GLN cc_start: 0.8557 (tt0) cc_final: 0.8205 (tm-30) REVERT: D 403 TYR cc_start: 0.9030 (p90) cc_final: 0.8783 (p90) REVERT: D 463 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: D 484 LEU cc_start: 0.8844 (tp) cc_final: 0.8565 (mp) REVERT: D 504 ARG cc_start: 0.8338 (mmt-90) cc_final: 0.7894 (mmt90) REVERT: D 531 LYS cc_start: 0.8527 (ptpp) cc_final: 0.8315 (ptpp) REVERT: D 579 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8124 (mmt180) REVERT: H 41 VAL cc_start: 0.6211 (t) cc_final: 0.5852 (m) REVERT: H 60 TYR cc_start: 0.7861 (m-80) cc_final: 0.7393 (m-80) REVERT: H 69 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6564 (t70) REVERT: H 73 TYR cc_start: 0.7635 (t80) cc_final: 0.7374 (t80) REVERT: H 74 ARG cc_start: 0.6724 (tpp-160) cc_final: 0.6370 (tpp-160) REVERT: H 199 TRP cc_start: 0.8032 (t-100) cc_final: 0.7741 (t60) REVERT: H 238 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7437 (mppt) outliers start: 75 outliers final: 34 residues processed: 433 average time/residue: 1.0702 time to fit residues: 542.7307 Evaluate side-chains 397 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 352 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 150 optimal weight: 0.6980 chunk 63 optimal weight: 20.0000 chunk 257 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 ASN ** E 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN A 37 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN A 182 ASN A 198 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 399 GLN D 505 GLN ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22454 Z= 0.364 Angle : 0.666 11.705 30500 Z= 0.345 Chirality : 0.045 0.257 3439 Planarity : 0.004 0.051 3904 Dihedral : 5.770 56.457 3832 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.00 % Allowed : 21.25 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.41 (0.16), residues: 2658 helix: 0.30 (0.26), residues: 383 sheet: -0.67 (0.18), residues: 778 loop : -0.07 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 199 HIS 0.014 0.001 HIS B 189 PHE 0.027 0.002 PHE A 110 TYR 0.029 0.002 TYR H 209 ARG 0.010 0.001 ARG H 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 356 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 PHE cc_start: 0.8828 (m-10) cc_final: 0.8276 (m-80) REVERT: E 123 GLN cc_start: 0.8005 (mt0) cc_final: 0.7724 (mm-40) REVERT: E 129 TRP cc_start: 0.7953 (p-90) cc_final: 0.7515 (p-90) REVERT: E 215 GLN cc_start: 0.8082 (tt0) cc_final: 0.7438 (tm-30) REVERT: E 256 MET cc_start: 0.8386 (ttt) cc_final: 0.7863 (tmt) REVERT: E 370 ASN cc_start: 0.8430 (t0) cc_final: 0.8220 (t0) REVERT: E 453 LYS cc_start: 0.9041 (pttt) cc_final: 0.8773 (ptmm) REVERT: E 525 MET cc_start: 0.7637 (mmm) cc_final: 0.7260 (mtp) REVERT: E 579 ARG cc_start: 0.7646 (mmm160) cc_final: 0.7239 (ttt90) REVERT: E 586 ASP cc_start: 0.8222 (p0) cc_final: 0.7778 (p0) REVERT: A 63 ARG cc_start: 0.8130 (mtp-110) cc_final: 0.6982 (mtt90) REVERT: A 72 GLU cc_start: 0.6607 (tp30) cc_final: 0.6336 (mm-30) REVERT: A 89 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8902 (pt) REVERT: A 97 ARG cc_start: 0.7579 (tpm170) cc_final: 0.7179 (tpp-160) REVERT: A 106 MET cc_start: 0.7067 (mpt) cc_final: 0.6817 (mmt) REVERT: A 111 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8316 (tm-30) REVERT: A 140 ARG cc_start: 0.7770 (mtt90) cc_final: 0.6964 (mpp80) REVERT: A 169 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7717 (mm-30) REVERT: A 173 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8353 (mm-30) REVERT: A 177 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8014 (tmmm) REVERT: A 178 TYR cc_start: 0.9378 (t80) cc_final: 0.9140 (t80) REVERT: A 181 GLU cc_start: 0.9525 (pp20) cc_final: 0.9319 (pp20) REVERT: A 257 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: A 374 ASN cc_start: 0.8881 (t0) cc_final: 0.8206 (p0) REVERT: A 380 LEU cc_start: 0.9000 (tp) cc_final: 0.8527 (mt) REVERT: B 89 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8966 (mm) REVERT: B 154 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8397 (mt-10) REVERT: B 214 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: B 215 GLN cc_start: 0.8268 (pt0) cc_final: 0.7701 (pp30) REVERT: B 235 PHE cc_start: 0.8882 (m-80) cc_final: 0.8633 (m-80) REVERT: B 251 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: B 339 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7463 (mtt-85) REVERT: B 351 THR cc_start: 0.8593 (p) cc_final: 0.8358 (p) REVERT: B 484 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8486 (mp) REVERT: C 195 ASP cc_start: 0.7740 (p0) cc_final: 0.7255 (p0) REVERT: C 212 MET cc_start: 0.8853 (mmm) cc_final: 0.8239 (mmt) REVERT: C 356 ASP cc_start: 0.7764 (m-30) cc_final: 0.7520 (m-30) REVERT: C 492 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7927 (pt0) REVERT: C 584 ASN cc_start: 0.8476 (t0) cc_final: 0.7615 (t0) REVERT: D 214 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.6734 (m-10) REVERT: D 215 GLN cc_start: 0.8583 (tt0) cc_final: 0.8203 (tm-30) REVERT: D 272 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: D 463 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: D 504 ARG cc_start: 0.8362 (mmt-90) cc_final: 0.8051 (mmt90) REVERT: D 531 LYS cc_start: 0.8582 (ptpp) cc_final: 0.8354 (ptpp) REVERT: H 41 VAL cc_start: 0.6367 (t) cc_final: 0.6108 (m) REVERT: H 60 TYR cc_start: 0.8049 (m-80) cc_final: 0.7467 (m-80) REVERT: H 69 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6530 (t70) REVERT: H 199 TRP cc_start: 0.8121 (t-100) cc_final: 0.7798 (t60) REVERT: H 238 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7384 (mppt) REVERT: H 243 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.7961 (ttm-80) outliers start: 93 outliers final: 54 residues processed: 420 average time/residue: 1.0875 time to fit residues: 533.8134 Evaluate side-chains 410 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 342 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 256 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 ASN ** E 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN A 37 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN A 182 ASN A 198 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22454 Z= 0.273 Angle : 0.652 14.107 30500 Z= 0.335 Chirality : 0.044 0.302 3439 Planarity : 0.004 0.045 3904 Dihedral : 5.628 55.317 3832 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 3.61 % Allowed : 21.98 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.42 (0.16), residues: 2658 helix: 0.28 (0.25), residues: 383 sheet: -0.65 (0.18), residues: 776 loop : -0.09 (0.17), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 199 HIS 0.014 0.001 HIS B 189 PHE 0.031 0.002 PHE A 256 TYR 0.024 0.002 TYR H 178 ARG 0.009 0.001 ARG H 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 353 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 PHE cc_start: 0.8804 (m-10) cc_final: 0.8260 (m-80) REVERT: E 123 GLN cc_start: 0.7983 (mt0) cc_final: 0.7710 (mm-40) REVERT: E 129 TRP cc_start: 0.7961 (p-90) cc_final: 0.7521 (p-90) REVERT: E 215 GLN cc_start: 0.8031 (tt0) cc_final: 0.7742 (tm-30) REVERT: E 256 MET cc_start: 0.8339 (ttt) cc_final: 0.7801 (tmt) REVERT: E 315 MET cc_start: 0.8420 (mmm) cc_final: 0.8212 (mmp) REVERT: E 370 ASN cc_start: 0.8367 (t0) cc_final: 0.8016 (t0) REVERT: E 453 LYS cc_start: 0.8993 (pttt) cc_final: 0.8752 (ptmm) REVERT: E 525 MET cc_start: 0.7551 (mmm) cc_final: 0.7136 (mtp) REVERT: E 586 ASP cc_start: 0.8300 (p0) cc_final: 0.7821 (p0) REVERT: A 63 ARG cc_start: 0.8118 (mtp-110) cc_final: 0.6988 (mtt90) REVERT: A 89 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8874 (pt) REVERT: A 97 ARG cc_start: 0.7412 (tpm170) cc_final: 0.6663 (tpp-160) REVERT: A 106 MET cc_start: 0.7012 (mpt) cc_final: 0.6811 (mmt) REVERT: A 111 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8217 (tm-30) REVERT: A 121 PHE cc_start: 0.6589 (t80) cc_final: 0.4933 (t80) REVERT: A 123 MET cc_start: 0.8803 (tpt) cc_final: 0.7875 (pmm) REVERT: A 140 ARG cc_start: 0.7704 (mtt90) cc_final: 0.6843 (mpp80) REVERT: A 169 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 173 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8346 (mm-30) REVERT: A 177 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7990 (tmmm) REVERT: A 178 TYR cc_start: 0.9385 (t80) cc_final: 0.9159 (t80) REVERT: A 181 GLU cc_start: 0.9542 (pp20) cc_final: 0.9331 (pp20) REVERT: A 213 GLU cc_start: 0.8507 (tp30) cc_final: 0.8207 (tp30) REVERT: A 257 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: A 374 ASN cc_start: 0.8864 (t0) cc_final: 0.8204 (p0) REVERT: A 380 LEU cc_start: 0.8984 (tp) cc_final: 0.8513 (mt) REVERT: B 89 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8939 (mm) REVERT: B 154 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8155 (mt-10) REVERT: B 215 GLN cc_start: 0.8237 (pt0) cc_final: 0.7656 (pp30) REVERT: B 235 PHE cc_start: 0.8827 (m-80) cc_final: 0.8607 (m-80) REVERT: B 251 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: B 266 LEU cc_start: 0.8877 (mt) cc_final: 0.8608 (mt) REVERT: B 351 THR cc_start: 0.8531 (p) cc_final: 0.8297 (p) REVERT: B 428 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: B 453 LYS cc_start: 0.8180 (ptmm) cc_final: 0.7636 (tttp) REVERT: B 484 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8478 (mp) REVERT: C 157 ILE cc_start: 0.8828 (mt) cc_final: 0.8608 (mt) REVERT: C 193 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8360 (m) REVERT: C 195 ASP cc_start: 0.7743 (p0) cc_final: 0.7254 (p0) REVERT: C 212 MET cc_start: 0.8839 (mmm) cc_final: 0.8206 (mmt) REVERT: C 356 ASP cc_start: 0.7746 (m-30) cc_final: 0.7244 (m-30) REVERT: C 584 ASN cc_start: 0.8451 (t0) cc_final: 0.7617 (t0) REVERT: D 214 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.6723 (m-10) REVERT: D 215 GLN cc_start: 0.8596 (tt0) cc_final: 0.8238 (tm-30) REVERT: D 272 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: D 463 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: D 504 ARG cc_start: 0.8370 (mmt-90) cc_final: 0.8024 (mmt90) REVERT: D 531 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8388 (ptpp) REVERT: H 41 VAL cc_start: 0.6397 (t) cc_final: 0.6103 (m) REVERT: H 60 TYR cc_start: 0.7931 (m-80) cc_final: 0.7437 (m-80) REVERT: H 69 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6491 (t70) REVERT: H 199 TRP cc_start: 0.8069 (t-100) cc_final: 0.7830 (t60) REVERT: H 238 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7601 (mppt) outliers start: 84 outliers final: 51 residues processed: 411 average time/residue: 1.1037 time to fit residues: 531.5329 Evaluate side-chains 403 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 339 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 256 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 8.9990 chunk 102 optimal weight: 0.0270 chunk 153 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 ASN ** E 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN A 198 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 22454 Z= 0.258 Angle : 0.651 12.781 30500 Z= 0.333 Chirality : 0.044 0.276 3439 Planarity : 0.004 0.052 3904 Dihedral : 5.508 54.942 3832 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 3.53 % Allowed : 22.45 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.37 (0.16), residues: 2658 helix: 0.30 (0.26), residues: 383 sheet: -0.57 (0.19), residues: 760 loop : -0.09 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 199 HIS 0.013 0.001 HIS B 189 PHE 0.025 0.002 PHE A 110 TYR 0.025 0.002 TYR A 131 ARG 0.010 0.000 ARG H 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 354 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 PHE cc_start: 0.8800 (m-10) cc_final: 0.8260 (m-80) REVERT: E 123 GLN cc_start: 0.7973 (mt0) cc_final: 0.7702 (mm-40) REVERT: E 129 TRP cc_start: 0.7975 (p-90) cc_final: 0.7476 (p-90) REVERT: E 215 GLN cc_start: 0.8065 (tt0) cc_final: 0.7791 (tm-30) REVERT: E 256 MET cc_start: 0.8355 (ttt) cc_final: 0.7800 (tmt) REVERT: E 315 MET cc_start: 0.8416 (mmm) cc_final: 0.8173 (mmp) REVERT: E 370 ASN cc_start: 0.8372 (t0) cc_final: 0.8013 (t0) REVERT: E 453 LYS cc_start: 0.8935 (pttt) cc_final: 0.8672 (ptmm) REVERT: E 525 MET cc_start: 0.7341 (mmm) cc_final: 0.7086 (mtp) REVERT: E 567 TRP cc_start: 0.6828 (m-90) cc_final: 0.5393 (m-90) REVERT: E 586 ASP cc_start: 0.8353 (p0) cc_final: 0.7870 (p0) REVERT: A 63 ARG cc_start: 0.7952 (mtp-110) cc_final: 0.6840 (mtt180) REVERT: A 72 GLU cc_start: 0.6387 (mm-30) cc_final: 0.4679 (tp30) REVERT: A 82 PHE cc_start: 0.7677 (m-80) cc_final: 0.7137 (m-80) REVERT: A 89 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9008 (pt) REVERT: A 97 ARG cc_start: 0.7401 (tpm170) cc_final: 0.7124 (tpp-160) REVERT: A 106 MET cc_start: 0.6796 (mpt) cc_final: 0.6282 (mmt) REVERT: A 111 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8237 (tm-30) REVERT: A 121 PHE cc_start: 0.6429 (t80) cc_final: 0.5988 (t80) REVERT: A 132 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8558 (tm) REVERT: A 140 ARG cc_start: 0.7721 (mtt90) cc_final: 0.6868 (mtm-85) REVERT: A 168 LEU cc_start: 0.8984 (tm) cc_final: 0.8630 (tm) REVERT: A 169 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 173 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8334 (mm-30) REVERT: A 213 GLU cc_start: 0.8598 (tp30) cc_final: 0.8299 (tp30) REVERT: A 374 ASN cc_start: 0.8879 (t0) cc_final: 0.8202 (p0) REVERT: A 380 LEU cc_start: 0.8981 (tp) cc_final: 0.8494 (mt) REVERT: B 89 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8922 (mm) REVERT: B 132 VAL cc_start: 0.8781 (t) cc_final: 0.8504 (m) REVERT: B 154 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8133 (mt-10) REVERT: B 215 GLN cc_start: 0.8200 (pt0) cc_final: 0.7637 (pp30) REVERT: B 235 PHE cc_start: 0.8861 (m-80) cc_final: 0.8635 (m-80) REVERT: B 251 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: B 339 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7348 (mtt-85) REVERT: B 351 THR cc_start: 0.8508 (p) cc_final: 0.8287 (p) REVERT: B 453 LYS cc_start: 0.8109 (ptmm) cc_final: 0.7673 (tttp) REVERT: B 484 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8470 (mp) REVERT: C 66 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8558 (p0) REVERT: C 157 ILE cc_start: 0.8806 (mt) cc_final: 0.8593 (mt) REVERT: C 195 ASP cc_start: 0.7865 (p0) cc_final: 0.7371 (p0) REVERT: C 209 GLU cc_start: 0.8556 (tt0) cc_final: 0.8326 (tt0) REVERT: C 212 MET cc_start: 0.8846 (mmm) cc_final: 0.8185 (mmt) REVERT: C 356 ASP cc_start: 0.7686 (m-30) cc_final: 0.7146 (m-30) REVERT: C 584 ASN cc_start: 0.8425 (t0) cc_final: 0.7586 (t0) REVERT: D 214 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.6697 (m-10) REVERT: D 215 GLN cc_start: 0.8591 (tt0) cc_final: 0.8213 (tm-30) REVERT: D 272 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: D 463 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: D 504 ARG cc_start: 0.8275 (mmt-90) cc_final: 0.7939 (mmt90) REVERT: H 41 VAL cc_start: 0.6564 (t) cc_final: 0.6261 (m) REVERT: H 60 TYR cc_start: 0.7922 (m-80) cc_final: 0.7429 (m-80) REVERT: H 69 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.6802 (t70) REVERT: H 199 TRP cc_start: 0.8056 (t-100) cc_final: 0.7817 (t60) REVERT: H 238 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7384 (mppt) REVERT: H 243 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.7797 (tpp80) REVERT: H 349 MET cc_start: 0.7335 (pmm) cc_final: 0.6730 (pmm) outliers start: 82 outliers final: 53 residues processed: 410 average time/residue: 1.1111 time to fit residues: 530.5889 Evaluate side-chains 401 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 336 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 256 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 7.9990 chunk 245 optimal weight: 9.9990 chunk 224 optimal weight: 0.9980 chunk 238 optimal weight: 50.0000 chunk 143 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 156 optimal weight: 0.0370 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 ASN E 584 ASN A 37 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN A 198 GLN B 215 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 GLN C 554 HIS D 307 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22454 Z= 0.302 Angle : 0.671 12.797 30500 Z= 0.343 Chirality : 0.044 0.259 3439 Planarity : 0.004 0.051 3904 Dihedral : 5.513 55.316 3832 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 3.35 % Allowed : 22.80 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.41 (0.16), residues: 2658 helix: 0.25 (0.25), residues: 383 sheet: -0.55 (0.19), residues: 759 loop : -0.15 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 199 HIS 0.013 0.001 HIS B 189 PHE 0.034 0.002 PHE A 256 TYR 0.032 0.002 TYR H 209 ARG 0.010 0.001 ARG H 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 338 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 PHE cc_start: 0.8842 (m-10) cc_final: 0.8316 (m-80) REVERT: E 123 GLN cc_start: 0.7979 (mt0) cc_final: 0.7676 (mm-40) REVERT: E 129 TRP cc_start: 0.8056 (p-90) cc_final: 0.7617 (p-90) REVERT: E 215 GLN cc_start: 0.8057 (tt0) cc_final: 0.7672 (tm-30) REVERT: E 256 MET cc_start: 0.8394 (ttt) cc_final: 0.7819 (tmt) REVERT: E 293 ASP cc_start: 0.8329 (m-30) cc_final: 0.7508 (p0) REVERT: E 370 ASN cc_start: 0.8443 (t0) cc_final: 0.8044 (t0) REVERT: E 453 LYS cc_start: 0.8933 (pttt) cc_final: 0.8693 (ptmm) REVERT: E 525 MET cc_start: 0.7417 (mmm) cc_final: 0.7119 (mtp) REVERT: E 567 TRP cc_start: 0.6866 (m-90) cc_final: 0.5466 (m-90) REVERT: E 586 ASP cc_start: 0.8358 (p0) cc_final: 0.7864 (p0) REVERT: A 63 ARG cc_start: 0.7992 (mtp-110) cc_final: 0.6843 (mpp-170) REVERT: A 72 GLU cc_start: 0.6573 (mm-30) cc_final: 0.5561 (tp30) REVERT: A 74 ARG cc_start: 0.7588 (mpp-170) cc_final: 0.6734 (tpm170) REVERT: A 82 PHE cc_start: 0.7725 (m-80) cc_final: 0.7084 (m-80) REVERT: A 89 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8934 (pt) REVERT: A 106 MET cc_start: 0.7010 (mpt) cc_final: 0.6532 (mmt) REVERT: A 111 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8244 (tm-30) REVERT: A 132 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8168 (tm) REVERT: A 140 ARG cc_start: 0.7738 (mtt90) cc_final: 0.6860 (mtm-85) REVERT: A 169 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 173 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8394 (mm-30) REVERT: A 177 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8099 (tptp) REVERT: A 213 GLU cc_start: 0.8542 (tp30) cc_final: 0.8257 (tp30) REVERT: A 374 ASN cc_start: 0.8879 (t0) cc_final: 0.8170 (p0) REVERT: A 380 LEU cc_start: 0.9001 (tp) cc_final: 0.8512 (mt) REVERT: B 89 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8854 (mm) REVERT: B 132 VAL cc_start: 0.8810 (t) cc_final: 0.8530 (m) REVERT: B 154 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 214 TYR cc_start: 0.8399 (m-10) cc_final: 0.8078 (m-80) REVERT: B 215 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7681 (pp30) REVERT: B 235 PHE cc_start: 0.8873 (m-80) cc_final: 0.8649 (m-80) REVERT: B 251 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: B 293 ASP cc_start: 0.7373 (t70) cc_final: 0.7084 (t0) REVERT: B 339 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7344 (mtt-85) REVERT: B 351 THR cc_start: 0.8532 (p) cc_final: 0.8315 (p) REVERT: B 453 LYS cc_start: 0.8114 (ptmm) cc_final: 0.7705 (tttp) REVERT: B 484 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8487 (mp) REVERT: B 586 ASP cc_start: 0.7291 (m-30) cc_final: 0.6728 (m-30) REVERT: C 157 ILE cc_start: 0.8858 (mt) cc_final: 0.8658 (mt) REVERT: C 195 ASP cc_start: 0.7903 (p0) cc_final: 0.7386 (p0) REVERT: C 212 MET cc_start: 0.8861 (mmm) cc_final: 0.8215 (mmt) REVERT: C 356 ASP cc_start: 0.7720 (m-30) cc_final: 0.7118 (m-30) REVERT: C 584 ASN cc_start: 0.8438 (t0) cc_final: 0.7597 (t0) REVERT: D 214 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.6709 (m-10) REVERT: D 215 GLN cc_start: 0.8610 (tt0) cc_final: 0.8231 (tm-30) REVERT: D 272 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8459 (mp0) REVERT: D 463 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: D 504 ARG cc_start: 0.8295 (mmt-90) cc_final: 0.7979 (mmt90) REVERT: H 41 VAL cc_start: 0.6583 (t) cc_final: 0.6291 (m) REVERT: H 60 TYR cc_start: 0.7910 (m-80) cc_final: 0.7436 (m-80) REVERT: H 69 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.6782 (t70) REVERT: H 75 ARG cc_start: 0.7946 (mpp80) cc_final: 0.7496 (mpp80) REVERT: H 199 TRP cc_start: 0.8115 (t-100) cc_final: 0.7873 (t60) REVERT: H 238 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7394 (mppt) REVERT: H 243 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.7787 (tpp80) REVERT: H 349 MET cc_start: 0.7374 (pmm) cc_final: 0.6982 (pmm) outliers start: 78 outliers final: 56 residues processed: 392 average time/residue: 1.1224 time to fit residues: 514.3137 Evaluate side-chains 411 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 342 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 256 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 0.2980 chunk 175 optimal weight: 3.9990 chunk 265 optimal weight: 30.0000 chunk 243 optimal weight: 9.9990 chunk 211 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 584 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 GLN C 554 HIS D 307 GLN ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22454 Z= 0.284 Angle : 0.680 15.416 30500 Z= 0.346 Chirality : 0.045 0.272 3439 Planarity : 0.004 0.052 3904 Dihedral : 5.475 55.226 3832 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 3.27 % Allowed : 22.88 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.43 (0.16), residues: 2658 helix: 0.23 (0.25), residues: 383 sheet: -0.54 (0.18), residues: 769 loop : -0.16 (0.17), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP A 199 HIS 0.013 0.001 HIS B 189 PHE 0.025 0.002 PHE A 110 TYR 0.036 0.002 TYR H 135 ARG 0.009 0.000 ARG H 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 351 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 PHE cc_start: 0.8847 (m-10) cc_final: 0.8316 (m-80) REVERT: E 123 GLN cc_start: 0.7973 (mt0) cc_final: 0.7704 (mm-40) REVERT: E 129 TRP cc_start: 0.8068 (p-90) cc_final: 0.7627 (p-90) REVERT: E 215 GLN cc_start: 0.8052 (tt0) cc_final: 0.7653 (tm-30) REVERT: E 256 MET cc_start: 0.8395 (ttt) cc_final: 0.7817 (tmt) REVERT: E 293 ASP cc_start: 0.8481 (m-30) cc_final: 0.7791 (p0) REVERT: E 315 MET cc_start: 0.8476 (mmm) cc_final: 0.8126 (mmp) REVERT: E 370 ASN cc_start: 0.8443 (t0) cc_final: 0.8040 (t0) REVERT: E 453 LYS cc_start: 0.8931 (pttt) cc_final: 0.8693 (ptmm) REVERT: E 525 MET cc_start: 0.7407 (mmm) cc_final: 0.7106 (mtp) REVERT: E 567 TRP cc_start: 0.6841 (m-90) cc_final: 0.5457 (m-90) REVERT: E 586 ASP cc_start: 0.8368 (p0) cc_final: 0.7865 (p0) REVERT: A 63 ARG cc_start: 0.8019 (mtp-110) cc_final: 0.6802 (mtm-85) REVERT: A 72 GLU cc_start: 0.6476 (mm-30) cc_final: 0.5579 (tp30) REVERT: A 74 ARG cc_start: 0.7411 (mpp-170) cc_final: 0.6648 (tpm170) REVERT: A 82 PHE cc_start: 0.7945 (m-80) cc_final: 0.7144 (m-80) REVERT: A 89 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8912 (pt) REVERT: A 106 MET cc_start: 0.6867 (mpt) cc_final: 0.6321 (mmt) REVERT: A 111 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8255 (tm-30) REVERT: A 121 PHE cc_start: 0.6401 (t80) cc_final: 0.5965 (t80) REVERT: A 132 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8043 (tm) REVERT: A 140 ARG cc_start: 0.7748 (mtt90) cc_final: 0.6852 (mtm-85) REVERT: A 168 LEU cc_start: 0.8972 (tm) cc_final: 0.8596 (tm) REVERT: A 169 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7671 (mm-30) REVERT: A 173 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8376 (mm-30) REVERT: A 177 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8207 (tptp) REVERT: A 213 GLU cc_start: 0.8516 (tp30) cc_final: 0.8224 (tp30) REVERT: A 374 ASN cc_start: 0.8859 (t0) cc_final: 0.8121 (p0) REVERT: A 380 LEU cc_start: 0.9039 (tp) cc_final: 0.8574 (mt) REVERT: B 89 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8846 (mm) REVERT: B 132 VAL cc_start: 0.8807 (t) cc_final: 0.8525 (m) REVERT: B 154 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8156 (mt-10) REVERT: B 215 GLN cc_start: 0.8094 (pt0) cc_final: 0.7775 (tm-30) REVERT: B 235 PHE cc_start: 0.8869 (m-80) cc_final: 0.8646 (m-80) REVERT: B 251 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: B 293 ASP cc_start: 0.7361 (t70) cc_final: 0.7079 (t0) REVERT: B 339 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7333 (mtt-85) REVERT: B 453 LYS cc_start: 0.8089 (ptmm) cc_final: 0.7686 (tttp) REVERT: B 484 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8490 (mp) REVERT: B 586 ASP cc_start: 0.7291 (m-30) cc_final: 0.6723 (m-30) REVERT: C 157 ILE cc_start: 0.8843 (mt) cc_final: 0.8641 (mt) REVERT: C 195 ASP cc_start: 0.7921 (p0) cc_final: 0.7389 (p0) REVERT: C 209 GLU cc_start: 0.8585 (tt0) cc_final: 0.8361 (tt0) REVERT: C 212 MET cc_start: 0.8857 (mmm) cc_final: 0.8178 (mmt) REVERT: C 356 ASP cc_start: 0.7714 (m-30) cc_final: 0.7103 (m-30) REVERT: C 584 ASN cc_start: 0.8454 (t0) cc_final: 0.7632 (t0) REVERT: D 214 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.6707 (m-10) REVERT: D 215 GLN cc_start: 0.8609 (tt0) cc_final: 0.8233 (tm-30) REVERT: D 463 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: D 504 ARG cc_start: 0.8281 (mmt-90) cc_final: 0.7967 (mmt90) REVERT: H 41 VAL cc_start: 0.6604 (t) cc_final: 0.6308 (m) REVERT: H 60 TYR cc_start: 0.7901 (m-80) cc_final: 0.7410 (m-80) REVERT: H 69 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.6771 (t70) REVERT: H 199 TRP cc_start: 0.8143 (t-100) cc_final: 0.7905 (t60) REVERT: H 238 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7494 (mppt) REVERT: H 243 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7876 (tpp80) REVERT: H 349 MET cc_start: 0.7430 (pmm) cc_final: 0.6738 (pmm) REVERT: H 350 GLU cc_start: 0.5851 (OUTLIER) cc_final: 0.5637 (tm-30) outliers start: 76 outliers final: 58 residues processed: 407 average time/residue: 1.0915 time to fit residues: 518.3554 Evaluate side-chains 412 residues out of total 2402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 342 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 339 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 256 PHE Chi-restraints excluded: chain H residue 350 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 194 optimal weight: 0.2980 chunk 31 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 211 optimal weight: 0.2980 chunk 88 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 185 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 ASN E 584 ASN A 37 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 GLN C 554 HIS ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.151897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108618 restraints weight = 40793.694| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.35 r_work: 0.3348 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22454 Z= 0.193 Angle : 0.661 14.878 30500 Z= 0.334 Chirality : 0.043 0.250 3439 Planarity : 0.004 0.050 3904 Dihedral : 5.312 54.112 3832 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 2.71 % Allowed : 23.61 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.39 (0.16), residues: 2658 helix: 0.28 (0.26), residues: 383 sheet: -0.51 (0.18), residues: 763 loop : -0.15 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 199 HIS 0.012 0.001 HIS B 189 PHE 0.034 0.002 PHE A 256 TYR 0.025 0.001 TYR H 209 ARG 0.009 0.000 ARG H 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9178.70 seconds wall clock time: 163 minutes 50.48 seconds (9830.48 seconds total)