Starting phenix.real_space_refine on Fri Aug 9 08:43:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm3_7516/08_2024/6cm3_7516_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm3_7516/08_2024/6cm3_7516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm3_7516/08_2024/6cm3_7516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm3_7516/08_2024/6cm3_7516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm3_7516/08_2024/6cm3_7516_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm3_7516/08_2024/6cm3_7516_neut.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 216 atoms to isotropic. 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 129 5.16 5 C 16002 2.51 5 N 4248 2.21 5 O 5076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25455 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2814 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 7, 'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "E" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2814 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 7, 'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "F" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2814 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 7, 'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "J" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "K" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 985 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "L" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "M" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 985 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "N" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain breaks: 1 Chain: "O" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 985 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "P" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "R" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "S" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "T" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "U" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "V" 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: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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 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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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 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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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 Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" C1 NAG Y 1 " occ=0.69 ... (12 atoms not shown) pdb=" O7 NAG Y 1 " occ=0.69 residue: pdb=" C1 NAG Y 2 " occ=0.65 ... (12 atoms not shown) pdb=" O7 NAG Y 2 " occ=0.65 residue: pdb=" C1 BMA Y 3 " occ=0.92 ... (9 atoms not shown) pdb=" O6 BMA Y 3 " occ=0.92 residue: pdb=" C1 MAN Y 4 " occ=0.85 ... (9 atoms not shown) pdb=" O6 MAN Y 4 " occ=0.85 residue: pdb=" C1 MAN Y 5 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN Y 5 " occ=0.79 residue: pdb=" C1 MAN Y 6 " occ=0.66 ... (9 atoms not shown) pdb=" O6 MAN Y 6 " occ=0.66 residue: pdb=" C1 NAG c 1 " occ=0.69 ... (12 atoms not shown) pdb=" O7 NAG c 1 " occ=0.69 residue: pdb=" C1 NAG c 2 " occ=0.65 ... (12 atoms not shown) pdb=" O7 NAG c 2 " occ=0.65 residue: pdb=" C1 BMA c 3 " occ=0.92 ... (9 atoms not shown) pdb=" O6 BMA c 3 " occ=0.92 residue: pdb=" C1 MAN c 4 " occ=0.85 ... (9 atoms not shown) pdb=" O6 MAN c 4 " occ=0.85 residue: pdb=" C1 MAN c 5 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN c 5 " occ=0.79 residue: pdb=" C1 MAN c 6 " occ=0.66 ... (9 atoms not shown) pdb=" O6 MAN c 6 " occ=0.66 ... (remaining 6 not shown) Time building chain proxies: 13.79, per 1000 atoms: 0.54 Number of scatterers: 25455 At special positions: 0 Unit cell: (157.2, 149.34, 138.86, 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 129 16.00 O 5076 8.00 N 4248 7.00 C 16002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS E 501 " distance=1.97 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS D 501 " distance=2.01 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS F 501 " distance=2.10 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.05 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.05 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.02 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 84 " distance=2.02 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 99 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 99 " distance=2.02 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 89 " distance=2.04 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 99 " distance=2.02 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 89 " 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=3, symmetry=0 Links applied ALPHA1-2 " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Z 4 " - " MAN Z 5 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN c 8 " - " MAN c 9 " " MAN d 4 " - " MAN d 5 " " MAN g 4 " - " MAN g 5 " " MAN g 5 " - " MAN g 6 " " MAN g 8 " - " MAN g 9 " " MAN h 4 " - " MAN h 5 " ALPHA1-3 " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 10 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 4 " " MAN c 7 " - " MAN c 10 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " BMA g 3 " - " MAN g 4 " " MAN g 7 " - " MAN g 10 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 8 " " BMA a 3 " - " MAN a 5 " " BMA c 3 " - " MAN c 7 " " MAN c 7 " - " MAN c 8 " " BMA e 3 " - " MAN e 5 " " BMA g 3 " - " MAN g 7 " " MAN g 7 " - " MAN g 8 " " BMA i 3 " - " MAN i 5 " BETA1-4 " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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 i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG D 621 " - " ASN D 295 " " NAG D 622 " - " ASN D 332 " " NAG D 623 " - " ASN D 339 " " NAG D 624 " - " ASN D 363 " " NAG D 627 " - " ASN D 392 " " NAG D 628 " - " ASN D 448 " " NAG E 621 " - " ASN E 295 " " NAG E 622 " - " ASN E 332 " " NAG E 623 " - " ASN E 339 " " NAG E 624 " - " ASN E 363 " " NAG E 627 " - " ASN E 392 " " NAG E 628 " - " ASN E 448 " " NAG F 621 " - " ASN F 295 " " NAG F 622 " - " ASN F 332 " " NAG F 623 " - " ASN F 339 " " NAG F 624 " - " ASN F 363 " " NAG F 627 " - " ASN F 392 " " NAG F 628 " - " ASN F 448 " " NAG V 1 " - " ASN A 637 " " NAG W 1 " - " ASN B 637 " " NAG X 1 " - " ASN C 637 " " NAG Y 1 " - " ASN D 234 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN D 276 " " NAG b 1 " - " ASN D 386 " " NAG c 1 " - " ASN E 234 " " NAG d 1 " - " ASN E 262 " " NAG e 1 " - " ASN E 276 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN F 234 " " NAG h 1 " - " ASN F 262 " " NAG i 1 " - " ASN F 276 " " NAG j 1 " - " ASN F 386 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.36 Conformation dependent library (CDL) restraints added in 4.5 seconds 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5838 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 60 sheets defined 15.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.843A pdb=" N GLY A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 525 " --> pdb=" O PHE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 544 removed outlier: 3.990A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 593 removed outlier: 3.985A pdb=" N VAL A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TRP A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 removed outlier: 3.726A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.843A pdb=" N GLY B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 544 removed outlier: 3.991A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 593 removed outlier: 3.986A pdb=" N VAL B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.726A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'C' and resid 520 through 526 removed outlier: 3.843A pdb=" N GLY C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 525 " --> pdb=" O PHE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 544 removed outlier: 3.991A pdb=" N THR C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 593 removed outlier: 3.985A pdb=" N VAL C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP C 571 " --> pdb=" O LYS C 567 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 626 removed outlier: 3.726A pdb=" N MET C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 649 Processing helix chain 'D' and resid 64 through 74 Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.598A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN D 98 " --> pdb=" O MET D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 94 through 98' Processing helix chain 'D' and resid 100 through 116 removed outlier: 3.613A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 354 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 475 through 480 removed outlier: 3.556A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.598A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN E 98 " --> pdb=" O MET E 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 94 through 98' Processing helix chain 'E' and resid 100 through 116 removed outlier: 3.613A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.556A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 74 Processing helix chain 'F' and resid 94 through 98 removed outlier: 3.598A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN F 98 " --> pdb=" O MET F 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 94 through 98' Processing helix chain 'F' and resid 100 through 116 removed outlier: 3.613A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 354 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 480 removed outlier: 3.556A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 64 removed outlier: 3.591A pdb=" N LEU G 61 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP G 63 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 64 removed outlier: 3.591A pdb=" N LEU H 61 " --> pdb=" O ARG H 58 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP H 63 " --> pdb=" O SER H 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 removed outlier: 3.591A pdb=" N LEU I 61 " --> pdb=" O ARG I 58 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP I 63 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.715A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.716A pdb=" N THR M 91 " --> pdb=" O SER M 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 30 No H-bonds generated for 'chain 'O' and resid 28 through 30' Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.715A pdb=" N THR O 91 " --> pdb=" O SER O 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 56 Processing helix chain 'R' and resid 53 through 56 Processing helix chain 'T' and resid 53 through 56 Processing sheet with id=AA1, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.712A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.678A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 199 through 202 removed outlier: 3.596A pdb=" N ILE D 201 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 120 " --> pdb=" O MET D 434 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.031A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS D 296 " --> pdb=" O CYS D 445 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE D 294 " --> pdb=" O SER D 447 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE D 453 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.031A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS D 296 " --> pdb=" O CYS D 445 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE D 294 " --> pdb=" O SER D 447 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE D 453 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.713A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.678A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 199 through 202 removed outlier: 3.596A pdb=" N ILE E 201 " --> pdb=" O LYS E 121 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL E 120 " --> pdb=" O MET E 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.030A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 294 " --> pdb=" O SER E 447 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.030A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 294 " --> pdb=" O SER E 447 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.712A pdb=" N LYS F 487 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 91 through 92 removed outlier: 3.678A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 199 through 202 removed outlier: 3.596A pdb=" N ILE F 201 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL F 120 " --> pdb=" O MET F 434 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.030A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS F 296 " --> pdb=" O CYS F 445 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 294 " --> pdb=" O SER F 447 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE F 453 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.030A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS F 296 " --> pdb=" O CYS F 445 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 294 " --> pdb=" O SER F 447 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.213A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.995A pdb=" N ILE F 453 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 2 through 5 removed outlier: 6.423A pdb=" N TRP G 28 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 12 through 17 removed outlier: 3.620A pdb=" N PHE G 67 " --> pdb=" O CYS G 16 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 2 through 5 removed outlier: 6.423A pdb=" N TRP H 28 " --> pdb=" O ILE H 36 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 12 through 17 removed outlier: 3.620A pdb=" N PHE H 67 " --> pdb=" O CYS H 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 2 through 5 removed outlier: 6.423A pdb=" N TRP I 28 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 12 through 17 removed outlier: 3.620A pdb=" N PHE I 67 " --> pdb=" O CYS I 16 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.564A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.666A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU K 10 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 33 " --> pdb=" O VAL K 99 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N TYR K 32 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE K 52 " --> pdb=" O TYR K 32 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU K 10 " --> pdb=" O LEU K 123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 18 through 20 Processing sheet with id=AD1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.565A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.665A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU M 10 " --> pdb=" O LEU M 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER M 33 " --> pdb=" O VAL M 99 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N TYR M 32 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE M 52 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU M 10 " --> pdb=" O LEU M 123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 18 through 20 Processing sheet with id=AD7, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.564A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.665A pdb=" N THR N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU O 10 " --> pdb=" O LEU O 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER O 33 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N TYR O 32 " --> pdb=" O ILE O 52 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE O 52 " --> pdb=" O TYR O 32 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE O 34 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG O 50 " --> pdb=" O PHE O 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.749A pdb=" N GLU O 10 " --> pdb=" O LEU O 123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 18 through 20 Processing sheet with id=AE4, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'P' and resid 10 through 12 removed outlier: 7.085A pdb=" N VAL P 35 " --> pdb=" O GLN P 51 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN P 51 " --> pdb=" O VAL P 35 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP P 37 " --> pdb=" O ILE P 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 10 through 12 Processing sheet with id=AE7, first strand: chain 'P' and resid 112 through 113 Processing sheet with id=AE8, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'Q' and resid 54 through 55 removed outlier: 6.502A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR Q 50 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR Q 98 " --> pdb=" O GLN Q 91 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 54 through 55 removed outlier: 6.502A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR Q 50 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE Q 87 " --> pdb=" O THR Q 103 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR Q 103 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AF3, first strand: chain 'R' and resid 10 through 12 removed outlier: 7.085A pdb=" N VAL R 35 " --> pdb=" O GLN R 51 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN R 51 " --> pdb=" O VAL R 35 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP R 37 " --> pdb=" O ILE R 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 10 through 12 Processing sheet with id=AF5, first strand: chain 'R' and resid 112 through 113 Processing sheet with id=AF6, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'S' and resid 54 through 55 removed outlier: 6.502A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR S 98 " --> pdb=" O GLN S 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 54 through 55 removed outlier: 6.502A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE S 87 " --> pdb=" O THR S 103 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR S 103 " --> pdb=" O PHE S 87 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 5 through 6 Processing sheet with id=AG1, first strand: chain 'T' and resid 10 through 12 removed outlier: 7.085A pdb=" N VAL T 35 " --> pdb=" O GLN T 51 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN T 51 " --> pdb=" O VAL T 35 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP T 37 " --> pdb=" O ILE T 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 10 through 12 Processing sheet with id=AG3, first strand: chain 'T' and resid 112 through 113 Processing sheet with id=AG4, first strand: chain 'U' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'U' and resid 54 through 55 removed outlier: 6.503A pdb=" N TRP U 36 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR U 50 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL U 34 " --> pdb=" O TYR U 50 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR U 98 " --> pdb=" O GLN U 91 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 54 through 55 removed outlier: 6.503A pdb=" N TRP U 36 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR U 50 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL U 34 " --> pdb=" O TYR U 50 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE U 87 " --> pdb=" O THR U 103 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR U 103 " --> pdb=" O PHE U 87 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2349 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: 9.31 Time building geometry restraints manager: 12.81 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: 7698 1.33 - 1.46: 6034 1.46 - 1.58: 12086 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 25986 Sorted by residual: bond pdb=" CB TRP E 45 " pdb=" CG TRP E 45 " ideal model delta sigma weight residual 1.498 1.405 0.093 3.10e-02 1.04e+03 8.95e+00 bond pdb=" CB TRP F 45 " pdb=" CG TRP F 45 " ideal model delta sigma weight residual 1.498 1.406 0.092 3.10e-02 1.04e+03 8.89e+00 bond pdb=" CB TRP D 45 " pdb=" CG TRP D 45 " ideal model delta sigma weight residual 1.498 1.406 0.092 3.10e-02 1.04e+03 8.87e+00 bond pdb=" CB TRP C 631 " pdb=" CG TRP C 631 " ideal model delta sigma weight residual 1.498 1.408 0.090 3.10e-02 1.04e+03 8.47e+00 bond pdb=" CB TRP B 631 " pdb=" CG TRP B 631 " ideal model delta sigma weight residual 1.498 1.408 0.090 3.10e-02 1.04e+03 8.44e+00 ... (remaining 25981 not shown) Histogram of bond angle deviations from ideal: 96.97 - 104.84: 408 104.84 - 112.72: 14811 112.72 - 120.60: 10388 120.60 - 128.48: 9460 128.48 - 136.36: 273 Bond angle restraints: 35340 Sorted by residual: angle pdb=" C CYS F 54 " pdb=" N ALA F 55 " pdb=" CA ALA F 55 " ideal model delta sigma weight residual 121.70 134.83 -13.13 1.80e+00 3.09e-01 5.32e+01 angle pdb=" C CYS D 54 " pdb=" N ALA D 55 " pdb=" CA ALA D 55 " ideal model delta sigma weight residual 121.70 134.82 -13.12 1.80e+00 3.09e-01 5.31e+01 angle pdb=" C CYS E 54 " pdb=" N ALA E 55 " pdb=" CA ALA E 55 " ideal model delta sigma weight residual 121.70 134.81 -13.11 1.80e+00 3.09e-01 5.31e+01 angle pdb=" C SER F 463 " pdb=" N THR F 464 " pdb=" CA THR F 464 " ideal model delta sigma weight residual 121.70 130.13 -8.43 1.80e+00 3.09e-01 2.19e+01 angle pdb=" C SER D 463 " pdb=" N THR D 464 " pdb=" CA THR D 464 " ideal model delta sigma weight residual 121.70 130.09 -8.39 1.80e+00 3.09e-01 2.17e+01 ... (remaining 35335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.09: 15939 22.09 - 44.17: 428 44.17 - 66.26: 52 66.26 - 88.35: 69 88.35 - 110.44: 36 Dihedral angle restraints: 16524 sinusoidal: 7443 harmonic: 9081 Sorted by residual: dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -158.89 72.89 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -158.89 72.89 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -158.88 72.88 1 1.00e+01 1.00e-02 6.77e+01 ... (remaining 16521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3991 0.124 - 0.248: 262 0.248 - 0.371: 16 0.371 - 0.495: 6 0.495 - 0.619: 3 Chirality restraints: 4278 Sorted by residual: chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN F 234 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN D 234 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.69e+00 ... (remaining 4275 not shown) Planarity restraints: 4383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 610 " 0.031 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP B 610 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 610 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 610 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 610 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 610 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 610 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 610 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 610 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 610 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 610 " 0.031 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP A 610 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 610 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 610 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 610 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 610 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 610 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 610 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 610 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 610 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 610 " -0.031 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP C 610 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 610 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 610 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 610 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 610 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 610 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 610 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 610 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 610 " 0.003 2.00e-02 2.50e+03 ... (remaining 4380 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 244 2.62 - 3.19: 20866 3.19 - 3.76: 37179 3.76 - 4.33: 52174 4.33 - 4.90: 87246 Nonbonded interactions: 197709 Sorted by model distance: nonbonded pdb=" OG SER L 22 " pdb=" OE2 GLU L 70 " model vdw 2.044 3.040 nonbonded pdb=" OG SER N 22 " pdb=" OE2 GLU N 70 " model vdw 2.045 3.040 nonbonded pdb=" OG SER J 22 " pdb=" OE2 GLU J 70 " model vdw 2.045 3.040 nonbonded pdb=" OD2 ASP A 632 " pdb=" NE1 TRP R 108 " model vdw 2.118 3.120 nonbonded pdb=" OD2 ASP B 632 " pdb=" NE1 TRP P 108 " model vdw 2.168 3.120 ... (remaining 197704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'b' selection = chain 'f' selection = chain 'j' } ncs_group { reference = chain 'Y' selection = chain 'c' selection = chain 'g' } ncs_group { reference = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'e' selection = chain 'h' selection = chain 'i' } 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=0.65 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 70.050 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.010 0.093 25986 Z= 0.626 Angle : 1.081 14.946 35340 Z= 0.540 Chirality : 0.070 0.619 4278 Planarity : 0.007 0.068 4350 Dihedral : 12.581 110.435 10551 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.11 % Allowed : 1.71 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % 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: -4.10 (0.13), residues: 3099 helix: -3.15 (0.16), residues: 450 sheet: -2.01 (0.15), residues: 1110 loop : -3.13 (0.13), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.005 TRP B 610 HIS 0.009 0.002 HIS D 216 PHE 0.041 0.005 PHE D 382 TYR 0.043 0.004 TYR N 98 ARG 0.009 0.001 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 943 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7647 (m-40) cc_final: 0.7246 (m-40) REVERT: A 620 SER cc_start: 0.8287 (m) cc_final: 0.7696 (t) REVERT: A 624 ASP cc_start: 0.8150 (m-30) cc_final: 0.7923 (m-30) REVERT: B 543 ASN cc_start: 0.7616 (m-40) cc_final: 0.7217 (m110) REVERT: B 620 SER cc_start: 0.8373 (m) cc_final: 0.8151 (t) REVERT: B 624 ASP cc_start: 0.7773 (m-30) cc_final: 0.7508 (m-30) REVERT: B 643 TYR cc_start: 0.9161 (m-10) cc_final: 0.8951 (m-10) REVERT: C 528 SER cc_start: 0.9335 (p) cc_final: 0.9018 (m) REVERT: C 586 TYR cc_start: 0.8178 (t80) cc_final: 0.7752 (t80) REVERT: C 620 SER cc_start: 0.8343 (m) cc_final: 0.8038 (p) REVERT: C 624 ASP cc_start: 0.7552 (m-30) cc_final: 0.7274 (m-30) REVERT: D 83 GLU cc_start: 0.7664 (tt0) cc_final: 0.7395 (tt0) REVERT: D 104 MET cc_start: 0.8145 (ptm) cc_final: 0.7696 (ttt) REVERT: D 193 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6197 (tm) REVERT: D 217 TYR cc_start: 0.7997 (m-80) cc_final: 0.7521 (m-80) REVERT: D 358 ILE cc_start: 0.7662 (mm) cc_final: 0.7412 (mt) REVERT: D 435 TYR cc_start: 0.8709 (m-10) cc_final: 0.8201 (m-10) REVERT: D 475 MET cc_start: 0.8319 (mmp) cc_final: 0.8066 (mmp) REVERT: E 83 GLU cc_start: 0.7701 (tt0) cc_final: 0.7332 (tt0) REVERT: E 107 ASP cc_start: 0.7813 (m-30) cc_final: 0.7193 (m-30) REVERT: E 193 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6186 (tm) REVERT: E 217 TYR cc_start: 0.7936 (m-80) cc_final: 0.7527 (m-80) REVERT: E 457 ASP cc_start: 0.7570 (m-30) cc_final: 0.7313 (m-30) REVERT: F 193 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6270 (tm) REVERT: F 264 SER cc_start: 0.8920 (m) cc_final: 0.8464 (p) REVERT: F 358 ILE cc_start: 0.7395 (mm) cc_final: 0.7066 (mt) REVERT: F 475 MET cc_start: 0.8450 (mmp) cc_final: 0.8066 (mmm) REVERT: H 24 ILE cc_start: 0.8917 (pt) cc_final: 0.8669 (tp) REVERT: H 42 SER cc_start: 0.9234 (p) cc_final: 0.8946 (t) REVERT: H 64 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8531 (mm-40) REVERT: I 2 LYS cc_start: 0.7073 (mttt) cc_final: 0.6855 (mmtm) REVERT: I 24 ILE cc_start: 0.8904 (pt) cc_final: 0.8364 (pt) REVERT: I 32 ASN cc_start: 0.8519 (m-40) cc_final: 0.8237 (t0) REVERT: J 23 CYS cc_start: 0.4532 (t) cc_final: 0.3046 (t) REVERT: J 32 ASP cc_start: 0.8026 (m-30) cc_final: 0.7668 (m-30) REVERT: J 37 GLN cc_start: 0.6901 (tt0) cc_final: 0.6533 (tt0) REVERT: J 61 ARG cc_start: 0.5879 (ptt-90) cc_final: 0.5388 (ptt90) REVERT: J 81 GLU cc_start: 0.7198 (pt0) cc_final: 0.6940 (mp0) REVERT: J 82 ASP cc_start: 0.5993 (m-30) cc_final: 0.4976 (m-30) REVERT: J 87 TYR cc_start: 0.7557 (m-80) cc_final: 0.7266 (m-10) REVERT: K 36 TRP cc_start: 0.7872 (m100) cc_final: 0.6852 (m100) REVERT: K 86 LEU cc_start: 0.8354 (mt) cc_final: 0.7883 (mt) REVERT: K 111 ASN cc_start: 0.8782 (t0) cc_final: 0.8415 (t0) REVERT: L 54 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.8088 (mtm-85) REVERT: M 86 LEU cc_start: 0.8166 (mt) cc_final: 0.7921 (mt) REVERT: M 115 LEU cc_start: 0.8833 (mt) cc_final: 0.8535 (mt) REVERT: N 53 THR cc_start: 0.8830 (t) cc_final: 0.8559 (p) REVERT: N 79 GLN cc_start: 0.6922 (mm-40) cc_final: 0.6585 (mm110) REVERT: O 67 ARG cc_start: 0.6887 (ptm160) cc_final: 0.5979 (ttt180) REVERT: O 87 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.7927 (mmp-170) REVERT: O 111 ASN cc_start: 0.8247 (t0) cc_final: 0.7832 (t0) REVERT: P 13 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7674 (mmtt) REVERT: Q 5 THR cc_start: 0.8596 (m) cc_final: 0.8389 (p) REVERT: R 52 ILE cc_start: 0.8685 (pt) cc_final: 0.7992 (mt) REVERT: R 93 ASP cc_start: 0.7863 (m-30) cc_final: 0.7355 (m-30) REVERT: T 93 ASP cc_start: 0.7932 (m-30) cc_final: 0.7600 (m-30) outliers start: 3 outliers final: 0 residues processed: 946 average time/residue: 0.4159 time to fit residues: 585.8069 Evaluate side-chains 591 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 588 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain F residue 193 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.9980 chunk 231 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 123 optimal weight: 0.0170 chunk 239 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 616 ASN B 577 GLN B 611 ASN B 616 ASN C 611 ASN C 616 ASN D 66 HIS D 103 GLN D 258 GLN D 279 ASN D 280 ASN D 293 GLN E 66 HIS E 85 HIS ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 279 ASN E 280 ASN F 66 HIS F 85 HIS F 279 ASN F 280 ASN F 293 GLN F 422 GLN G 32 ASN G 94 GLN H 32 ASN H 94 GLN I 39 ASN I 73 ASN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN L 89 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN N 89 GLN O 65 GLN P 28 ASN R 62 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25986 Z= 0.236 Angle : 0.750 14.976 35340 Z= 0.383 Chirality : 0.049 0.380 4278 Planarity : 0.005 0.074 4350 Dihedral : 11.670 82.520 5178 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.20 % Allowed : 11.20 % Favored : 85.60 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.14), residues: 3099 helix: -0.93 (0.25), residues: 390 sheet: -1.43 (0.16), residues: 1017 loop : -2.50 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Q 36 HIS 0.006 0.001 HIS R 62 PHE 0.018 0.002 PHE O 114 TYR 0.028 0.002 TYR N 49 ARG 0.005 0.001 ARG H 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 715 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7652 (m-40) cc_final: 0.7278 (m110) REVERT: A 610 TRP cc_start: 0.6382 (OUTLIER) cc_final: 0.5936 (m100) REVERT: A 620 SER cc_start: 0.8272 (m) cc_final: 0.7622 (t) REVERT: A 624 ASP cc_start: 0.7895 (m-30) cc_final: 0.7628 (m-30) REVERT: B 620 SER cc_start: 0.8163 (m) cc_final: 0.7777 (p) REVERT: B 624 ASP cc_start: 0.7734 (m-30) cc_final: 0.7333 (m-30) REVERT: B 643 TYR cc_start: 0.9134 (m-10) cc_final: 0.8930 (m-10) REVERT: C 528 SER cc_start: 0.9282 (p) cc_final: 0.9082 (m) REVERT: C 624 ASP cc_start: 0.7578 (m-30) cc_final: 0.7287 (m-30) REVERT: D 358 ILE cc_start: 0.7465 (mm) cc_final: 0.7214 (mt) REVERT: D 430 ILE cc_start: 0.9065 (mm) cc_final: 0.8792 (mm) REVERT: E 82 GLN cc_start: 0.8016 (mt0) cc_final: 0.7767 (pt0) REVERT: E 107 ASP cc_start: 0.7903 (m-30) cc_final: 0.6971 (m-30) REVERT: E 217 TYR cc_start: 0.7845 (m-80) cc_final: 0.7629 (m-80) REVERT: E 358 ILE cc_start: 0.7224 (mm) cc_final: 0.6848 (mt) REVERT: E 475 MET cc_start: 0.8103 (mmt) cc_final: 0.7640 (mmt) REVERT: F 264 SER cc_start: 0.8818 (m) cc_final: 0.8397 (p) REVERT: F 358 ILE cc_start: 0.7088 (mm) cc_final: 0.6765 (mt) REVERT: F 477 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8433 (m-30) REVERT: G 40 GLN cc_start: 0.8526 (mt0) cc_final: 0.8066 (mt0) REVERT: G 60 SER cc_start: 0.9298 (p) cc_final: 0.9087 (p) REVERT: H 32 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.8023 (t0) REVERT: H 40 GLN cc_start: 0.8483 (mt0) cc_final: 0.7823 (mt0) REVERT: H 64 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8683 (mm-40) REVERT: H 80 ASP cc_start: 0.7833 (t0) cc_final: 0.7600 (m-30) REVERT: I 32 ASN cc_start: 0.8552 (m-40) cc_final: 0.8194 (t0) REVERT: I 40 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7841 (mt0) REVERT: I 89 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7409 (mp10) REVERT: J 21 LEU cc_start: 0.6608 (tp) cc_final: 0.6300 (tp) REVERT: J 37 GLN cc_start: 0.6540 (tt0) cc_final: 0.6287 (tt0) REVERT: J 81 GLU cc_start: 0.7243 (pt0) cc_final: 0.7040 (mp0) REVERT: J 82 ASP cc_start: 0.5884 (m-30) cc_final: 0.4690 (m-30) REVERT: K 12 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8371 (mmmt) REVERT: K 13 LYS cc_start: 0.8034 (mmtm) cc_final: 0.7564 (mmtm) REVERT: K 19 LYS cc_start: 0.8665 (tptt) cc_final: 0.8416 (tptp) REVERT: K 31 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7495 (mtt180) REVERT: K 84 ARG cc_start: 0.7669 (ptp-170) cc_final: 0.7376 (ptt-90) REVERT: K 86 LEU cc_start: 0.8340 (mt) cc_final: 0.7922 (mt) REVERT: K 101 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7626 (mm-30) REVERT: K 111 ASN cc_start: 0.8715 (t0) cc_final: 0.8120 (t0) REVERT: L 5 THR cc_start: 0.8132 (p) cc_final: 0.7891 (m) REVERT: L 24 ARG cc_start: 0.7932 (tpp-160) cc_final: 0.7173 (tpp-160) REVERT: L 54 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.7943 (mtm-85) REVERT: M 13 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8409 (mmtm) REVERT: M 86 LEU cc_start: 0.8142 (mt) cc_final: 0.7710 (mt) REVERT: M 110 ASP cc_start: 0.7983 (m-30) cc_final: 0.7313 (t0) REVERT: M 111 ASN cc_start: 0.7857 (t0) cc_final: 0.7617 (t0) REVERT: M 114 PHE cc_start: 0.8214 (p90) cc_final: 0.7988 (p90) REVERT: M 120 GLN cc_start: 0.6975 (mm110) cc_final: 0.6751 (mp10) REVERT: N 53 THR cc_start: 0.8847 (t) cc_final: 0.8618 (p) REVERT: N 54 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: N 90 GLN cc_start: 0.8442 (pp30) cc_final: 0.8173 (pp30) REVERT: O 3 GLN cc_start: 0.6966 (mp10) cc_final: 0.6664 (mp10) REVERT: O 12 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7011 (mmmt) REVERT: O 13 LYS cc_start: 0.8896 (mmtm) cc_final: 0.8639 (mmtm) REVERT: O 86 LEU cc_start: 0.8131 (mt) cc_final: 0.7081 (mt) REVERT: O 87 ARG cc_start: 0.8405 (mtp-110) cc_final: 0.7850 (mmm160) REVERT: O 101 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7591 (mm-30) REVERT: O 111 ASN cc_start: 0.8330 (t0) cc_final: 0.8014 (t0) REVERT: P 13 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7767 (mmmt) REVERT: R 89 LEU cc_start: 0.8378 (tp) cc_final: 0.8137 (tp) REVERT: T 89 LEU cc_start: 0.8579 (mm) cc_final: 0.8269 (mm) REVERT: U 40 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7831 (mmm-85) outliers start: 84 outliers final: 40 residues processed: 756 average time/residue: 0.3742 time to fit residues: 436.6331 Evaluate side-chains 644 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 600 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 610 TRP Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain T residue 94 THR Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 61 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 278 optimal weight: 0.6980 chunk 300 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 276 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 616 ASN C 616 ASN E 103 GLN F 293 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 94 GLN I 73 ASN I 94 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN M 65 GLN ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25986 Z= 0.249 Angle : 0.725 19.542 35340 Z= 0.363 Chirality : 0.048 0.322 4278 Planarity : 0.004 0.035 4350 Dihedral : 10.569 79.895 5178 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.00 % Allowed : 12.76 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.15), residues: 3099 helix: -0.21 (0.27), residues: 408 sheet: -1.32 (0.17), residues: 1038 loop : -2.20 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 610 HIS 0.003 0.001 HIS P 62 PHE 0.017 0.002 PHE J 83 TYR 0.028 0.002 TYR J 49 ARG 0.004 0.000 ARG E 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 663 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7578 (m-40) cc_final: 0.7286 (m110) REVERT: A 620 SER cc_start: 0.8208 (m) cc_final: 0.7597 (t) REVERT: A 624 ASP cc_start: 0.7869 (m-30) cc_final: 0.7459 (m-30) REVERT: B 591 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8400 (tp40) REVERT: B 608 VAL cc_start: 0.9108 (t) cc_final: 0.8752 (p) REVERT: B 620 SER cc_start: 0.8061 (m) cc_final: 0.7721 (p) REVERT: B 624 ASP cc_start: 0.7679 (m-30) cc_final: 0.7307 (m-30) REVERT: C 585 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7929 (tpp-160) REVERT: C 624 ASP cc_start: 0.7533 (m-30) cc_final: 0.7233 (m-30) REVERT: D 358 ILE cc_start: 0.7480 (mm) cc_final: 0.7228 (mt) REVERT: D 430 ILE cc_start: 0.9187 (mm) cc_final: 0.8902 (mm) REVERT: E 107 ASP cc_start: 0.8016 (m-30) cc_final: 0.6975 (m-30) REVERT: E 217 TYR cc_start: 0.7873 (m-80) cc_final: 0.7589 (m-80) REVERT: F 78 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7874 (t70) REVERT: F 358 ILE cc_start: 0.6963 (mm) cc_final: 0.6683 (mt) REVERT: G 32 ASN cc_start: 0.8285 (t0) cc_final: 0.8033 (t0) REVERT: G 40 GLN cc_start: 0.8468 (mt0) cc_final: 0.7926 (mt0) REVERT: G 60 SER cc_start: 0.9374 (p) cc_final: 0.9140 (p) REVERT: H 40 GLN cc_start: 0.8441 (mt0) cc_final: 0.7758 (mt0) REVERT: H 64 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8671 (mm-40) REVERT: I 32 ASN cc_start: 0.8583 (m-40) cc_final: 0.8219 (t0) REVERT: I 40 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7911 (mm-40) REVERT: J 21 LEU cc_start: 0.6693 (tp) cc_final: 0.6350 (tp) REVERT: J 24 ARG cc_start: 0.8441 (tpm170) cc_final: 0.7654 (tpm170) REVERT: J 32 ASP cc_start: 0.8072 (m-30) cc_final: 0.7862 (m-30) REVERT: J 37 GLN cc_start: 0.6667 (tt0) cc_final: 0.6340 (tt0) REVERT: J 87 TYR cc_start: 0.7270 (m-80) cc_final: 0.6800 (m-80) REVERT: K 12 LYS cc_start: 0.8699 (mmmt) cc_final: 0.8314 (mmmt) REVERT: K 13 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7619 (mmtm) REVERT: K 19 LYS cc_start: 0.8661 (tptt) cc_final: 0.8254 (tptp) REVERT: K 86 LEU cc_start: 0.8431 (mt) cc_final: 0.7926 (mt) REVERT: K 101 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7616 (mm-30) REVERT: K 111 ASN cc_start: 0.8725 (t0) cc_final: 0.8202 (t0) REVERT: L 54 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.8117 (mtm-85) REVERT: L 90 GLN cc_start: 0.8231 (pp30) cc_final: 0.7866 (pp30) REVERT: M 19 LYS cc_start: 0.8322 (tppt) cc_final: 0.8048 (tptp) REVERT: M 86 LEU cc_start: 0.7958 (mt) cc_final: 0.7747 (mt) REVERT: M 101 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7427 (mm-30) REVERT: M 110 ASP cc_start: 0.7920 (m-30) cc_final: 0.7263 (t0) REVERT: M 114 PHE cc_start: 0.8253 (p90) cc_final: 0.8008 (p90) REVERT: N 61 ARG cc_start: 0.6092 (ptt90) cc_final: 0.5608 (ptt90) REVERT: N 90 GLN cc_start: 0.8409 (pp30) cc_final: 0.8132 (pp30) REVERT: O 3 GLN cc_start: 0.6864 (mp10) cc_final: 0.6562 (mp10) REVERT: O 19 LYS cc_start: 0.8797 (tptt) cc_final: 0.8463 (tptp) REVERT: O 86 LEU cc_start: 0.8058 (mt) cc_final: 0.6766 (mt) REVERT: O 87 ARG cc_start: 0.8383 (mtp-110) cc_final: 0.8036 (mmp-170) REVERT: O 110 ASP cc_start: 0.8126 (m-30) cc_final: 0.7474 (t0) REVERT: O 111 ASN cc_start: 0.8340 (t0) cc_final: 0.7948 (t0) REVERT: O 116 LYS cc_start: 0.8728 (tptm) cc_final: 0.8307 (tmtt) REVERT: P 13 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7607 (mmtt) REVERT: Q 3 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7483 (mm-40) REVERT: R 89 LEU cc_start: 0.8381 (tp) cc_final: 0.8133 (tp) REVERT: S 78 ASN cc_start: 0.7942 (t0) cc_final: 0.7650 (t0) REVERT: T 89 LEU cc_start: 0.8564 (mm) cc_final: 0.8300 (mm) REVERT: U 4 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7947 (ttm) outliers start: 105 outliers final: 66 residues processed: 715 average time/residue: 0.3736 time to fit residues: 411.7148 Evaluate side-chains 671 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 602 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 67 ARG Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 61 HIS Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 4 MET Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 61 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 616 ASN D 330 HIS ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 293 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN I 73 ASN I 94 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN M 111 ASN ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN ** T 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 25986 Z= 0.576 Angle : 0.878 19.922 35340 Z= 0.439 Chirality : 0.054 0.495 4278 Planarity : 0.005 0.041 4350 Dihedral : 10.309 78.599 5178 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.65 % Favored : 90.32 % Rotamer: Outliers : 5.14 % Allowed : 13.71 % Favored : 81.14 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.15), residues: 3099 helix: -0.60 (0.24), residues: 450 sheet: -1.17 (0.17), residues: 1008 loop : -2.40 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP K 36 HIS 0.005 0.001 HIS R 3 PHE 0.028 0.003 PHE R 98 TYR 0.031 0.003 TYR F 217 ARG 0.011 0.001 ARG T 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 609 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7843 (m-40) cc_final: 0.7488 (m110) REVERT: A 610 TRP cc_start: 0.6618 (OUTLIER) cc_final: 0.6332 (t60) REVERT: A 620 SER cc_start: 0.8401 (m) cc_final: 0.7846 (t) REVERT: A 624 ASP cc_start: 0.8050 (m-30) cc_final: 0.7601 (m-30) REVERT: B 624 ASP cc_start: 0.7896 (m-30) cc_final: 0.7554 (m-30) REVERT: C 585 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7807 (tpp-160) REVERT: C 610 TRP cc_start: 0.6969 (OUTLIER) cc_final: 0.6549 (t60) REVERT: C 624 ASP cc_start: 0.7722 (m-30) cc_final: 0.7472 (m-30) REVERT: D 64 GLU cc_start: 0.7978 (tp30) cc_final: 0.7765 (tt0) REVERT: D 99 ASN cc_start: 0.9003 (t0) cc_final: 0.8726 (t0) REVERT: D 358 ILE cc_start: 0.7449 (mm) cc_final: 0.7243 (mt) REVERT: D 430 ILE cc_start: 0.9279 (mm) cc_final: 0.9026 (mm) REVERT: D 435 TYR cc_start: 0.8826 (m-10) cc_final: 0.8520 (m-10) REVERT: E 78 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8013 (t70) REVERT: E 107 ASP cc_start: 0.8091 (m-30) cc_final: 0.7166 (m-30) REVERT: F 78 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7817 (t70) REVERT: F 217 TYR cc_start: 0.8331 (m-80) cc_final: 0.8128 (m-80) REVERT: F 358 ILE cc_start: 0.7523 (mm) cc_final: 0.7245 (mt) REVERT: G 32 ASN cc_start: 0.8651 (t0) cc_final: 0.8337 (t0) REVERT: G 40 GLN cc_start: 0.8690 (mt0) cc_final: 0.8208 (mt0) REVERT: G 60 SER cc_start: 0.9389 (p) cc_final: 0.9173 (p) REVERT: H 40 GLN cc_start: 0.8751 (mt0) cc_final: 0.7865 (mt0) REVERT: H 64 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8604 (mm-40) REVERT: I 32 ASN cc_start: 0.8811 (m-40) cc_final: 0.8604 (t0) REVERT: J 21 LEU cc_start: 0.6557 (tp) cc_final: 0.6204 (tp) REVERT: J 24 ARG cc_start: 0.8439 (tpm170) cc_final: 0.8038 (tpp-160) REVERT: J 32 ASP cc_start: 0.8014 (m-30) cc_final: 0.7617 (m-30) REVERT: J 37 GLN cc_start: 0.6642 (tt0) cc_final: 0.6265 (tt0) REVERT: J 48 ILE cc_start: 0.7667 (mm) cc_final: 0.7408 (mm) REVERT: J 87 TYR cc_start: 0.7424 (m-80) cc_final: 0.6975 (m-80) REVERT: K 3 GLN cc_start: 0.7068 (mp10) cc_final: 0.6807 (mp10) REVERT: K 12 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8222 (mmmt) REVERT: K 13 LYS cc_start: 0.7961 (mmtm) cc_final: 0.7655 (mmtm) REVERT: K 19 LYS cc_start: 0.8642 (tptt) cc_final: 0.8382 (tptp) REVERT: K 31 ARG cc_start: 0.8281 (mtt180) cc_final: 0.8025 (mtt180) REVERT: K 86 LEU cc_start: 0.8375 (mt) cc_final: 0.7870 (mt) REVERT: K 101 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7742 (mm-30) REVERT: K 111 ASN cc_start: 0.8781 (t0) cc_final: 0.8178 (t0) REVERT: L 24 ARG cc_start: 0.7953 (tpp-160) cc_final: 0.7477 (tpp-160) REVERT: L 53 THR cc_start: 0.8621 (t) cc_final: 0.8319 (p) REVERT: L 90 GLN cc_start: 0.8406 (pp30) cc_final: 0.8089 (pp30) REVERT: M 3 GLN cc_start: 0.7156 (mp10) cc_final: 0.6688 (mp10) REVERT: M 19 LYS cc_start: 0.8449 (tppt) cc_final: 0.8096 (tptp) REVERT: M 86 LEU cc_start: 0.7982 (mt) cc_final: 0.7750 (mt) REVERT: M 101 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7701 (mm-30) REVERT: M 110 ASP cc_start: 0.8104 (m-30) cc_final: 0.7378 (t0) REVERT: M 114 PHE cc_start: 0.8115 (p90) cc_final: 0.7888 (p90) REVERT: N 23 CYS cc_start: 0.4586 (t) cc_final: 0.3699 (t) REVERT: N 61 ARG cc_start: 0.5568 (ptt90) cc_final: 0.5320 (ptt90) REVERT: N 88 CYS cc_start: 0.2800 (p) cc_final: 0.1972 (p) REVERT: N 90 GLN cc_start: 0.8602 (pp30) cc_final: 0.8376 (pp30) REVERT: O 3 GLN cc_start: 0.6821 (mp10) cc_final: 0.6581 (mp10) REVERT: O 21 SER cc_start: 0.7810 (OUTLIER) cc_final: 0.7340 (t) REVERT: O 86 LEU cc_start: 0.8163 (mt) cc_final: 0.6725 (mt) REVERT: O 87 ARG cc_start: 0.8387 (mtp-110) cc_final: 0.8031 (mmp-170) REVERT: O 101 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7653 (mm-30) REVERT: O 110 ASP cc_start: 0.8213 (m-30) cc_final: 0.7610 (t0) REVERT: O 111 ASN cc_start: 0.8365 (t0) cc_final: 0.7816 (t0) REVERT: O 116 LYS cc_start: 0.8740 (tptm) cc_final: 0.8280 (tmtt) REVERT: P 13 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7664 (mmmt) REVERT: R 89 LEU cc_start: 0.8642 (tp) cc_final: 0.8430 (tp) REVERT: S 62 ARG cc_start: 0.8175 (ptp90) cc_final: 0.7760 (ptp90) REVERT: S 83 ASP cc_start: 0.7942 (m-30) cc_final: 0.7272 (m-30) REVERT: T 89 LEU cc_start: 0.8551 (mm) cc_final: 0.8143 (mm) REVERT: U 40 ARG cc_start: 0.8267 (tpp80) cc_final: 0.7869 (mmm-85) outliers start: 135 outliers final: 80 residues processed: 687 average time/residue: 0.3908 time to fit residues: 416.7664 Evaluate side-chains 642 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 557 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain C residue 610 TRP Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 111 ASN Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 67 ARG Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain R residue 61 HIS Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 61 SER Chi-restraints excluded: chain U residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 220 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 252 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 265 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 94 GLN I 73 ASN I 94 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 ASN Q 80 GLN ** T 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25986 Z= 0.237 Angle : 0.745 21.421 35340 Z= 0.373 Chirality : 0.049 0.501 4278 Planarity : 0.004 0.040 4350 Dihedral : 9.222 72.236 5178 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.89 % Allowed : 15.24 % Favored : 80.88 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % 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: -2.16 (0.15), residues: 3099 helix: 0.07 (0.26), residues: 414 sheet: -1.07 (0.17), residues: 1023 loop : -2.11 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 610 HIS 0.007 0.001 HIS T 62 PHE 0.016 0.002 PHE F 382 TYR 0.026 0.002 TYR J 49 ARG 0.010 0.001 ARG M 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 646 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7731 (m-40) cc_final: 0.7388 (m110) REVERT: A 620 SER cc_start: 0.8401 (m) cc_final: 0.7734 (t) REVERT: A 624 ASP cc_start: 0.7936 (m-30) cc_final: 0.7486 (m-30) REVERT: B 624 ASP cc_start: 0.7724 (m-30) cc_final: 0.7372 (m-30) REVERT: C 585 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7928 (tpp-160) REVERT: C 592 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8189 (mm) REVERT: C 624 ASP cc_start: 0.7618 (m-30) cc_final: 0.7309 (m-30) REVERT: D 99 ASN cc_start: 0.8845 (t0) cc_final: 0.8630 (t0) REVERT: D 358 ILE cc_start: 0.7522 (mm) cc_final: 0.7320 (mt) REVERT: D 430 ILE cc_start: 0.9203 (mm) cc_final: 0.8946 (mm) REVERT: D 435 TYR cc_start: 0.8710 (m-10) cc_final: 0.8486 (m-10) REVERT: F 78 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7630 (t70) REVERT: F 435 TYR cc_start: 0.8700 (m-80) cc_final: 0.8478 (m-80) REVERT: G 32 ASN cc_start: 0.8616 (t0) cc_final: 0.8269 (t0) REVERT: G 40 GLN cc_start: 0.8535 (mt0) cc_final: 0.7924 (mt0) REVERT: G 60 SER cc_start: 0.9365 (p) cc_final: 0.9132 (p) REVERT: H 40 GLN cc_start: 0.8618 (mt0) cc_final: 0.7909 (mt0) REVERT: H 64 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8576 (mm-40) REVERT: I 32 ASN cc_start: 0.8791 (m-40) cc_final: 0.8565 (t0) REVERT: J 24 ARG cc_start: 0.8402 (tpm170) cc_final: 0.7974 (tpp-160) REVERT: J 32 ASP cc_start: 0.7841 (m-30) cc_final: 0.7545 (m-30) REVERT: J 37 GLN cc_start: 0.6578 (tt0) cc_final: 0.6191 (tt0) REVERT: J 48 ILE cc_start: 0.7619 (mm) cc_final: 0.7332 (mm) REVERT: J 90 GLN cc_start: 0.8632 (pp30) cc_final: 0.7938 (pp30) REVERT: K 12 LYS cc_start: 0.8490 (mmmt) cc_final: 0.7927 (mmmt) REVERT: K 13 LYS cc_start: 0.7895 (mmtm) cc_final: 0.7327 (mmtm) REVERT: K 19 LYS cc_start: 0.8608 (tptt) cc_final: 0.8368 (tptp) REVERT: K 86 LEU cc_start: 0.8318 (mt) cc_final: 0.7764 (mt) REVERT: K 95 PHE cc_start: 0.8678 (m-80) cc_final: 0.7956 (m-80) REVERT: K 101 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7588 (mm-30) REVERT: K 111 ASN cc_start: 0.8802 (t0) cc_final: 0.8380 (t0) REVERT: L 53 THR cc_start: 0.8743 (t) cc_final: 0.8425 (p) REVERT: L 61 ARG cc_start: 0.6227 (ptt-90) cc_final: 0.5970 (ptt-90) REVERT: L 90 GLN cc_start: 0.8393 (pp30) cc_final: 0.7783 (pp30) REVERT: M 3 GLN cc_start: 0.7150 (mp10) cc_final: 0.6649 (mp10) REVERT: M 19 LYS cc_start: 0.8399 (tppt) cc_final: 0.8026 (tptp) REVERT: M 101 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7655 (mm-30) REVERT: M 110 ASP cc_start: 0.8091 (m-30) cc_final: 0.7298 (t0) REVERT: N 61 ARG cc_start: 0.5501 (ptt90) cc_final: 0.5134 (ptt90) REVERT: N 90 GLN cc_start: 0.8597 (pp30) cc_final: 0.8379 (pp30) REVERT: O 3 GLN cc_start: 0.7078 (mp10) cc_final: 0.6822 (mp10) REVERT: O 19 LYS cc_start: 0.8719 (tptm) cc_final: 0.8322 (tptp) REVERT: O 86 LEU cc_start: 0.8137 (mt) cc_final: 0.7768 (mt) REVERT: O 101 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7171 (mm-30) REVERT: O 110 ASP cc_start: 0.8237 (m-30) cc_final: 0.7649 (t0) REVERT: O 111 ASN cc_start: 0.8484 (t0) cc_final: 0.7876 (t0) REVERT: O 116 LYS cc_start: 0.8663 (tptm) cc_final: 0.8214 (tmtt) REVERT: P 13 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7559 (mmtt) REVERT: Q 3 GLN cc_start: 0.7892 (tp40) cc_final: 0.7563 (mm-40) REVERT: Q 6 GLN cc_start: 0.7946 (tt0) cc_final: 0.7560 (tt0) REVERT: R 89 LEU cc_start: 0.8641 (tp) cc_final: 0.8428 (tp) REVERT: S 62 ARG cc_start: 0.8123 (ptp90) cc_final: 0.7635 (ptp90) REVERT: S 83 ASP cc_start: 0.8211 (m-30) cc_final: 0.7487 (m-30) REVERT: S 101 GLN cc_start: 0.7873 (mt0) cc_final: 0.7428 (mm-40) REVERT: T 38 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.8117 (m) REVERT: T 89 LEU cc_start: 0.8571 (mm) cc_final: 0.8290 (mm) REVERT: U 4 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7939 (ttm) REVERT: U 40 ARG cc_start: 0.8170 (tpp80) cc_final: 0.7836 (mmm-85) outliers start: 102 outliers final: 75 residues processed: 700 average time/residue: 0.3742 time to fit residues: 405.1627 Evaluate side-chains 671 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 592 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 647 GLU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 67 ARG Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 4 MET Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.9980 chunk 266 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 173 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 296 optimal weight: 0.4980 chunk 245 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 94 GLN I 73 ASN I 94 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN K 117 HIS ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25986 Z= 0.223 Angle : 0.722 21.983 35340 Z= 0.360 Chirality : 0.047 0.459 4278 Planarity : 0.004 0.037 4350 Dihedral : 8.699 70.444 5178 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.19 % Allowed : 16.00 % Favored : 79.81 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.97 (0.15), residues: 3099 helix: 0.38 (0.27), residues: 414 sheet: -0.92 (0.17), residues: 1014 loop : -2.04 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP K 36 HIS 0.004 0.001 HIS T 62 PHE 0.020 0.002 PHE K 114 TYR 0.033 0.002 TYR J 49 ARG 0.009 0.001 ARG M 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 635 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7776 (m-40) cc_final: 0.7476 (m110) REVERT: A 620 SER cc_start: 0.8189 (m) cc_final: 0.7799 (p) REVERT: A 624 ASP cc_start: 0.7935 (m-30) cc_final: 0.7459 (m-30) REVERT: B 528 SER cc_start: 0.9335 (p) cc_final: 0.9121 (m) REVERT: B 612 SER cc_start: 0.8972 (t) cc_final: 0.8465 (t) REVERT: C 585 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7819 (tpp-160) REVERT: C 624 ASP cc_start: 0.7604 (m-30) cc_final: 0.7241 (m-30) REVERT: D 358 ILE cc_start: 0.7494 (mm) cc_final: 0.7290 (mt) REVERT: D 430 ILE cc_start: 0.9119 (mm) cc_final: 0.8830 (mm) REVERT: E 346 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8374 (p) REVERT: F 78 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7575 (t70) REVERT: F 481 SER cc_start: 0.8260 (m) cc_final: 0.7976 (t) REVERT: G 32 ASN cc_start: 0.8575 (t0) cc_final: 0.8215 (t0) REVERT: G 40 GLN cc_start: 0.8539 (mt0) cc_final: 0.8031 (mt0) REVERT: H 40 GLN cc_start: 0.8467 (mt0) cc_final: 0.7722 (mt0) REVERT: H 64 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8569 (mm-40) REVERT: I 32 ASN cc_start: 0.8762 (m-40) cc_final: 0.8535 (t0) REVERT: I 40 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8257 (mm-40) REVERT: J 32 ASP cc_start: 0.7806 (m-30) cc_final: 0.7485 (m-30) REVERT: J 37 GLN cc_start: 0.6611 (tt0) cc_final: 0.6171 (tt0) REVERT: J 48 ILE cc_start: 0.7650 (mm) cc_final: 0.7378 (mm) REVERT: J 90 GLN cc_start: 0.8415 (pp30) cc_final: 0.7997 (pp30) REVERT: J 102 GLN cc_start: 0.7864 (mp10) cc_final: 0.7569 (mp10) REVERT: K 3 GLN cc_start: 0.7001 (mp10) cc_final: 0.6506 (pm20) REVERT: K 12 LYS cc_start: 0.8351 (mmmt) cc_final: 0.7824 (mmmt) REVERT: K 13 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7767 (mmtm) REVERT: K 19 LYS cc_start: 0.8669 (tptt) cc_final: 0.8418 (tptp) REVERT: K 67 ARG cc_start: 0.7355 (mtm110) cc_final: 0.6953 (mtm110) REVERT: K 85 ASN cc_start: 0.7247 (t0) cc_final: 0.6964 (t0) REVERT: K 86 LEU cc_start: 0.8346 (mt) cc_final: 0.7874 (mt) REVERT: K 111 ASN cc_start: 0.8814 (t0) cc_final: 0.8402 (t0) REVERT: L 61 ARG cc_start: 0.6132 (ptt-90) cc_final: 0.5805 (ptt180) REVERT: L 90 GLN cc_start: 0.8098 (pp30) cc_final: 0.7883 (pp30) REVERT: M 19 LYS cc_start: 0.8505 (tppt) cc_final: 0.8190 (tptp) REVERT: M 101 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7652 (mm-30) REVERT: M 110 ASP cc_start: 0.8133 (m-30) cc_final: 0.7289 (t0) REVERT: M 111 ASN cc_start: 0.8006 (t0) cc_final: 0.7578 (t0) REVERT: N 53 THR cc_start: 0.8780 (t) cc_final: 0.8489 (p) REVERT: O 3 GLN cc_start: 0.7158 (mp10) cc_final: 0.6921 (mp10) REVERT: O 19 LYS cc_start: 0.8682 (tptm) cc_final: 0.8216 (tptt) REVERT: O 86 LEU cc_start: 0.8142 (mt) cc_final: 0.7774 (mt) REVERT: O 101 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7143 (mm-30) REVERT: O 111 ASN cc_start: 0.8445 (t0) cc_final: 0.7794 (t0) REVERT: O 116 LYS cc_start: 0.8660 (tptm) cc_final: 0.8222 (tmtt) REVERT: P 13 LYS cc_start: 0.7883 (mmtt) cc_final: 0.7544 (mmtt) REVERT: P 121 SER cc_start: 0.8781 (t) cc_final: 0.8554 (p) REVERT: Q 62 ARG cc_start: 0.8518 (ptp90) cc_final: 0.8062 (ptp-170) REVERT: Q 80 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8488 (mm110) REVERT: S 12 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8283 (t) REVERT: S 62 ARG cc_start: 0.8107 (ptp90) cc_final: 0.7720 (ptp90) REVERT: S 83 ASP cc_start: 0.8303 (m-30) cc_final: 0.7645 (m-30) REVERT: S 101 GLN cc_start: 0.7859 (mt0) cc_final: 0.7434 (mm-40) REVERT: T 89 LEU cc_start: 0.8544 (mm) cc_final: 0.8264 (mm) REVERT: U 4 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.8004 (ttm) outliers start: 110 outliers final: 84 residues processed: 696 average time/residue: 0.3848 time to fit residues: 413.7666 Evaluate side-chains 685 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 597 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain M residue 67 ARG Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 67 ARG Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain T residue 102 THR Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 4 MET Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 61 SER Chi-restraints excluded: chain U residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 168 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 136 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 73 ASN H 94 GLN I 73 ASN I 94 GLN J 38 GLN J 89 GLN K 39 GLN ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25986 Z= 0.210 Angle : 0.721 21.102 35340 Z= 0.357 Chirality : 0.048 0.494 4278 Planarity : 0.004 0.036 4350 Dihedral : 8.344 68.793 5178 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.08 % Allowed : 16.95 % Favored : 78.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % 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: -1.82 (0.15), residues: 3099 helix: 0.56 (0.26), residues: 435 sheet: -0.70 (0.18), residues: 963 loop : -2.06 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.001 TRP K 36 HIS 0.006 0.001 HIS K 117 PHE 0.017 0.002 PHE N 71 TYR 0.033 0.002 TYR J 49 ARG 0.006 0.000 ARG S 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6198 Ramachandran restraints generated. 3099 Oldfield, 0 Emsley, 3099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 627 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.7709 (m-40) cc_final: 0.7418 (m110) REVERT: A 620 SER cc_start: 0.8158 (m) cc_final: 0.7805 (p) REVERT: A 624 ASP cc_start: 0.7927 (m-30) cc_final: 0.7466 (m-30) REVERT: B 612 SER cc_start: 0.8754 (t) cc_final: 0.8296 (t) REVERT: C 585 ARG cc_start: 0.8021 (tpp80) cc_final: 0.7772 (tpp-160) REVERT: D 95 MET cc_start: 0.8669 (ptm) cc_final: 0.8224 (ttm) REVERT: D 358 ILE cc_start: 0.7400 (mm) cc_final: 0.7185 (mt) REVERT: D 422 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: D 430 ILE cc_start: 0.9113 (mm) cc_final: 0.8828 (mm) REVERT: E 346 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8318 (p) REVERT: E 485 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8690 (mtpp) REVERT: F 481 SER cc_start: 0.8273 (m) cc_final: 0.7878 (t) REVERT: G 32 ASN cc_start: 0.8565 (t0) cc_final: 0.8192 (t0) REVERT: G 40 GLN cc_start: 0.8537 (mt0) cc_final: 0.8044 (mt0) REVERT: H 40 GLN cc_start: 0.8463 (mt0) cc_final: 0.7766 (mt0) REVERT: H 64 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8571 (mm-40) REVERT: J 24 ARG cc_start: 0.8536 (tpm170) cc_final: 0.8025 (mmm160) REVERT: J 37 GLN cc_start: 0.6557 (tt0) cc_final: 0.6333 (tt0) REVERT: J 48 ILE cc_start: 0.7626 (mm) cc_final: 0.7352 (mm) REVERT: J 86 TYR cc_start: 0.6711 (m-80) cc_final: 0.6492 (m-80) REVERT: J 90 GLN cc_start: 0.8316 (pp30) cc_final: 0.8090 (pp30) REVERT: J 102 GLN cc_start: 0.7837 (mp10) cc_final: 0.7544 (mp10) REVERT: K 3 GLN cc_start: 0.7006 (mp10) cc_final: 0.6542 (pm20) REVERT: K 12 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7818 (mmmt) REVERT: K 13 LYS cc_start: 0.8192 (mmtm) cc_final: 0.7784 (mmtm) REVERT: K 67 ARG cc_start: 0.7494 (mtm110) cc_final: 0.7175 (mtm110) REVERT: K 86 LEU cc_start: 0.8274 (mt) cc_final: 0.7833 (mt) REVERT: K 101 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6963 (mm-30) REVERT: K 111 ASN cc_start: 0.8728 (t0) cc_final: 0.8410 (t0) REVERT: L 36 TYR cc_start: 0.7705 (m-80) cc_final: 0.6889 (m-10) REVERT: L 61 ARG cc_start: 0.6186 (ptt-90) cc_final: 0.5908 (ptt180) REVERT: L 90 GLN cc_start: 0.8119 (pp30) cc_final: 0.7886 (pp30) REVERT: M 19 LYS cc_start: 0.8503 (tppt) cc_final: 0.8171 (tptp) REVERT: M 84 ARG cc_start: 0.7665 (ptt-90) cc_final: 0.7120 (ptt-90) REVERT: M 87 ARG cc_start: 0.7408 (mmp80) cc_final: 0.6921 (mtm-85) REVERT: M 101 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7517 (mm-30) REVERT: M 111 ASN cc_start: 0.7907 (t0) cc_final: 0.7406 (t0) REVERT: N 24 ARG cc_start: 0.8127 (tpp-160) cc_final: 0.7917 (mmm160) REVERT: N 53 THR cc_start: 0.8766 (t) cc_final: 0.8410 (p) REVERT: O 19 LYS cc_start: 0.8638 (tptm) cc_final: 0.8128 (tptt) REVERT: O 86 LEU cc_start: 0.8120 (mt) cc_final: 0.7745 (mt) REVERT: O 101 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7173 (mm-30) REVERT: O 111 ASN cc_start: 0.8528 (t0) cc_final: 0.7934 (t0) REVERT: O 120 GLN cc_start: 0.6924 (mp10) cc_final: 0.6597 (mp10) REVERT: P 13 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7536 (mmtt) REVERT: Q 78 ASN cc_start: 0.7798 (t0) cc_final: 0.7574 (t0) REVERT: S 3 GLN cc_start: 0.8468 (tp-100) cc_final: 0.8247 (mm-40) REVERT: S 62 ARG cc_start: 0.8117 (ptp90) cc_final: 0.7756 (ptp90) REVERT: S 83 ASP cc_start: 0.8264 (m-30) cc_final: 0.7585 (m-30) REVERT: S 101 GLN cc_start: 0.7766 (mt0) cc_final: 0.7443 (mm-40) REVERT: U 40 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7863 (mtp180) outliers start: 107 outliers final: 83 residues processed: 683 average time/residue: 0.3020 time to fit residues: 320.7150 Evaluate side-chains 674 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 588 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 601 LYS Chi-restraints excluded: chain C residue 605 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain D residue 35 TRP Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 485 LYS Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain H residue 20 GLN Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 108 ILE Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 63 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 63 HIS Chi-restraints excluded: chain O residue 67 ARG Chi-restraints excluded: chain O residue 74 LYS Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 94 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 99 CYS Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain T residue 56 LYS Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 96 VAL Chi-restraints excluded: chain U residue 2 ILE Chi-restraints excluded: chain U residue 11 LEU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 14 SER Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 61 SER Chi-restraints excluded: chain U residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 187 optimal weight: 0.2980 chunk 200 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 231 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: