Starting phenix.real_space_refine on Tue Feb 20 05:48:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybh_33721/02_2024/7ybh_33721.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybh_33721/02_2024/7ybh_33721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybh_33721/02_2024/7ybh_33721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybh_33721/02_2024/7ybh_33721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybh_33721/02_2024/7ybh_33721.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybh_33721/02_2024/7ybh_33721.pdb" } resolution = 3.5 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= 0.001 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 17099 2.51 5 N 4366 2.21 5 O 5385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 981": "OE1" <-> "OE2" Residue "A GLU 1085": "OE1" <-> "OE2" Residue "B GLU 911": "OE1" <-> "OE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C GLU 718": "OE1" <-> "OE2" Residue "C GLU 1024": "OE1" <-> "OE2" Residue "C TYR 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26964 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 8596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8596 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1046} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 8578 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 1101, 8578 Classifications: {'peptide': 1101} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 59, 'TRANS': 1041} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 8497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8497 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 58, 'TRANS': 1032} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" 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: 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "I" 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: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "L" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "Q" 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: "R" 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "T" 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: "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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "W" 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: "X" 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: "Y" 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: "Z" 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: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "b" 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "f" 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: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 13.36, per 1000 atoms: 0.50 Number of scatterers: 26964 At special positions: 0 Unit cell: (157.29, 147.66, 219.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5385 8.00 N 4366 7.00 C 17099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 518 " distance=2.04 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 583 " distance=2.04 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 642 " distance=2.02 Simple disulfide: pdb=" SG CYS A 655 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 753 " distance=2.04 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 833 " - pdb=" SG CYS A 844 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 284 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 583 " distance=2.03 Simple disulfide: pdb=" SG CYS B 610 " - pdb=" SG CYS B 642 " distance=2.03 Simple disulfide: pdb=" SG CYS B 655 " - pdb=" SG CYS B 664 " distance=2.03 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 284 " - pdb=" SG CYS C 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 481 " distance=2.03 Simple disulfide: pdb=" SG CYS C 531 " - pdb=" SG CYS C 583 " distance=2.07 Simple disulfide: pdb=" SG CYS C 610 " - pdb=" SG CYS C 642 " distance=2.03 Simple disulfide: pdb=" SG CYS C 655 " - pdb=" SG CYS C 664 " distance=2.04 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 275 " " NAG A1306 " - " ASN A 596 " " NAG A1307 " - " ASN A 650 " " NAG A1308 " - " ASN A 609 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 336 " " NAG B1303 " - " ASN B 596 " " NAG B1304 " - " ASN B 650 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 324 " " NAG C1304 " - " ASN C 596 " " NAG C1305 " - " ASN C 650 " " NAG D 1 " - " ASN A 336 " " NAG E 1 " - " ASN A 702 " " NAG G 1 " - " ASN A 710 " " NAG H 1 " - " ASN A 794 " " NAG I 1 " - " ASN A1067 " " NAG J 1 " - " ASN A1091 " " NAG K 1 " - " ASN A1127 " " NAG L 1 " - " ASN B 324 " " NAG M 1 " - " ASN B 702 " " NAG O 1 " - " ASN B 165 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 275 " " NAG R 1 " - " ASN B 609 " " NAG S 1 " - " ASN B 710 " " NAG T 1 " - " ASN B 794 " " NAG U 1 " - " ASN B1067 " " NAG V 1 " - " ASN B1091 " " NAG W 1 " - " ASN B1127 " " NAG X 1 " - " ASN C 275 " " NAG Y 1 " - " ASN C 336 " " NAG Z 1 " - " ASN C 702 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 609 " " NAG d 1 " - " ASN C 710 " " NAG e 1 " - " ASN C 794 " " NAG f 1 " - " ASN C1067 " " NAG g 1 " - " ASN C1091 " " NAG h 1 " - " ASN C1127 " Time building additional restraints: 12.48 Conformation dependent library (CDL) restraints added in 5.0 seconds 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6176 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 43 sheets defined 26.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 376 through 383 removed outlier: 5.095A pdb=" N ASN A 381 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 removed outlier: 5.334A pdb=" N ARG A 401 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 404 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.655A pdb=" N VAL A 613 " --> pdb=" O CYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 736 Processing helix chain 'A' and resid 739 through 747 Processing helix chain 'A' and resid 752 through 776 removed outlier: 3.697A pdb=" N ASP A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 819 Processing helix chain 'A' and resid 823 through 828 removed outlier: 4.057A pdb=" N ILE A 827 " --> pdb=" O ASP A 823 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 823 through 828' Processing helix chain 'A' and resid 829 through 835 Processing helix chain 'A' and resid 843 through 849 removed outlier: 3.615A pdb=" N ASN A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 878 Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.536A pdb=" N GLY A 882 " --> pdb=" O TRP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 903 removed outlier: 3.600A pdb=" N GLN A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 934 removed outlier: 3.731A pdb=" N TYR A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LYS A 914 " --> pdb=" O TYR A 910 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 922 " --> pdb=" O ASN A 918 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY A 925 " --> pdb=" O ASN A 921 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 926 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 929 " --> pdb=" O GLY A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 937 No H-bonds generated for 'chain 'A' and resid 935 through 937' Processing helix chain 'A' and resid 938 through 959 removed outlier: 4.452A pdb=" N VAL A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN A 948 " --> pdb=" O VAL A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 976 removed outlier: 3.633A pdb=" N ILE A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1026 removed outlier: 4.026A pdb=" N GLN A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1154 removed outlier: 4.156A pdb=" N GLU A1137 " --> pdb=" O PRO A1133 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A1154 " --> pdb=" O LYS A1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.818A pdb=" N VAL B 334 " --> pdb=" O PRO B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.632A pdb=" N TRP B 346 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.867A pdb=" N SER B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 382 removed outlier: 4.542A pdb=" N ASN B 381 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 404 removed outlier: 4.573A pdb=" N ARG B 401 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 415 removed outlier: 3.568A pdb=" N ASN B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 612 through 618 Processing helix chain 'B' and resid 619 through 622 Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.935A pdb=" N TYR B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 737 Processing helix chain 'B' and resid 740 through 747 Processing helix chain 'B' and resid 748 through 750 No H-bonds generated for 'chain 'B' and resid 748 through 750' Processing helix chain 'B' and resid 751 through 776 removed outlier: 3.680A pdb=" N GLN B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 819 Processing helix chain 'B' and resid 845 through 849 Processing helix chain 'B' and resid 859 through 878 Processing helix chain 'B' and resid 879 through 884 removed outlier: 4.095A pdb=" N ALA B 883 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 903 Processing helix chain 'B' and resid 906 through 912 removed outlier: 3.578A pdb=" N TYR B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 934 removed outlier: 3.614A pdb=" N ILE B 927 " --> pdb=" O ALA B 923 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN B 928 " --> pdb=" O ILE B 924 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 929 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 934 " --> pdb=" O SER B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 959 removed outlier: 4.393A pdb=" N VAL B 944 " --> pdb=" O LYS B 940 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 977 removed outlier: 3.794A pdb=" N ILE B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1026 removed outlier: 4.918A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN B 985 " --> pdb=" O GLU B 981 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP B 987 " --> pdb=" O GLU B 983 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1111 No H-bonds generated for 'chain 'B' and resid 1109 through 1111' Processing helix chain 'B' and resid 1133 through 1154 removed outlier: 4.024A pdb=" N SER B1154 " --> pdb=" O LYS B1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.680A pdb=" N LEU C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 342 through 346 removed outlier: 3.621A pdb=" N TRP C 346 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 364 removed outlier: 4.380A pdb=" N LEU C 361 " --> pdb=" O ASP C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 383 removed outlier: 4.151A pdb=" N ASN C 381 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 383 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 404 removed outlier: 4.424A pdb=" N ARG C 401 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 404 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 415 Processing helix chain 'C' and resid 611 through 616 Processing helix chain 'C' and resid 731 through 737 Processing helix chain 'C' and resid 740 through 746 Processing helix chain 'C' and resid 747 through 749 No H-bonds generated for 'chain 'C' and resid 747 through 749' Processing helix chain 'C' and resid 751 through 776 removed outlier: 3.949A pdb=" N ASN C 757 " --> pdb=" O CYS C 753 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 768 " --> pdb=" O ALA C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 819 Processing helix chain 'C' and resid 859 through 878 removed outlier: 3.580A pdb=" N GLY C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 883 removed outlier: 3.920A pdb=" N GLY C 882 " --> pdb=" O TRP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 902 removed outlier: 3.781A pdb=" N ILE C 902 " --> pdb=" O ARG C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 removed outlier: 3.517A pdb=" N TYR C 910 " --> pdb=" O GLN C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 934 removed outlier: 3.686A pdb=" N ILE C 927 " --> pdb=" O ALA C 923 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN C 928 " --> pdb=" O ILE C 924 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 929 " --> pdb=" O GLY C 925 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 932 " --> pdb=" O GLN C 928 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 934 " --> pdb=" O SER C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 958 removed outlier: 4.090A pdb=" N VAL C 944 " --> pdb=" O LYS C 940 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN C 948 " --> pdb=" O VAL C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 961 No H-bonds generated for 'chain 'C' and resid 959 through 961' Processing helix chain 'C' and resid 969 through 975 removed outlier: 3.603A pdb=" N ILE C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 984 through 1026 removed outlier: 3.674A pdb=" N VAL C1026 " --> pdb=" O MET C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1154 removed outlier: 4.304A pdb=" N SER C1154 " --> pdb=" O LYS C1150 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.033A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 257 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 95 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.074A pdb=" N ASP A 280 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.935A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.355A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 312 removed outlier: 5.323A pdb=" N ASN A 310 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A 586 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLY A 587 " --> pdb=" O GLN A 606 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 606 " --> pdb=" O GLY A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 321 removed outlier: 5.680A pdb=" N ASP A 567 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE A 558 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 347 through 351 removed outlier: 4.146A pdb=" N ASN A 387 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS A 425 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA9, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AB1, first strand: chain 'A' and resid 647 through 648 removed outlier: 3.660A pdb=" N GLU A 647 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 694 through 695 removed outlier: 6.524A pdb=" N ALA A 694 " --> pdb=" O ILE C 781 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 704 through 708 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 721 removed outlier: 6.940A pdb=" N GLY A1052 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER A1048 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A1054 " --> pdb=" O PRO A1046 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A1056 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER A1044 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A1058 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1113 through 1118 removed outlier: 5.487A pdb=" N VAL A1115 " --> pdb=" O PHE A1082 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE A1082 " --> pdb=" O VAL A1115 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLY A1117 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A1074 " --> pdb=" O HIS A1081 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1087 through 1089 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.241A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN B 61 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR B 262 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 257 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 95 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.970A pdb=" N ASP B 280 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.114A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 141 through 144 removed outlier: 6.722A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.832A pdb=" N GLY B 304 " --> pdb=" O THR B 592 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 592 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 317 through 321 removed outlier: 4.038A pdb=" N VAL B 532 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY B 543 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 347 through 351 Processing sheet with id=AC5, first strand: chain 'B' and resid 384 through 385 Processing sheet with id=AC6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AC7, first strand: chain 'B' and resid 647 through 648 removed outlier: 5.726A pdb=" N GLU B 647 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N THR B 689 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ALA B 665 " --> pdb=" O PRO B 658 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 704 through 721 removed outlier: 6.454A pdb=" N SER B 704 " --> pdb=" O THR B1069 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR B1069 " --> pdb=" O SER B 704 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 706 " --> pdb=" O ASN B1067 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN B1067 " --> pdb=" O ALA B 706 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU B1065 " --> pdb=" O PRO B 708 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN B 710 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY B1052 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER B1048 " --> pdb=" O GLY B1052 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B1054 " --> pdb=" O PRO B1046 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B1056 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER B1044 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B1058 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1074 through 1075 Processing sheet with id=AD1, first strand: chain 'B' and resid 1080 through 1083 removed outlier: 3.800A pdb=" N ALA B1080 " --> pdb=" O SER B1116 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1087 through 1090 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.516A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA C 257 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 95 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.995A pdb=" N ASP C 280 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.605A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 140 through 143 Processing sheet with id=AD7, first strand: chain 'C' and resid 306 through 312 removed outlier: 4.436A pdb=" N VAL C 588 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASN C 310 " --> pdb=" O GLY C 586 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY C 586 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY C 587 " --> pdb=" O GLN C 606 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 318 through 321 Processing sheet with id=AD9, first strand: chain 'C' and resid 347 through 351 removed outlier: 3.656A pdb=" N VAL C 388 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 355 removed outlier: 6.824A pdb=" N CYS C 354 " --> pdb=" O CYS C 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 445 through 447 Processing sheet with id=AE3, first strand: chain 'C' and resid 657 through 660 removed outlier: 6.498A pdb=" N ILE C 663 " --> pdb=" O ILE C 659 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 721 removed outlier: 6.012A pdb=" N TYR C1060 " --> pdb=" O HIS C1041 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS C1041 " --> pdb=" O TYR C1060 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1069 through 1070 Processing sheet with id=AE7, first strand: chain 'C' and resid 1113 through 1118 removed outlier: 4.825A pdb=" N ALA C1080 " --> pdb=" O SER C1116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C1074 " --> pdb=" O HIS C1081 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2727 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: 12.10 Time building geometry restraints manager: 13.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6897 1.33 - 1.46: 6893 1.46 - 1.58: 13633 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 27564 Sorted by residual: bond pdb=" N PRO C 935 " pdb=" CD PRO C 935 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" N PRO B 935 " pdb=" CD PRO B 935 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" N PRO B 810 " pdb=" CD PRO B 810 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.47e+01 bond pdb=" N PRO A 810 " pdb=" CD PRO A 810 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" N PRO A 892 " pdb=" CD PRO A 892 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.44e+01 ... (remaining 27559 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.90: 884 106.90 - 114.70: 16663 114.70 - 122.50: 16055 122.50 - 130.29: 3857 130.29 - 138.09: 72 Bond angle restraints: 37531 Sorted by residual: angle pdb=" CA PRO C 935 " pdb=" N PRO C 935 " pdb=" CD PRO C 935 " ideal model delta sigma weight residual 112.00 99.11 12.89 1.40e+00 5.10e-01 8.48e+01 angle pdb=" CA PRO B 935 " pdb=" N PRO B 935 " pdb=" CD PRO B 935 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.33e+01 angle pdb=" CA PRO B 810 " pdb=" N PRO B 810 " pdb=" CD PRO B 810 " ideal model delta sigma weight residual 112.00 99.35 12.65 1.40e+00 5.10e-01 8.17e+01 angle pdb=" CA PRO A 810 " pdb=" N PRO A 810 " pdb=" CD PRO A 810 " ideal model delta sigma weight residual 112.00 99.35 12.65 1.40e+00 5.10e-01 8.16e+01 angle pdb=" CA PRO A 892 " pdb=" N PRO A 892 " pdb=" CD PRO A 892 " ideal model delta sigma weight residual 112.00 99.37 12.63 1.40e+00 5.10e-01 8.14e+01 ... (remaining 37526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 16165 22.08 - 44.17: 1104 44.17 - 66.25: 158 66.25 - 88.33: 169 88.33 - 110.42: 98 Dihedral angle restraints: 17694 sinusoidal: 8093 harmonic: 9601 Sorted by residual: dihedral pdb=" CB CYS A 731 " pdb=" SG CYS A 731 " pdb=" SG CYS A 753 " pdb=" CB CYS A 753 " ideal model delta sinusoidal sigma weight residual -86.00 1.98 -87.98 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CA CYS C 583 " pdb=" C CYS C 583 " pdb=" N SER C 584 " pdb=" CA SER C 584 " ideal model delta harmonic sigma weight residual -180.00 -137.49 -42.51 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 20.07 72.93 1 1.00e+01 1.00e-02 6.78e+01 ... (remaining 17691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4386 0.112 - 0.224: 121 0.224 - 0.336: 20 0.336 - 0.447: 1 0.447 - 0.559: 1 Chirality restraints: 4529 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 324 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.82e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 324 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 702 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4526 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 312 " 1.009 9.50e-02 1.11e+02 4.52e-01 1.24e+02 pdb=" NE ARG C 312 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG C 312 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG C 312 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 312 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 321 " -0.971 9.50e-02 1.11e+02 4.35e-01 1.14e+02 pdb=" NE ARG A 321 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 321 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 321 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 321 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 891 " 0.117 5.00e-02 4.00e+02 1.65e-01 4.34e+01 pdb=" N PRO B 892 " -0.284 5.00e-02 4.00e+02 pdb=" CA PRO B 892 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO B 892 " 0.080 5.00e-02 4.00e+02 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 168 2.51 - 3.11: 20298 3.11 - 3.70: 39300 3.70 - 4.30: 53018 4.30 - 4.90: 88947 Nonbonded interactions: 201731 Sorted by model distance: nonbonded pdb=" OG SER C 809 " pdb=" CD PRO C 810 " model vdw 1.909 3.440 nonbonded pdb=" O ASP C 283 " pdb=" OG SER C 290 " model vdw 2.064 2.440 nonbonded pdb=" OG SER A 809 " pdb=" OE1 GLU A 812 " model vdw 2.119 2.440 nonbonded pdb=" OG SER B 462 " pdb=" OE1 GLU B 464 " model vdw 2.147 2.440 nonbonded pdb=" O TYR C1040 " pdb=" OG1 THR C1059 " model vdw 2.149 2.440 ... (remaining 201726 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 14 through 546 or (resid 547 and (name N or name CA or nam \ e C or name O or name CB )) or resid 548 through 821 or (resid 846 and (name N o \ r name CA or name C or name O or name CB )) or resid 847 through 1155 or resid 1 \ 301 through 1304)) selection = (chain 'B' and (resid 14 through 546 or (resid 547 and (name N or name CA or nam \ e C or name O or name CB )) or resid 548 through 616 or resid 634 through 842 or \ (resid 846 and (name N or name CA or name C or name O or name CB )) or resid 84 \ 7 through 1155 or resid 1301 through 1304)) selection = (chain 'C' and (resid 14 through 616 or resid 634 through 1155 or resid 1301 thr \ ough 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'f' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 8.300 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 74.170 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.005 0.062 27564 Z= 0.312 Angle : 0.774 13.088 37531 Z= 0.405 Chirality : 0.051 0.559 4529 Planarity : 0.012 0.452 4744 Dihedral : 18.854 110.416 11392 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.46 % Favored : 92.42 % Rotamer: Outliers : 0.42 % Allowed : 0.45 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.97 (0.14), residues: 3271 helix: 0.98 (0.20), residues: 736 sheet: -0.04 (0.20), residues: 649 loop : -1.60 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 429 HIS 0.007 0.001 HIS A 245 PHE 0.030 0.002 PHE A 157 TYR 0.016 0.001 TYR A1060 ARG 0.013 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 482 time to evaluate : 2.825 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: A 53 ASP cc_start: 0.6831 (t0) cc_final: 0.6596 (t0) REVERT: A 577 ILE cc_start: 0.8285 (mm) cc_final: 0.7743 (mt) REVERT: B 52 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7747 (pp30) REVERT: B 177 MET cc_start: 0.7083 (pmm) cc_final: 0.4404 (mmm) REVERT: B 335 PHE cc_start: 0.8024 (m-80) cc_final: 0.7752 (m-80) REVERT: B 385 PHE cc_start: 0.6832 (m-80) cc_final: 0.5795 (m-80) REVERT: B 446 TYR cc_start: 0.8439 (p90) cc_final: 0.8238 (p90) REVERT: C 313 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8625 (t) REVERT: C 490 PHE cc_start: 0.4148 (m-80) cc_final: 0.3155 (m-80) REVERT: C 769 LYS cc_start: 0.8948 (tppp) cc_final: 0.8712 (tptm) outliers start: 12 outliers final: 5 residues processed: 494 average time/residue: 0.3617 time to fit residues: 285.2084 Evaluate side-chains 235 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 229 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 156 optimal weight: 0.0270 chunk 191 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 668 GLN ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 ASN B1057 HIS ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 121 ASN C 310 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27564 Z= 0.305 Angle : 0.755 11.412 37531 Z= 0.372 Chirality : 0.050 0.424 4529 Planarity : 0.005 0.120 4744 Dihedral : 12.252 92.446 5522 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.97 % Favored : 93.00 % Rotamer: Outliers : 2.03 % Allowed : 11.61 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3271 helix: 1.04 (0.19), residues: 751 sheet: -0.14 (0.21), residues: 610 loop : -1.72 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 64 HIS 0.011 0.001 HIS A 66 PHE 0.028 0.002 PHE A1141 TYR 0.033 0.002 TYR B 362 ARG 0.024 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 266 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7126 (m-80) cc_final: 0.6662 (m-10) REVERT: A 577 ILE cc_start: 0.8446 (mm) cc_final: 0.7910 (mt) REVERT: B 21 ARG cc_start: 0.5463 (mtt180) cc_final: 0.4897 (mmm160) REVERT: B 52 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7716 (pp30) REVERT: B 177 MET cc_start: 0.7285 (pmm) cc_final: 0.4719 (tpt) REVERT: B 385 PHE cc_start: 0.7917 (m-80) cc_final: 0.7618 (m-80) REVERT: B 972 ASP cc_start: 0.7830 (t0) cc_final: 0.7412 (t0) REVERT: C 449 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7559 (t80) REVERT: C 769 LYS cc_start: 0.9002 (tppp) cc_final: 0.8797 (tptm) outliers start: 58 outliers final: 37 residues processed: 310 average time/residue: 0.3502 time to fit residues: 178.2150 Evaluate side-chains 234 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 196 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 860 ASP Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 166 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 248 optimal weight: 0.0980 chunk 203 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 299 optimal weight: 5.9990 chunk 323 optimal weight: 0.6980 chunk 266 optimal weight: 9.9990 chunk 296 optimal weight: 7.9990 chunk 102 optimal weight: 0.1980 chunk 240 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN B 245 HIS ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 GLN C 948 ASN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27564 Z= 0.172 Angle : 0.620 9.275 37531 Z= 0.304 Chirality : 0.046 0.370 4529 Planarity : 0.004 0.059 4744 Dihedral : 9.757 91.114 5516 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.63 % Favored : 94.34 % Rotamer: Outliers : 2.13 % Allowed : 14.34 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3271 helix: 1.51 (0.20), residues: 742 sheet: -0.10 (0.21), residues: 601 loop : -1.58 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 251 HIS 0.003 0.001 HIS B1081 PHE 0.021 0.001 PHE A 32 TYR 0.019 0.001 TYR A1060 ARG 0.004 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 227 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4741 (pmm) cc_final: 0.3168 (tpt) REVERT: A 577 ILE cc_start: 0.8446 (mm) cc_final: 0.7884 (mt) REVERT: A 1024 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: B 52 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7714 (pp30) REVERT: B 177 MET cc_start: 0.7134 (pmm) cc_final: 0.4397 (tpt) REVERT: B 972 ASP cc_start: 0.7679 (t0) cc_final: 0.7360 (t0) REVERT: C 168 PHE cc_start: 0.7167 (t80) cc_final: 0.6676 (t80) REVERT: C 449 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7565 (t80) outliers start: 61 outliers final: 36 residues processed: 270 average time/residue: 0.3315 time to fit residues: 150.5976 Evaluate side-chains 236 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 198 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 860 ASP Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 295 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 33 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 300 optimal weight: 0.7980 chunk 318 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN B 748 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 27564 Z= 0.265 Angle : 0.658 10.397 37531 Z= 0.326 Chirality : 0.046 0.382 4529 Planarity : 0.004 0.059 4744 Dihedral : 8.354 84.849 5516 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.94 % Favored : 93.03 % Rotamer: Outliers : 3.46 % Allowed : 15.45 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3271 helix: 1.47 (0.19), residues: 743 sheet: -0.16 (0.20), residues: 624 loop : -1.69 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 251 HIS 0.004 0.001 HIS B1051 PHE 0.027 0.002 PHE A 826 TYR 0.021 0.001 TYR C1060 ARG 0.005 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 210 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 ILE cc_start: 0.8528 (mm) cc_final: 0.7971 (mt) REVERT: A 1024 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6335 (mp0) REVERT: A 1137 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6728 (mm-30) REVERT: B 52 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7814 (pp30) REVERT: B 177 MET cc_start: 0.6954 (pmm) cc_final: 0.4545 (tpt) REVERT: B 385 PHE cc_start: 0.8135 (m-80) cc_final: 0.7743 (m-10) REVERT: B 446 TYR cc_start: 0.8414 (p90) cc_final: 0.8024 (p90) REVERT: B 860 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7420 (p0) REVERT: B 972 ASP cc_start: 0.7863 (t0) cc_final: 0.7617 (t0) REVERT: C 866 TYR cc_start: 0.9263 (OUTLIER) cc_final: 0.8858 (m-10) outliers start: 99 outliers final: 57 residues processed: 288 average time/residue: 0.3278 time to fit residues: 161.7994 Evaluate side-chains 248 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 188 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 860 ASP Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 264 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 236 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 219 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 162 optimal weight: 10.0000 chunk 285 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN B 948 ASN B1057 HIS ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN C1099 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 27564 Z= 0.482 Angle : 0.841 13.052 37531 Z= 0.423 Chirality : 0.051 0.427 4529 Planarity : 0.006 0.072 4744 Dihedral : 9.042 82.033 5516 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.84 % Favored : 91.13 % Rotamer: Outliers : 4.65 % Allowed : 16.50 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3271 helix: 0.96 (0.19), residues: 736 sheet: -0.61 (0.20), residues: 655 loop : -2.00 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 64 HIS 0.010 0.002 HIS B1051 PHE 0.027 0.003 PHE B 92 TYR 0.028 0.002 TYR C1060 ARG 0.009 0.001 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 201 time to evaluate : 3.242 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: A 312 ARG cc_start: 0.7939 (ptp90) cc_final: 0.7520 (ptp90) REVERT: A 461 ILE cc_start: 0.3428 (OUTLIER) cc_final: 0.3057 (pt) REVERT: A 895 MET cc_start: 0.9030 (tpt) cc_final: 0.8694 (tpt) REVERT: A 1024 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: B 177 MET cc_start: 0.7081 (pmm) cc_final: 0.4825 (tpt) REVERT: B 385 PHE cc_start: 0.8561 (m-80) cc_final: 0.8178 (m-10) REVERT: B 446 TYR cc_start: 0.8474 (p90) cc_final: 0.8065 (p90) REVERT: B 508 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7734 (p90) REVERT: C 128 ILE cc_start: 0.8622 (mm) cc_final: 0.8343 (mm) REVERT: C 558 PHE cc_start: 0.6987 (m-10) cc_final: 0.6760 (m-10) REVERT: C 579 ASP cc_start: 0.6240 (m-30) cc_final: 0.6033 (m-30) REVERT: C 866 TYR cc_start: 0.9337 (OUTLIER) cc_final: 0.9008 (m-10) REVERT: C 995 GLN cc_start: 0.8224 (tp40) cc_final: 0.7953 (mm-40) outliers start: 133 outliers final: 86 residues processed: 318 average time/residue: 0.3454 time to fit residues: 185.2450 Evaluate side-chains 258 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 168 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 648 HIS Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1010 GLU Chi-restraints excluded: chain C residue 1099 GLN Chi-restraints excluded: chain C residue 1118 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 106 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 318 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1099 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27564 Z= 0.198 Angle : 0.651 9.982 37531 Z= 0.322 Chirality : 0.046 0.398 4529 Planarity : 0.004 0.048 4744 Dihedral : 7.994 78.583 5516 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 3.36 % Allowed : 19.06 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3271 helix: 1.45 (0.19), residues: 742 sheet: -0.35 (0.21), residues: 638 loop : -1.82 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 251 HIS 0.003 0.001 HIS B 648 PHE 0.026 0.001 PHE C 555 TYR 0.019 0.001 TYR B 373 ARG 0.004 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 205 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7854 (p0) cc_final: 0.7629 (p0) REVERT: A 812 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: A 895 MET cc_start: 0.8954 (tpt) cc_final: 0.8706 (tpt) REVERT: A 995 GLN cc_start: 0.7438 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 1024 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6354 (mp0) REVERT: A 1137 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6963 (mm-30) REVERT: B 21 ARG cc_start: 0.3507 (mmm160) cc_final: 0.3179 (mmm160) REVERT: B 177 MET cc_start: 0.6977 (pmm) cc_final: 0.4932 (mmm) REVERT: B 189 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8127 (tp) REVERT: B 351 ILE cc_start: 0.8616 (mm) cc_final: 0.8263 (mt) REVERT: B 385 PHE cc_start: 0.8440 (m-80) cc_final: 0.8136 (m-10) REVERT: B 446 TYR cc_start: 0.8455 (p90) cc_final: 0.8079 (p90) REVERT: B 508 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7775 (p90) REVERT: C 866 TYR cc_start: 0.9276 (OUTLIER) cc_final: 0.8850 (m-10) REVERT: C 1118 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.7895 (p0) outliers start: 96 outliers final: 65 residues processed: 280 average time/residue: 0.3654 time to fit residues: 170.6768 Evaluate side-chains 255 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 184 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1010 GLU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1118 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 306 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 232 optimal weight: 20.0000 chunk 180 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 317 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 193 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27564 Z= 0.254 Angle : 0.671 9.474 37531 Z= 0.331 Chirality : 0.046 0.396 4529 Planarity : 0.004 0.052 4744 Dihedral : 7.714 74.627 5516 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 3.60 % Allowed : 19.44 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3271 helix: 1.57 (0.19), residues: 735 sheet: -0.31 (0.21), residues: 618 loop : -1.84 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.005 0.001 HIS C 512 PHE 0.025 0.001 PHE C 92 TYR 0.041 0.001 TYR A 416 ARG 0.005 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 187 time to evaluate : 2.996 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: A 228 ASP cc_start: 0.7824 (p0) cc_final: 0.7618 (p0) REVERT: A 461 ILE cc_start: 0.3392 (OUTLIER) cc_final: 0.3060 (pt) REVERT: A 741 GLU cc_start: 0.7462 (pm20) cc_final: 0.6942 (pm20) REVERT: A 812 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: A 995 GLN cc_start: 0.7356 (tm-30) cc_final: 0.7094 (tm-30) REVERT: A 998 GLN cc_start: 0.8279 (tp40) cc_final: 0.8013 (mm-40) REVERT: A 1024 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: A 1137 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6942 (mm-30) REVERT: B 21 ARG cc_start: 0.3277 (mmm160) cc_final: 0.2949 (tpp-160) REVERT: B 177 MET cc_start: 0.7101 (pmm) cc_final: 0.4975 (mmm) REVERT: B 189 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8158 (tp) REVERT: B 385 PHE cc_start: 0.8411 (m-80) cc_final: 0.8115 (m-10) REVERT: B 446 TYR cc_start: 0.8402 (p90) cc_final: 0.8079 (p90) REVERT: B 508 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7809 (p90) REVERT: B 958 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8376 (tm-30) REVERT: B 1067 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8520 (p0) REVERT: C 128 ILE cc_start: 0.8616 (mm) cc_final: 0.8368 (mm) REVERT: C 866 TYR cc_start: 0.9263 (OUTLIER) cc_final: 0.9043 (m-10) REVERT: C 1118 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7869 (p0) outliers start: 103 outliers final: 76 residues processed: 269 average time/residue: 0.3378 time to fit residues: 153.0356 Evaluate side-chains 262 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 178 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 766 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1067 ASN Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1010 GLU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1118 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 196 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 chunk 156 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27564 Z= 0.180 Angle : 0.636 17.097 37531 Z= 0.311 Chirality : 0.045 0.384 4529 Planarity : 0.004 0.056 4744 Dihedral : 7.185 68.837 5516 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.79 % Rotamer: Outliers : 2.90 % Allowed : 20.21 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3271 helix: 1.73 (0.19), residues: 735 sheet: -0.18 (0.20), residues: 639 loop : -1.78 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 251 HIS 0.004 0.001 HIS C 512 PHE 0.026 0.001 PHE C 92 TYR 0.028 0.001 TYR B 373 ARG 0.007 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 195 time to evaluate : 2.976 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: A 895 MET cc_start: 0.8967 (tpt) cc_final: 0.8725 (tpt) REVERT: A 995 GLN cc_start: 0.7326 (tm-30) cc_final: 0.7014 (tm-30) REVERT: A 1024 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6159 (mp0) REVERT: A 1137 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7009 (mm-30) REVERT: B 21 ARG cc_start: 0.3309 (mmm160) cc_final: 0.3029 (tpp80) REVERT: B 177 MET cc_start: 0.6886 (pmm) cc_final: 0.4907 (mmm) REVERT: B 385 PHE cc_start: 0.8328 (m-80) cc_final: 0.8114 (m-10) REVERT: B 446 TYR cc_start: 0.8400 (p90) cc_final: 0.8081 (p90) REVERT: B 508 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7826 (p90) REVERT: B 874 THR cc_start: 0.8338 (m) cc_final: 0.8103 (m) REVERT: B 958 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8277 (tm-30) REVERT: C 866 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8951 (m-10) REVERT: C 1118 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7853 (p0) outliers start: 83 outliers final: 68 residues processed: 261 average time/residue: 0.3459 time to fit residues: 152.7790 Evaluate side-chains 256 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 184 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 766 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1010 GLU Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1118 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 288 optimal weight: 0.9990 chunk 303 optimal weight: 0.7980 chunk 277 optimal weight: 0.5980 chunk 295 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 279 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27564 Z= 0.178 Angle : 0.627 13.043 37531 Z= 0.308 Chirality : 0.045 0.377 4529 Planarity : 0.004 0.056 4744 Dihedral : 6.746 62.310 5516 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 3.08 % Allowed : 20.31 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3271 helix: 1.74 (0.19), residues: 749 sheet: -0.09 (0.21), residues: 607 loop : -1.72 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 251 HIS 0.003 0.001 HIS C 512 PHE 0.027 0.001 PHE C 168 TYR 0.030 0.001 TYR A 170 ARG 0.007 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 193 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.5594 (OUTLIER) cc_final: 0.5365 (p0) REVERT: A 461 ILE cc_start: 0.3771 (OUTLIER) cc_final: 0.3448 (pt) REVERT: A 812 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: A 1024 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6079 (mp0) REVERT: A 1137 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7033 (mm-30) REVERT: B 21 ARG cc_start: 0.3417 (mmm160) cc_final: 0.3104 (tpp80) REVERT: B 177 MET cc_start: 0.6924 (pmm) cc_final: 0.4954 (mmm) REVERT: B 446 TYR cc_start: 0.8433 (p90) cc_final: 0.8091 (p90) REVERT: B 508 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7877 (p90) REVERT: B 895 MET cc_start: 0.8979 (tpp) cc_final: 0.8601 (tpt) REVERT: B 958 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 234 ASN cc_start: 0.7122 (OUTLIER) cc_final: 0.6722 (p0) REVERT: C 987 ASP cc_start: 0.7215 (m-30) cc_final: 0.6953 (m-30) REVERT: C 1118 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7854 (p0) outliers start: 88 outliers final: 67 residues processed: 263 average time/residue: 0.3292 time to fit residues: 146.1213 Evaluate side-chains 250 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 176 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1118 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 194 optimal weight: 0.3980 chunk 312 optimal weight: 5.9990 chunk 190 optimal weight: 0.0010 chunk 148 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 327 optimal weight: 6.9990 chunk 301 optimal weight: 0.7980 chunk 261 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 770 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27564 Z= 0.162 Angle : 0.621 12.762 37531 Z= 0.304 Chirality : 0.044 0.370 4529 Planarity : 0.004 0.057 4744 Dihedral : 6.329 58.135 5516 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 2.41 % Allowed : 20.84 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3271 helix: 1.84 (0.20), residues: 744 sheet: -0.05 (0.20), residues: 628 loop : -1.65 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 251 HIS 0.003 0.001 HIS C 512 PHE 0.027 0.001 PHE C 92 TYR 0.016 0.001 TYR C1060 ARG 0.008 0.000 ARG C 758 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 187 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.5589 (OUTLIER) cc_final: 0.5386 (p0) REVERT: A 461 ILE cc_start: 0.3917 (OUTLIER) cc_final: 0.3556 (pt) REVERT: A 812 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: A 1137 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7000 (mm-30) REVERT: B 124 THR cc_start: 0.4829 (OUTLIER) cc_final: 0.4620 (m) REVERT: B 177 MET cc_start: 0.6396 (pmm) cc_final: 0.4674 (mmm) REVERT: B 446 TYR cc_start: 0.8424 (p90) cc_final: 0.8093 (p90) REVERT: B 508 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8075 (p90) REVERT: B 895 MET cc_start: 0.8910 (tpp) cc_final: 0.8594 (tpt) REVERT: B 958 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8322 (tm-30) REVERT: C 234 ASN cc_start: 0.7131 (OUTLIER) cc_final: 0.6749 (p0) REVERT: C 987 ASP cc_start: 0.7103 (m-30) cc_final: 0.6884 (m-30) REVERT: C 1118 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7920 (p0) outliers start: 69 outliers final: 57 residues processed: 243 average time/residue: 0.3322 time to fit residues: 137.7827 Evaluate side-chains 243 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 179 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 549 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1118 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 207 optimal weight: 5.9990 chunk 278 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 363 ASN ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1099 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 GLN C 770 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** 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 = 0.4017 r_free = 0.4017 target = 0.128516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.091179 restraints weight = 71002.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.091735 restraints weight = 45168.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.092192 restraints weight = 28907.929| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 27564 Z= 0.396 Angle : 0.760 12.063 37531 Z= 0.379 Chirality : 0.048 0.409 4529 Planarity : 0.005 0.058 4744 Dihedral : 7.043 59.861 5515 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.01 % Favored : 91.96 % Rotamer: Outliers : 2.83 % Allowed : 20.63 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3271 helix: 1.42 (0.19), residues: 747 sheet: -0.40 (0.20), residues: 640 loop : -1.88 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 64 HIS 0.008 0.002 HIS B1051 PHE 0.034 0.002 PHE C 385 TYR 0.027 0.002 TYR C1060 ARG 0.018 0.001 ARG A1100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4831.14 seconds wall clock time: 89 minutes 44.42 seconds (5384.42 seconds total)