Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 15:48:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm3_7516/04_2023/6cm3_7516_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm3_7516/04_2023/6cm3_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_7516/04_2023/6cm3_7516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm3_7516/04_2023/6cm3_7516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm3_7516/04_2023/6cm3_7516_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm3_7516/04_2023/6cm3_7516_neut.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 12.99, per 1000 atoms: 0.51 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: 10.95 Conformation dependent library (CDL) restraints added in 3.9 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: 1.89 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: 11.94 Time building geometry restraints manager: 11.61 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 - 14.58: 13843 14.58 - 29.17: 650 29.17 - 43.75: 180 43.75 - 58.34: 27 58.34 - 72.92: 18 Dihedral angle restraints: 14718 sinusoidal: 5637 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 14715 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 2.440 nonbonded pdb=" OG SER N 22 " pdb=" OE2 GLU N 70 " model vdw 2.045 2.440 nonbonded pdb=" OG SER J 22 " pdb=" OE2 GLU J 70 " model vdw 2.045 2.440 nonbonded pdb=" OD2 ASP A 632 " pdb=" NE1 TRP R 108 " model vdw 2.118 2.520 nonbonded pdb=" OD2 ASP B 632 " pdb=" NE1 TRP P 108 " model vdw 2.168 2.520 ... (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 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 7.680 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 67.990 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.370 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.370 ------------------------------------------------------------------------------- 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 : 9.439 72.919 8745 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 % 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 *********************** 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 : 2.815 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 outliers start: 3 outliers final: 0 residues processed: 946 average time/residue: 0.4190 time to fit residues: 590.9329 Evaluate side-chains 579 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 579 time to evaluate : 2.871 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 128 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 239 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN F 280 ASN F 293 GLN F 422 GLN G 32 ASN G 89 GLN G 94 GLN H 32 ASN H 64 GLN 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 111 ASN ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN L 89 GLN L 90 GLN ** M 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN N 89 GLN N 90 GLN O 65 GLN P 28 ASN R 62 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 25986 Z= 0.260 Angle : 0.751 15.174 35340 Z= 0.380 Chirality : 0.048 0.438 4278 Planarity : 0.004 0.042 4350 Dihedral : 5.888 27.514 3366 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer Outliers : 3.39 % 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: -2.93 (0.14), residues: 3099 helix: -1.18 (0.23), residues: 414 sheet: -1.43 (0.17), residues: 1002 loop : -2.52 (0.13), residues: 1683 *********************** 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 784 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 695 time to evaluate : 3.145 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 outliers start: 89 outliers final: 43 residues processed: 743 average time/residue: 0.3910 time to fit residues: 449.6457 Evaluate side-chains 628 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 585 time to evaluate : 2.990 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2532 time to fit residues: 23.3587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 278 optimal weight: 0.9980 chunk 300 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN B 616 ASN C 616 ASN D 103 GLN E 478 ASN F 99 ASN F 103 GLN F 293 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN I 73 ASN J 38 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 111 ASN K 117 HIS K 120 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 25986 Z= 0.305 Angle : 0.750 16.952 35340 Z= 0.375 Chirality : 0.048 0.289 4278 Planarity : 0.004 0.042 4350 Dihedral : 5.673 26.322 3366 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 3.20 % 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: -2.60 (0.15), residues: 3099 helix: -0.61 (0.25), residues: 450 sheet: -1.29 (0.17), residues: 1035 loop : -2.39 (0.14), residues: 1614 *********************** 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 726 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 642 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 38 residues processed: 681 average time/residue: 0.3805 time to fit residues: 403.2012 Evaluate side-chains 625 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 587 time to evaluate : 2.674 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2220 time to fit residues: 19.5820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.0470 chunk 209 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 295 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 543 ASN B 616 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS F 103 GLN ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN H 94 GLN I 73 ASN I 94 GLN K 39 GLN K 63 HIS K 111 ASN K 120 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN N 90 GLN ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 25986 Z= 0.251 Angle : 0.736 19.382 35340 Z= 0.368 Chirality : 0.047 0.438 4278 Planarity : 0.004 0.039 4350 Dihedral : 5.566 36.468 3366 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 2.32 % 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: -2.27 (0.15), residues: 3099 helix: -0.11 (0.26), residues: 432 sheet: -1.08 (0.17), residues: 1032 loop : -2.21 (0.14), residues: 1635 *********************** 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 695 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 634 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 26 residues processed: 666 average time/residue: 0.3767 time to fit residues: 390.8930 Evaluate side-chains 609 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 583 time to evaluate : 2.978 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2639 time to fit residues: 16.1689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 220 optimal weight: 0.0970 chunk 122 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 265 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 591 GLN B 616 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 246 GLN G 32 ASN H 32 ASN H 94 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN I 94 GLN K 111 ASN K 120 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN M 117 HIS ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 62 HIS Q 80 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 25986 Z= 0.267 Angle : 0.718 13.538 35340 Z= 0.357 Chirality : 0.047 0.388 4278 Planarity : 0.004 0.038 4350 Dihedral : 5.420 34.814 3366 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % 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: -2.04 (0.15), residues: 3099 helix: 0.33 (0.27), residues: 402 sheet: -0.94 (0.17), residues: 1011 loop : -2.09 (0.14), residues: 1686 *********************** 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 696 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 631 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 35 residues processed: 662 average time/residue: 0.4048 time to fit residues: 420.2528 Evaluate side-chains 614 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 579 time to evaluate : 2.970 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2709 time to fit residues: 21.2798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.4980 chunk 266 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 296 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN C 616 ASN ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 94 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN I 73 ASN I 94 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN K 111 ASN K 120 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 25986 Z= 0.209 Angle : 0.709 20.834 35340 Z= 0.351 Chirality : 0.047 0.403 4278 Planarity : 0.004 0.058 4350 Dihedral : 5.251 37.286 3366 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 1.33 % 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: -1.89 (0.15), residues: 3099 helix: 0.60 (0.28), residues: 402 sheet: -0.80 (0.17), residues: 999 loop : -2.06 (0.14), residues: 1698 *********************** 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 665 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 630 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 648 average time/residue: 0.3884 time to fit residues: 389.9927 Evaluate side-chains 610 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 595 time to evaluate : 2.805 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2517 time to fit residues: 10.6722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.0970 chunk 33 optimal weight: 0.0970 chunk 168 optimal weight: 0.9990 chunk 216 optimal weight: 20.0000 chunk 167 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 294 optimal weight: 0.5980 chunk 184 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 0.0970 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN F 293 GLN G 32 ASN G 94 GLN H 73 ASN H 94 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN I 73 ASN I 94 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN K 111 ASN K 120 GLN L 90 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN Q 80 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 25986 Z= 0.175 Angle : 0.708 20.501 35340 Z= 0.347 Chirality : 0.046 0.443 4278 Planarity : 0.004 0.038 4350 Dihedral : 5.123 45.237 3366 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.15), residues: 3099 helix: 0.76 (0.27), residues: 420 sheet: -0.64 (0.18), residues: 957 loop : -2.09 (0.14), residues: 1722 *********************** 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 678 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 647 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 13 residues processed: 662 average time/residue: 0.3994 time to fit residues: 414.3260 Evaluate side-chains 614 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 601 time to evaluate : 3.190 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2932 time to fit residues: 10.7982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 187 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 268 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN G 94 GLN H 64 GLN H 73 ASN H 94 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN I 73 ASN I 94 GLN J 37 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 GLN L 89 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS Q 3 GLN S 3 GLN S 80 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 25986 Z= 0.223 Angle : 0.719 13.148 35340 Z= 0.351 Chirality : 0.047 0.432 4278 Planarity : 0.004 0.041 4350 Dihedral : 5.069 40.092 3366 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 1.10 % 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: -1.72 (0.15), residues: 3099 helix: 0.82 (0.27), residues: 423 sheet: -0.73 (0.17), residues: 1008 loop : -1.97 (0.15), residues: 1668 *********************** REFINEMENT MACRO_CYCLE 8 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 639 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 610 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 622 average time/residue: 0.3931 time to fit residues: 379.2494 Evaluate side-chains 597 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 584 time to evaluate : 2.948 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2973 time to fit residues: 10.4170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 2.9990 chunk 257 optimal weight: 0.6980 chunk 274 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 215 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 543 ASN ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 HIS ** F 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN I 94 GLN J 37 GLN ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 ASN Q 80 GLN S 80 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 25986 Z= 0.220 Angle : 0.773 24.620 35340 Z= 0.377 Chirality : 0.047 0.407 4278 Planarity : 0.004 0.063 4350 Dihedral : 5.167 52.184 3366 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.70 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.68 (0.15), residues: 3099 helix: 0.65 (0.26), residues: 441 sheet: -0.64 (0.17), residues: 1023 loop : -1.97 (0.15), residues: 1635 *********************** REFINEMENT MACRO_CYCLE 9 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 624 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 602 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 611 average time/residue: 0.3890 time to fit residues: 368.6697 Evaluate side-chains 587 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 577 time to evaluate : 2.868 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2271 time to fit residues: 8.1252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.0370 chunk 177 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 187 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 616 ASN G 94 GLN H 64 GLN H 73 ASN H 94 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN I 94 GLN J 37 GLN ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 65 GLN R 36 ASN S 3 GLN T 62 HIS U 3 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 25986 Z= 0.285 Angle : 0.768 15.687 35340 Z= 0.375 Chirality : 0.048 0.392 4278 Planarity : 0.004 0.045 4350 Dihedral : 5.198 55.672 3366 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.10 % 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: -1.66 (0.15), residues: 3099 helix: 0.85 (0.27), residues: 423 sheet: -0.73 (0.17), residues: 1080 loop : -1.93 (0.15), residues: 1596 ********************** REFINEMENT MACRO_CYCLE 10 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 593 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 579 time to evaluate : 2.864 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 583 average time/residue: 0.3866 time to fit residues: 348.9213 Evaluate side-chains 571 residues out of total 2727 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 563 time to evaluate : 2.909 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2576 time to fit residues: 7.5527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 6.9990 chunk 74 optimal weight: 0.0270 chunk 223 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN C 616 ASN D 478 ASN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 GLN H 73 ASN H 94 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN I 94 GLN K 63 HIS K 117 HIS ** L 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 ASN Q 80 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097982 restraints weight = 41509.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101208 restraints weight = 22780.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102647 restraints weight = 14735.890| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 25986 Z= 0.239 Angle : 0.748 12.759 35340 Z= 0.367 Chirality : 0.047 0.352 4278 Planarity : 0.004 0.045 4350 Dihedral : 5.154 47.426 3366 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 0.50 % 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: -1.57 (0.15), residues: 3099 helix: 0.92 (0.27), residues: 423 sheet: -0.56 (0.17), residues: 1059 loop : -1.96 (0.15), residues: 1617 =============================================================================== Job complete usr+sys time: 6724.33 seconds wall clock time: 122 minutes 23.82 seconds (7343.82 seconds total)