Starting phenix.real_space_refine (version: dev) on Mon May 16 20:23:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/05_2022/6o81_0649_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/05_2022/6o81_0649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/05_2022/6o81_0649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/05_2022/6o81_0649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/05_2022/6o81_0649_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/05_2022/6o81_0649_neut_updated.pdb" } resolution = 3.21 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= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 55": "NH1" <-> "NH2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 362": "OD1" <-> "OD2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E GLU 445": "OE1" <-> "OE2" Residue "E ASP 450": "OD1" <-> "OD2" Residue "E ASP 458": "OD1" <-> "OD2" Residue "E ASP 459": "OD1" <-> "OD2" Residue "E ASP 461": "OD1" <-> "OD2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E ASP 498": "OD1" <-> "OD2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F ASP 331": "OD1" <-> "OD2" Residue "F PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 362": "OD1" <-> "OD2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 417": "NH1" <-> "NH2" Residue "F ASP 450": "OD1" <-> "OD2" Residue "F ASP 459": "OD1" <-> "OD2" Residue "F ASP 461": "OD1" <-> "OD2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 46": "NH1" <-> "NH2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G ASP 121": "OD1" <-> "OD2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 245": "OD1" <-> "OD2" Residue "G PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 299": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 46": "NH1" <-> "NH2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 108": "NH1" <-> "NH2" Residue "H ASP 121": "OD1" <-> "OD2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 245": "OD1" <-> "OD2" Residue "H PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 299": "OE1" <-> "OE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I ASP 119": "OD1" <-> "OD2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J ASP 119": "OD1" <-> "OD2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 33693 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4055 Classifications: {'peptide': 590} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 177} Link IDs: {'PTRANS': 20, 'TRANS': 567, 'PCIS': 2} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 832 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 9, 'GLU:plan': 23, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 391 Chain: "B" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4055 Classifications: {'peptide': 590} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 177} Link IDs: {'PTRANS': 20, 'TRANS': 567, 'PCIS': 2} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 832 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 9, 'GLU:plan': 23, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 391 Chain: "C" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2462 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 302, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 303, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2775 Classifications: {'peptide': 357} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 338, 'PCIS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2776 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 338, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2051 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 50, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "H" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2051 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 50, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "I" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1634 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 164 Chain: "J" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1634 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 164 Chain: "L" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1651 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 168} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 25, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 296 Chain: "M" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1651 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 168} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 25, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 296 Chain: "S" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2113 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 328} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1054 Unresolved non-hydrogen angles: 1342 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 14, 'HIS:plan': 9, 'PHE:plan': 6, 'GLU:plan': 26, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 423 Chain: "T" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2113 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 328} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1054 Unresolved non-hydrogen angles: 1342 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 14, 'HIS:plan': 9, 'PHE:plan': 6, 'GLU:plan': 26, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 423 Chain: "d" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 60 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C09AC7B C 401 " occ=0.50 ... (58 atoms not shown) pdb="CL2 BC7B C 401 " occ=0.50 Time building chain proxies: 19.28, per 1000 atoms: 0.57 Number of scatterers: 33693 At special positions: 0 Unit cell: (261.396, 189.06, 124.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 128 16.00 O 6243 8.00 N 6093 7.00 C 21225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.58 Conformation dependent library (CDL) restraints added in 5.8 seconds 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9404 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 50 sheets defined 37.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.558A pdb=" N ASP A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.607A pdb=" N VAL A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 314 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 550 through 566 Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 589 through 607 Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 614 through 627 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 629 through 635 Processing helix chain 'A' and resid 639 through 655 Processing helix chain 'A' and resid 657 through 670 removed outlier: 5.200A pdb=" N ILE A 661 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 664 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 666 " --> pdb=" O MET A 663 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 668 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE A 670 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'A' and resid 701 through 714 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.558A pdb=" N ASP B 262 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 278 removed outlier: 3.607A pdb=" N VAL B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 314 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 550 through 566 Processing helix chain 'B' and resid 571 through 585 Processing helix chain 'B' and resid 589 through 607 Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 614 through 627 Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 629 through 635 Processing helix chain 'B' and resid 639 through 655 Processing helix chain 'B' and resid 657 through 670 removed outlier: 5.199A pdb=" N ILE B 661 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 664 " --> pdb=" O ILE B 661 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 666 " --> pdb=" O MET B 663 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 668 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE B 670 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 686 Processing helix chain 'B' and resid 693 through 698 Processing helix chain 'B' and resid 701 through 714 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 77 through 97 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'C' and resid 148 through 157 removed outlier: 4.464A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 183 removed outlier: 4.518A pdb=" N ARG C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.562A pdb=" N LYS C 209 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 301 through 303 No H-bonds generated for 'chain 'C' and resid 301 through 303' Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 349 removed outlier: 3.807A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.598A pdb=" N ASP D 48 " --> pdb=" O GLN D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.517A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 Processing helix chain 'D' and resid 127 through 145 Processing helix chain 'D' and resid 147 through 157 removed outlier: 4.429A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 183 removed outlier: 4.161A pdb=" N ARG D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 219 through 226 removed outlier: 3.907A pdb=" N ILE D 222 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE D 223 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 192 through 195 removed outlier: 3.853A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 192 through 195' Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 222 through 238 Processing helix chain 'E' and resid 248 through 266 removed outlier: 4.763A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 271 through 285 Processing helix chain 'E' and resid 293 through 324 removed outlier: 5.518A pdb=" N ALA E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 352 Processing helix chain 'E' and resid 369 through 377 Processing helix chain 'E' and resid 391 through 394 No H-bonds generated for 'chain 'E' and resid 391 through 394' Processing helix chain 'E' and resid 421 through 429 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 460 through 462 No H-bonds generated for 'chain 'E' and resid 460 through 462' Processing helix chain 'E' and resid 509 through 517 Proline residue: E 513 - end of helix Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 192 through 195 Processing helix chain 'F' and resid 205 through 215 Processing helix chain 'F' and resid 222 through 238 Processing helix chain 'F' and resid 248 through 266 removed outlier: 4.665A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 271 through 285 Processing helix chain 'F' and resid 293 through 324 removed outlier: 5.462A pdb=" N ALA F 315 " --> pdb=" O LYS F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 352 Processing helix chain 'F' and resid 369 through 377 Processing helix chain 'F' and resid 391 through 394 No H-bonds generated for 'chain 'F' and resid 391 through 394' Processing helix chain 'F' and resid 421 through 429 Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 460 through 462 No H-bonds generated for 'chain 'F' and resid 460 through 462' Processing helix chain 'F' and resid 509 through 517 Proline residue: F 513 - end of helix Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 22 through 37 Processing helix chain 'G' and resid 43 through 59 WARNING: missing atoms! Processing helix chain 'G' and resid 63 through 82 Processing helix chain 'G' and resid 86 through 105 removed outlier: 4.011A pdb=" N LYS G 91 " --> pdb=" O SER G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 118 removed outlier: 3.705A pdb=" N HIS G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 161 through 169 Processing helix chain 'G' and resid 212 through 221 Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 278 through 280 No H-bonds generated for 'chain 'G' and resid 278 through 280' Processing helix chain 'G' and resid 295 through 303 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 22 through 37 Processing helix chain 'H' and resid 43 through 59 WARNING: missing atoms! Processing helix chain 'H' and resid 63 through 82 Processing helix chain 'H' and resid 86 through 105 removed outlier: 4.011A pdb=" N LYS H 91 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 118 removed outlier: 3.705A pdb=" N HIS H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 161 through 169 Processing helix chain 'H' and resid 212 through 221 Processing helix chain 'H' and resid 232 through 234 No H-bonds generated for 'chain 'H' and resid 232 through 234' Processing helix chain 'H' and resid 278 through 280 No H-bonds generated for 'chain 'H' and resid 278 through 280' Processing helix chain 'H' and resid 295 through 303 Processing helix chain 'I' and resid 35 through 45 Proline residue: I 39 - end of helix Processing helix chain 'I' and resid 63 through 69 removed outlier: 3.846A pdb=" N MET I 69 " --> pdb=" O ALA I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 Processing helix chain 'I' and resid 94 through 96 No H-bonds generated for 'chain 'I' and resid 94 through 96' Processing helix chain 'I' and resid 115 through 123 Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 209 through 217 Processing helix chain 'I' and resid 224 through 227 No H-bonds generated for 'chain 'I' and resid 224 through 227' Processing helix chain 'I' and resid 230 through 235 Processing helix chain 'I' and resid 282 through 291 removed outlier: 3.996A pdb=" N ARG I 286 " --> pdb=" O TRP I 282 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 45 Proline residue: J 39 - end of helix Processing helix chain 'J' and resid 63 through 69 removed outlier: 3.846A pdb=" N MET J 69 " --> pdb=" O ALA J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 92 Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 115 through 123 Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'J' and resid 209 through 217 Processing helix chain 'J' and resid 224 through 227 No H-bonds generated for 'chain 'J' and resid 224 through 227' Processing helix chain 'J' and resid 230 through 235 Processing helix chain 'J' and resid 282 through 291 removed outlier: 3.996A pdb=" N ARG J 286 " --> pdb=" O TRP J 282 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP J 290 " --> pdb=" O ARG J 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 60 No H-bonds generated for 'chain 'L' and resid 58 through 60' Processing helix chain 'L' and resid 91 through 118 Processing helix chain 'L' and resid 123 through 133 Processing helix chain 'L' and resid 135 through 140 Processing helix chain 'L' and resid 146 through 157 removed outlier: 3.770A pdb=" N SER L 157 " --> pdb=" O LYS L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 164 No H-bonds generated for 'chain 'L' and resid 162 through 164' Processing helix chain 'L' and resid 169 through 182 removed outlier: 4.091A pdb=" N GLU L 173 " --> pdb=" O GLU L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 216 Processing helix chain 'L' and resid 243 through 263 removed outlier: 3.842A pdb=" N SER L 248 " --> pdb=" O THR L 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 60 No H-bonds generated for 'chain 'M' and resid 58 through 60' Processing helix chain 'M' and resid 91 through 118 Processing helix chain 'M' and resid 123 through 133 Processing helix chain 'M' and resid 135 through 140 Processing helix chain 'M' and resid 146 through 157 removed outlier: 3.769A pdb=" N SER M 157 " --> pdb=" O LYS M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 164 No H-bonds generated for 'chain 'M' and resid 162 through 164' Processing helix chain 'M' and resid 169 through 182 removed outlier: 4.092A pdb=" N GLU M 173 " --> pdb=" O GLU M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 216 Processing helix chain 'M' and resid 243 through 263 removed outlier: 3.842A pdb=" N SER M 248 " --> pdb=" O THR M 244 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 61 Processing helix chain 'S' and resid 138 through 145 Processing helix chain 'S' and resid 166 through 178 Processing helix chain 'S' and resid 196 through 216 Processing helix chain 'S' and resid 229 through 242 Processing helix chain 'T' and resid 54 through 61 Processing helix chain 'T' and resid 138 through 145 Processing helix chain 'T' and resid 166 through 178 Processing helix chain 'T' and resid 196 through 216 Processing helix chain 'T' and resid 229 through 242 Processing helix chain 'd' and resid 4 through 15 Processing helix chain 'e' and resid 4 through 15 Processing sheet with id= A, first strand: chain 'A' and resid 149 through 152 removed outlier: 6.665A pdb=" N GLU A 90 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU A 47 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE A 92 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 119 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL A 93 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG A 121 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N CYS A 95 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 123 " --> pdb=" O CYS A 95 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 155 through 157 Processing sheet with id= C, first strand: chain 'A' and resid 288 through 292 Processing sheet with id= D, first strand: chain 'A' and resid 239 through 241 Processing sheet with id= E, first strand: chain 'A' and resid 335 through 337 removed outlier: 6.216A pdb=" N VAL A 360 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLY A 345 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU A 362 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 407 through 409 removed outlier: 5.721A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 411 through 413 removed outlier: 6.751A pdb=" N SER A 429 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 447 " --> pdb=" O VAL A 430 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.665A pdb=" N GLU B 90 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU B 47 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE B 92 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 119 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL B 93 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG B 121 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N CYS B 95 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 123 " --> pdb=" O CYS B 95 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 155 through 157 Processing sheet with id= J, first strand: chain 'B' and resid 288 through 292 Processing sheet with id= K, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= L, first strand: chain 'B' and resid 335 through 337 removed outlier: 6.216A pdb=" N VAL B 360 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLY B 345 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 362 " --> pdb=" O GLY B 345 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 407 through 409 removed outlier: 5.721A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 411 through 413 removed outlier: 6.752A pdb=" N SER B 429 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER B 447 " --> pdb=" O VAL B 430 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.755A pdb=" N HIS C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR C 167 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE C 190 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 231 through 234 removed outlier: 7.607A pdb=" N ILE C 234 " --> pdb=" O PRO C 264 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE C 266 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 245 through 248 Processing sheet with id= R, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.662A pdb=" N HIS D 188 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR D 167 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 190 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N THR D 215 " --> pdb=" O VAL D 191 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 232 through 234 removed outlier: 7.276A pdb=" N LEU D 323 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 245 through 248 Processing sheet with id= U, first strand: chain 'E' and resid 332 through 336 removed outlier: 6.638A pdb=" N ARG E 357 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL E 335 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL E 359 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL E 360 " --> pdb=" O PRO E 382 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER E 384 " --> pdb=" O VAL E 360 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASP E 362 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU E 386 " --> pdb=" O ASP E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 400 through 404 removed outlier: 7.876A pdb=" N LEU E 403 " --> pdb=" O PRO E 433 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 435 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU E 499 " --> pdb=" O VAL E 436 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 332 through 336 removed outlier: 6.539A pdb=" N ARG F 357 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL F 335 " --> pdb=" O ARG F 357 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL F 359 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL F 360 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER F 384 " --> pdb=" O VAL F 360 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP F 362 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU F 386 " --> pdb=" O ASP F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 401 through 404 removed outlier: 6.144A pdb=" N LEU F 499 " --> pdb=" O VAL F 436 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 289 through 291 removed outlier: 3.587A pdb=" N LEU G 283 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL G 229 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU G 192 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU G 126 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 206 through 208 removed outlier: 3.683A pdb=" N ASN G 208 " --> pdb=" O ASP G 274 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 289 through 291 removed outlier: 3.588A pdb=" N LEU H 283 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL H 229 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU H 192 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU H 126 " --> pdb=" O LEU H 192 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 206 through 208 removed outlier: 3.684A pdb=" N ASN H 208 " --> pdb=" O ASP H 274 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 75 through 78 removed outlier: 6.943A pdb=" N VAL I 51 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE I 78 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL I 53 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE I 52 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA I 5 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL I 54 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL I 7 " --> pdb=" O VAL I 54 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP I 100 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL I 6 " --> pdb=" O ASP I 100 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU I 102 " --> pdb=" O VAL I 6 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 193 through 196 removed outlier: 5.730A pdb=" N ASP I 161 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU I 167 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 75 through 78 removed outlier: 6.944A pdb=" N VAL J 51 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ILE J 78 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL J 53 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE J 52 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA J 5 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL J 54 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL J 7 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP J 100 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL J 6 " --> pdb=" O ASP J 100 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU J 102 " --> pdb=" O VAL J 6 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 193 through 196 removed outlier: 5.730A pdb=" N ASP J 161 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU J 167 " --> pdb=" O ASP J 161 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 41 through 46 removed outlier: 3.867A pdb=" N ILE L 41 " --> pdb=" O LEU L 35 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER L 34 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL L 23 " --> pdb=" O SER L 34 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP L 83 " --> pdb=" O ILE L 73 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL L 75 " --> pdb=" O TYR L 81 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR L 81 " --> pdb=" O VAL L 75 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 224 through 227 Processing sheet with id= AI, first strand: chain 'M' and resid 41 through 46 removed outlier: 3.867A pdb=" N ILE M 41 " --> pdb=" O LEU M 35 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER M 34 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL M 23 " --> pdb=" O SER M 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP M 83 " --> pdb=" O ILE M 73 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL M 75 " --> pdb=" O TYR M 81 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR M 81 " --> pdb=" O VAL M 75 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 224 through 227 Processing sheet with id= AK, first strand: chain 'S' and resid 42 through 46 removed outlier: 4.656A pdb=" N CYS S 135 " --> pdb=" O THR S 46 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL S 127 " --> pdb=" O ILE S 88 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE S 88 " --> pdb=" O VAL S 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS S 129 " --> pdb=" O ALA S 86 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA S 86 " --> pdb=" O HIS S 129 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER S 131 " --> pdb=" O ALA S 84 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ALA S 84 " --> pdb=" O SER S 131 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL S 133 " --> pdb=" O GLY S 82 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY S 82 " --> pdb=" O VAL S 133 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'S' and resid 155 through 159 Processing sheet with id= AM, first strand: chain 'S' and resid 256 through 258 Processing sheet with id= AN, first strand: chain 'S' and resid 293 through 295 removed outlier: 3.600A pdb=" N SER S 316 " --> pdb=" O ILE S 294 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'S' and resid 300 through 302 Processing sheet with id= AP, first strand: chain 'S' and resid 461 through 465 removed outlier: 4.143A pdb=" N GLU S 370 " --> pdb=" O VAL S 463 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE S 465 " --> pdb=" O PHE S 368 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE S 368 " --> pdb=" O ILE S 465 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR S 369 " --> pdb=" O LEU S 429 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA S 419 " --> pdb=" O LYS S 426 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL S 428 " --> pdb=" O VAL S 417 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL S 417 " --> pdb=" O VAL S 428 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'S' and resid 440 through 446 removed outlier: 5.654A pdb=" N ARG S 445 " --> pdb=" O LEU S 453 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU S 453 " --> pdb=" O ARG S 445 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'T' and resid 42 through 46 removed outlier: 4.655A pdb=" N CYS T 135 " --> pdb=" O THR T 46 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL T 127 " --> pdb=" O ILE T 88 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE T 88 " --> pdb=" O VAL T 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS T 129 " --> pdb=" O ALA T 86 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA T 86 " --> pdb=" O HIS T 129 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER T 131 " --> pdb=" O ALA T 84 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA T 84 " --> pdb=" O SER T 131 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL T 133 " --> pdb=" O GLY T 82 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY T 82 " --> pdb=" O VAL T 133 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'T' and resid 155 through 159 Processing sheet with id= AT, first strand: chain 'T' and resid 256 through 258 Processing sheet with id= AU, first strand: chain 'T' and resid 293 through 295 removed outlier: 3.599A pdb=" N SER T 316 " --> pdb=" O ILE T 294 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'T' and resid 300 through 302 Processing sheet with id= AW, first strand: chain 'T' and resid 461 through 465 removed outlier: 4.143A pdb=" N GLU T 370 " --> pdb=" O VAL T 463 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE T 465 " --> pdb=" O PHE T 368 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE T 368 " --> pdb=" O ILE T 465 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR T 369 " --> pdb=" O LEU T 429 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA T 419 " --> pdb=" O LYS T 426 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL T 428 " --> pdb=" O VAL T 417 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL T 417 " --> pdb=" O VAL T 428 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'T' and resid 440 through 446 removed outlier: 5.653A pdb=" N ARG T 445 " --> pdb=" O LEU T 453 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU T 453 " --> pdb=" O ARG T 445 " (cutoff:3.500A) 1410 hydrogen bonds defined for protein. 4032 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: 13.20 Time building geometry restraints manager: 14.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5769 1.31 - 1.44: 8466 1.44 - 1.56: 19758 1.56 - 1.69: 1 1.69 - 1.82: 200 Bond restraints: 34194 Sorted by residual: bond pdb=" C16AC7B C 401 " pdb=" N08AC7B C 401 " ideal model delta sigma weight residual 1.341 1.464 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C16BC7B C 401 " pdb=" N08BC7B C 401 " ideal model delta sigma weight residual 1.341 1.463 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C15AC7B C 401 " pdb=" N07AC7B C 401 " ideal model delta sigma weight residual 1.341 1.454 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C15BC7B C 401 " pdb=" N07BC7B C 401 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CD2 TRP M 135 " pdb=" CE2 TRP M 135 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.70e-02 3.46e+03 1.91e+01 ... (remaining 34189 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.49: 567 105.49 - 112.62: 18215 112.62 - 119.75: 10495 119.75 - 126.88: 17100 126.88 - 134.01: 300 Bond angle restraints: 46677 Sorted by residual: angle pdb=" CD2 TRP L 135 " pdb=" CE3 TRP L 135 " pdb=" CZ3 TRP L 135 " ideal model delta sigma weight residual 118.60 129.48 -10.88 1.30e+00 5.92e-01 7.01e+01 angle pdb=" CD2 TRP M 135 " pdb=" CE3 TRP M 135 " pdb=" CZ3 TRP M 135 " ideal model delta sigma weight residual 118.60 129.41 -10.81 1.30e+00 5.92e-01 6.92e+01 angle pdb=" CE2 TRP M 135 " pdb=" CD2 TRP M 135 " pdb=" CE3 TRP M 135 " ideal model delta sigma weight residual 118.80 124.83 -6.03 1.00e+00 1.00e+00 3.63e+01 angle pdb=" CE2 TRP L 135 " pdb=" CD2 TRP L 135 " pdb=" CE3 TRP L 135 " ideal model delta sigma weight residual 118.80 124.76 -5.96 1.00e+00 1.00e+00 3.56e+01 angle pdb=" N ILE F 388 " pdb=" CA ILE F 388 " pdb=" C ILE F 388 " ideal model delta sigma weight residual 108.88 119.48 -10.60 2.16e+00 2.14e-01 2.41e+01 ... (remaining 46672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.83: 19990 29.83 - 59.66: 332 59.66 - 89.49: 29 89.49 - 119.32: 4 119.32 - 149.15: 2 Dihedral angle restraints: 20357 sinusoidal: 5918 harmonic: 14439 Sorted by residual: dihedral pdb=" CA LYS S 421 " pdb=" C LYS S 421 " pdb=" N ALA S 422 " pdb=" CA ALA S 422 " ideal model delta harmonic sigma weight residual 180.00 151.71 28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS T 421 " pdb=" C LYS T 421 " pdb=" N ALA T 422 " pdb=" CA ALA T 422 " ideal model delta harmonic sigma weight residual 180.00 151.73 28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS E 311 " pdb=" C LYS E 311 " pdb=" N ILE E 312 " pdb=" CA ILE E 312 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 20354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 5694 1.020 - 2.040: 0 2.040 - 3.059: 0 3.059 - 4.079: 0 4.079 - 5.099: 4 Chirality restraints: 5698 Sorted by residual: chirality pdb=" C09BC7B C 401 " pdb=" C13BC7B C 401 " pdb=" C14BC7B C 401 " pdb=" N07BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.63 5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" C09AC7B C 401 " pdb=" C13AC7B C 401 " pdb=" C14AC7B C 401 " pdb=" N07AC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.61 5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" C10BC7B C 401 " pdb=" C11BC7B C 401 " pdb=" C12BC7B C 401 " pdb=" N08BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.44 4.90 2.00e-01 2.50e+01 6.01e+02 ... (remaining 5695 not shown) Planarity restraints: 6130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 395 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO F 396 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 396 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 396 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 395 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO E 396 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 396 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 396 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS S 421 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C LYS S 421 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS S 421 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA S 422 " 0.014 2.00e-02 2.50e+03 ... (remaining 6127 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9856 2.81 - 3.33: 28657 3.33 - 3.85: 56037 3.85 - 4.38: 59971 4.38 - 4.90: 106049 Nonbonded interactions: 260570 Sorted by model distance: nonbonded pdb=" OG SER A 411 " pdb=" OG SER A 429 " model vdw 2.285 2.440 nonbonded pdb=" OG SER B 411 " pdb=" OG SER B 429 " model vdw 2.286 2.440 nonbonded pdb=" O GLU H 202 " pdb=" OG SER H 297 " model vdw 2.289 2.440 nonbonded pdb=" O GLU G 202 " pdb=" OG SER G 297 " model vdw 2.290 2.440 nonbonded pdb=" OG SER B 130 " pdb=" O GLN B 267 " model vdw 2.302 2.440 ... (remaining 260565 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' } ncs_group { reference = (chain 'C' and resid 8 through 351) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 166 through 521 or (resid 522 and (name N or name CA or na \ me C or name O )))) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'd' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 128 5.16 5 Cl 4 4.86 5 C 21225 2.51 5 N 6093 2.21 5 O 6243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 29.360 Check model and map are aligned: 0.480 Convert atoms to be neutral: 0.250 Process input model: 89.600 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 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 : 0.004 0.123 34194 Z= 0.243 Angle : 0.714 17.013 46677 Z= 0.387 Chirality : 0.142 5.099 5698 Planarity : 0.006 0.080 6130 Dihedral : 11.978 149.152 10953 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.09), residues: 4881 helix: -2.63 (0.08), residues: 1898 sheet: -2.54 (0.17), residues: 746 loop : -2.70 (0.11), residues: 2237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1017 time to evaluate : 4.181 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 outliers start: 9 outliers final: 1 residues processed: 1020 average time/residue: 0.4660 time to fit residues: 751.8128 Evaluate side-chains 588 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 587 time to evaluate : 3.849 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2895 time to fit residues: 5.7781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 20.0000 chunk 372 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 251 optimal weight: 0.5980 chunk 199 optimal weight: 6.9990 chunk 385 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 446 optimal weight: 8.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN A 409 HIS ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS B 376 ASN C 158 HIS C 261 HIS C 277 GLN D 132 ASN D 138 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 261 HIS D 331 ASN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN E 274 HIS ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN F 406 HIS F 430 HIS F 475 ASN F 477 GLN G 156 GLN H 156 GLN I 41 ASN I 115 HIS I 172 ASN ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.124 34194 Z= 0.530 Angle : 0.881 23.453 46677 Z= 0.452 Chirality : 0.053 0.475 5698 Planarity : 0.007 0.117 6130 Dihedral : 6.168 169.013 5231 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 6.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.11), residues: 4881 helix: -0.67 (0.11), residues: 1921 sheet: -1.96 (0.18), residues: 707 loop : -2.30 (0.12), residues: 2253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 508 time to evaluate : 4.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 164 outliers final: 85 residues processed: 637 average time/residue: 0.4672 time to fit residues: 485.2612 Evaluate side-chains 457 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 372 time to evaluate : 3.821 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 0 residues processed: 85 average time/residue: 0.3125 time to fit residues: 55.7492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 371 optimal weight: 4.9990 chunk 304 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 447 optimal weight: 9.9990 chunk 483 optimal weight: 6.9990 chunk 398 optimal weight: 7.9990 chunk 443 optimal weight: 40.0000 chunk 152 optimal weight: 0.8980 chunk 359 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS A 337 HIS B 72 ASN C 277 GLN D 154 GLN E 234 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN L 10 HIS ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 9 GLN M 40 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.111 34194 Z= 0.211 Angle : 0.571 11.788 46677 Z= 0.290 Chirality : 0.044 0.173 5698 Planarity : 0.004 0.105 6130 Dihedral : 5.456 169.079 5231 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.04 % Favored : 95.94 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.12), residues: 4881 helix: 0.45 (0.12), residues: 1942 sheet: -1.61 (0.19), residues: 698 loop : -2.01 (0.12), residues: 2241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 410 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 35 residues processed: 463 average time/residue: 0.4471 time to fit residues: 339.2173 Evaluate side-chains 385 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 350 time to evaluate : 4.137 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3218 time to fit residues: 25.8859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 20.0000 chunk 336 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 49 optimal weight: 50.0000 chunk 213 optimal weight: 2.9990 chunk 300 optimal weight: 0.5980 chunk 449 optimal weight: 40.0000 chunk 475 optimal weight: 30.0000 chunk 234 optimal weight: 10.0000 chunk 425 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 255 GLN B 337 HIS C 150 ASN C 230 ASN C 260 HIS C 261 HIS C 277 GLN C 309 HIS D 154 GLN E 254 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.7751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 34194 Z= 0.424 Angle : 0.657 11.293 46677 Z= 0.338 Chirality : 0.047 0.230 5698 Planarity : 0.005 0.102 6130 Dihedral : 5.700 173.936 5231 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.78 % Favored : 94.18 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.12), residues: 4881 helix: 0.83 (0.12), residues: 1950 sheet: -1.65 (0.18), residues: 740 loop : -1.80 (0.13), residues: 2191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 377 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 49 residues processed: 447 average time/residue: 0.4586 time to fit residues: 335.5563 Evaluate side-chains 374 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 325 time to evaluate : 4.039 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.3016 time to fit residues: 33.7311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 7.9990 chunk 269 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 354 optimal weight: 7.9990 chunk 196 optimal weight: 0.7980 chunk 405 optimal weight: 5.9990 chunk 328 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 242 optimal weight: 0.5980 chunk 426 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN D 150 ASN D 154 GLN E 325 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 HIS ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.8004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.105 34194 Z= 0.253 Angle : 0.564 12.008 46677 Z= 0.286 Chirality : 0.044 0.165 5698 Planarity : 0.004 0.102 6130 Dihedral : 5.431 172.503 5231 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.12), residues: 4881 helix: 1.27 (0.12), residues: 1950 sheet: -1.45 (0.18), residues: 715 loop : -1.67 (0.13), residues: 2216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 375 time to evaluate : 4.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 21 residues processed: 413 average time/residue: 0.4478 time to fit residues: 300.2807 Evaluate side-chains 366 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 345 time to evaluate : 4.210 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3306 time to fit residues: 18.5353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 3.9990 chunk 428 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 chunk 279 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 476 optimal weight: 50.0000 chunk 395 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 249 optimal weight: 0.6980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 128 GLN C 277 GLN E 234 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 10 HIS ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.8597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 34194 Z= 0.359 Angle : 0.620 12.950 46677 Z= 0.314 Chirality : 0.046 0.178 5698 Planarity : 0.004 0.082 6130 Dihedral : 5.559 175.164 5231 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.57 % Favored : 94.39 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.12), residues: 4881 helix: 1.40 (0.12), residues: 1951 sheet: -1.51 (0.18), residues: 718 loop : -1.51 (0.13), residues: 2212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 364 time to evaluate : 4.254 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 25 residues processed: 405 average time/residue: 0.4541 time to fit residues: 302.9805 Evaluate side-chains 362 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 337 time to evaluate : 3.953 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2914 time to fit residues: 19.2216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 271 optimal weight: 0.6980 chunk 347 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 chunk 400 optimal weight: 6.9990 chunk 265 optimal weight: 0.7980 chunk 474 optimal weight: 30.0000 chunk 296 optimal weight: 0.7980 chunk 289 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN D 261 HIS D 331 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 HIS ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN M 40 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.8620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.126 34194 Z= 0.175 Angle : 0.549 15.337 46677 Z= 0.273 Chirality : 0.043 0.150 5698 Planarity : 0.004 0.092 6130 Dihedral : 5.279 175.339 5231 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.20 % Favored : 95.76 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 4881 helix: 1.83 (0.12), residues: 1927 sheet: -1.33 (0.19), residues: 685 loop : -1.39 (0.13), residues: 2269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 376 time to evaluate : 5.676 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 392 average time/residue: 0.4797 time to fit residues: 309.7876 Evaluate side-chains 354 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 345 time to evaluate : 3.960 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3353 time to fit residues: 10.8412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 283 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 301 optimal weight: 8.9990 chunk 323 optimal weight: 1.9990 chunk 234 optimal weight: 10.0000 chunk 44 optimal weight: 40.0000 chunk 372 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 GLN M 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.8792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.138 34194 Z= 0.252 Angle : 0.572 15.083 46677 Z= 0.285 Chirality : 0.044 0.166 5698 Planarity : 0.004 0.098 6130 Dihedral : 5.290 175.495 5231 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.00 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 4881 helix: 1.90 (0.12), residues: 1933 sheet: -1.34 (0.18), residues: 695 loop : -1.32 (0.13), residues: 2253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 346 time to evaluate : 4.179 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 363 average time/residue: 0.4552 time to fit residues: 270.6171 Evaluate side-chains 352 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 338 time to evaluate : 3.879 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2990 time to fit residues: 13.0195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 40.0000 chunk 454 optimal weight: 10.0000 chunk 414 optimal weight: 10.0000 chunk 441 optimal weight: 30.0000 chunk 265 optimal weight: 0.5980 chunk 192 optimal weight: 7.9990 chunk 346 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 399 optimal weight: 20.0000 chunk 417 optimal weight: 20.0000 chunk 440 optimal weight: 40.0000 overall best weight: 5.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN F 464 GLN ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 HIS H 213 ASN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.9527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.107 34194 Z= 0.694 Angle : 0.828 15.478 46677 Z= 0.420 Chirality : 0.052 0.227 5698 Planarity : 0.006 0.116 6130 Dihedral : 6.153 175.925 5231 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.31 % Favored : 92.64 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.12), residues: 4881 helix: 1.20 (0.12), residues: 1913 sheet: -1.45 (0.18), residues: 698 loop : -1.65 (0.13), residues: 2270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 317 time to evaluate : 3.882 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 346 average time/residue: 0.4597 time to fit residues: 258.9488 Evaluate side-chains 310 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 293 time to evaluate : 3.896 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3014 time to fit residues: 14.7676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 0.7980 chunk 467 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 324 optimal weight: 9.9990 chunk 490 optimal weight: 20.0000 chunk 451 optimal weight: 50.0000 chunk 390 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 301 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.9426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.152 34194 Z= 0.211 Angle : 0.601 16.190 46677 Z= 0.302 Chirality : 0.045 0.223 5698 Planarity : 0.004 0.132 6130 Dihedral : 5.572 179.870 5231 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.71 % Favored : 95.25 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.12), residues: 4881 helix: 1.75 (0.12), residues: 1918 sheet: -1.37 (0.18), residues: 733 loop : -1.32 (0.13), residues: 2230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 342 time to evaluate : 4.091 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 347 average time/residue: 0.4790 time to fit residues: 272.3019 Evaluate side-chains 327 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 321 time to evaluate : 4.153 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3001 time to fit residues: 8.9450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 20.0000 chunk 415 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 359 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 390 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 401 optimal weight: 7.9990 chunk 49 optimal weight: 50.0000 chunk 72 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.077931 restraints weight = 136437.215| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.88 r_work: 0.3190 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work: 0.3162 rms_B_bonded: 3.59 restraints_weight: 0.1250 r_work: 0.3148 rms_B_bonded: 3.66 restraints_weight: 0.0625 r_work: 0.3134 rms_B_bonded: 3.76 restraints_weight: 0.0312 r_work: 0.3119 rms_B_bonded: 3.91 restraints_weight: 0.0156 r_work: 0.3103 rms_B_bonded: 4.08 restraints_weight: 0.0078 r_work: 0.3087 rms_B_bonded: 4.30 restraints_weight: 0.0039 r_work: 0.3069 rms_B_bonded: 4.55 restraints_weight: 0.0020 r_work: 0.3051 rms_B_bonded: 4.84 restraints_weight: 0.0010 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.9783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.137 34194 Z= 0.592 Angle : 0.767 16.480 46677 Z= 0.387 Chirality : 0.050 0.217 5698 Planarity : 0.005 0.132 6130 Dihedral : 6.021 178.736 5231 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.48 % Favored : 92.48 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4881 helix: 1.34 (0.12), residues: 1918 sheet: -1.56 (0.18), residues: 728 loop : -1.51 (0.13), residues: 2235 =============================================================================== Job complete usr+sys time: 7786.35 seconds wall clock time: 141 minutes 15.17 seconds (8475.17 seconds total)