Starting phenix.real_space_refine on Tue Mar 19 00:30:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/03_2024/6ve3_21153.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/03_2024/6ve3_21153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/03_2024/6ve3_21153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/03_2024/6ve3_21153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/03_2024/6ve3_21153.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/03_2024/6ve3_21153.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 13328 2.51 5 N 4578 2.21 5 O 4578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22484 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "B" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "C" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "D" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "E" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "F" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "G" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "H" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "I" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "J" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "K" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "L" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "M" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Chain: "N" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Time building chain proxies: 12.52, per 1000 atoms: 0.56 Number of scatterers: 22484 At special positions: 0 Unit cell: (143.55, 143.55, 129.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 4578 8.00 N 4578 7.00 C 13328 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: 8.70 Conformation dependent library (CDL) restraints added in 5.6 seconds 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8344 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 57 sheets defined 25.4% alpha, 65.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 Processing helix chain 'A' and resid 44 through 59 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'B' and resid 12 through 27 Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'C' and resid 12 through 27 Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS C 107 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 removed outlier: 4.220A pdb=" N VAL C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG C 297 " --> pdb=" O PRO C 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 298 " --> pdb=" O TYR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 44 through 59 Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG D 297 " --> pdb=" O PRO D 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 298 " --> pdb=" O TYR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'E' and resid 12 through 27 Processing helix chain 'E' and resid 44 through 59 Processing helix chain 'E' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS E 107 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 246 Processing helix chain 'E' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU E 292 " --> pdb=" O PHE E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG E 297 " --> pdb=" O PRO E 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 298 " --> pdb=" O TYR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 325 Processing helix chain 'F' and resid 12 through 27 Processing helix chain 'F' and resid 44 through 59 Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS F 107 " --> pdb=" O ASN F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL F 136 " --> pdb=" O PRO F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'F' and resid 286 through 292 removed outlier: 3.688A pdb=" N LEU F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 299 removed outlier: 3.617A pdb=" N ARG F 297 " --> pdb=" O PRO F 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 298 " --> pdb=" O TYR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 325 Processing helix chain 'G' and resid 12 through 27 Processing helix chain 'G' and resid 44 through 59 Processing helix chain 'G' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 removed outlier: 4.217A pdb=" N VAL G 136 " --> pdb=" O PRO G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 246 Processing helix chain 'G' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU G 292 " --> pdb=" O PHE G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG G 297 " --> pdb=" O PRO G 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU G 298 " --> pdb=" O TYR G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 325 Processing helix chain 'H' and resid 12 through 27 Processing helix chain 'H' and resid 44 through 59 Processing helix chain 'H' and resid 103 through 115 removed outlier: 3.817A pdb=" N LYS H 107 " --> pdb=" O ASN H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL H 136 " --> pdb=" O PRO H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 246 Processing helix chain 'H' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU H 292 " --> pdb=" O PHE H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG H 297 " --> pdb=" O PRO H 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 298 " --> pdb=" O TYR H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 325 Processing helix chain 'I' and resid 12 through 27 Processing helix chain 'I' and resid 44 through 59 Processing helix chain 'I' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS I 107 " --> pdb=" O ASN I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL I 136 " --> pdb=" O PRO I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 246 Processing helix chain 'I' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU I 292 " --> pdb=" O PHE I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 299 removed outlier: 3.617A pdb=" N ARG I 297 " --> pdb=" O PRO I 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU I 298 " --> pdb=" O TYR I 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 325 Processing helix chain 'J' and resid 12 through 27 Processing helix chain 'J' and resid 44 through 59 Processing helix chain 'J' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS J 107 " --> pdb=" O ASN J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 246 Processing helix chain 'J' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU J 292 " --> pdb=" O PHE J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG J 297 " --> pdb=" O PRO J 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU J 298 " --> pdb=" O TYR J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 325 Processing helix chain 'K' and resid 12 through 27 Processing helix chain 'K' and resid 44 through 59 Processing helix chain 'K' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS K 107 " --> pdb=" O ASN K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL K 136 " --> pdb=" O PRO K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 246 Processing helix chain 'K' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU K 292 " --> pdb=" O PHE K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 299 removed outlier: 3.617A pdb=" N ARG K 297 " --> pdb=" O PRO K 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU K 298 " --> pdb=" O TYR K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 320 through 325 Processing helix chain 'L' and resid 12 through 27 Processing helix chain 'L' and resid 44 through 59 Processing helix chain 'L' and resid 103 through 115 removed outlier: 3.814A pdb=" N LYS L 107 " --> pdb=" O ASN L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL L 136 " --> pdb=" O PRO L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 286 through 292 removed outlier: 3.688A pdb=" N LEU L 292 " --> pdb=" O PHE L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 299 removed outlier: 3.614A pdb=" N ARG L 297 " --> pdb=" O PRO L 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU L 298 " --> pdb=" O TYR L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 325 Processing helix chain 'M' and resid 12 through 27 Processing helix chain 'M' and resid 44 through 59 Processing helix chain 'M' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS M 107 " --> pdb=" O ASN M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 142 removed outlier: 4.220A pdb=" N VAL M 136 " --> pdb=" O PRO M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 246 Processing helix chain 'M' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU M 292 " --> pdb=" O PHE M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG M 297 " --> pdb=" O PRO M 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 325 Processing helix chain 'N' and resid 12 through 27 Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS N 107 " --> pdb=" O ASN N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL N 136 " --> pdb=" O PRO N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 246 Processing helix chain 'N' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU N 292 " --> pdb=" O PHE N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG N 297 " --> pdb=" O PRO N 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU N 298 " --> pdb=" O TYR N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 320 through 325 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 152 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP A 302 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL A 84 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG A 300 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 272 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU A 315 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL A 270 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 271 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 152 Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP B 302 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL B 84 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 300 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 272 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU B 315 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL B 270 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE B 271 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 152 Processing sheet with id=AA7, first strand: chain 'C' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP C 302 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL C 84 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG C 300 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY C 272 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU C 315 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL C 270 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 271 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 166 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 152 Processing sheet with id=AA9, first strand: chain 'D' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP D 302 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL D 84 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG D 300 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY D 272 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU D 315 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL D 270 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE D 271 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU E 166 " --> pdb=" O LYS D 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 148 through 152 Processing sheet with id=AB2, first strand: chain 'E' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP E 302 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL E 84 " --> pdb=" O ARG E 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG E 300 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY E 272 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU E 315 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL E 270 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE E 271 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 166 " --> pdb=" O LYS E 285 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 148 through 152 Processing sheet with id=AB4, first strand: chain 'F' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP F 302 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL F 84 " --> pdb=" O ARG F 300 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG F 300 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY F 272 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU F 315 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL F 270 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE F 271 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 148 through 152 Processing sheet with id=AB6, first strand: chain 'G' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP G 302 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL G 84 " --> pdb=" O ARG G 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG G 300 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY G 272 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU G 315 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL G 270 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE G 271 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU H 166 " --> pdb=" O LYS G 285 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 148 through 152 Processing sheet with id=AB8, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.581A pdb=" N ASP H 302 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL H 84 " --> pdb=" O ARG H 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG H 300 " --> pdb=" O VAL H 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY H 272 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU H 315 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 270 " --> pdb=" O LEU H 315 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE H 271 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 148 through 152 Processing sheet with id=AC1, first strand: chain 'I' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP I 302 " --> pdb=" O LEU I 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL I 84 " --> pdb=" O ARG I 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG I 300 " --> pdb=" O VAL I 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY I 272 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU I 315 " --> pdb=" O VAL I 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL I 270 " --> pdb=" O LEU I 315 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE I 271 " --> pdb=" O VAL J 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 148 through 152 Processing sheet with id=AC3, first strand: chain 'J' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP J 302 " --> pdb=" O LEU J 82 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL J 84 " --> pdb=" O ARG J 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG J 300 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY J 272 " --> pdb=" O VAL J 313 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU J 315 " --> pdb=" O VAL J 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL J 270 " --> pdb=" O LEU J 315 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE J 271 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU K 166 " --> pdb=" O LYS J 285 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 148 through 152 Processing sheet with id=AC5, first strand: chain 'K' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP K 302 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL K 84 " --> pdb=" O ARG K 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG K 300 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY K 272 " --> pdb=" O VAL K 313 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU K 315 " --> pdb=" O VAL K 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL K 270 " --> pdb=" O LEU K 315 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE K 271 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU L 166 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 148 through 152 Processing sheet with id=AC7, first strand: chain 'L' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP L 302 " --> pdb=" O LEU L 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL L 84 " --> pdb=" O ARG L 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG L 300 " --> pdb=" O VAL L 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY L 272 " --> pdb=" O VAL L 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU L 315 " --> pdb=" O VAL L 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL L 270 " --> pdb=" O LEU L 315 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE L 271 " --> pdb=" O VAL M 180 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU M 166 " --> pdb=" O LYS L 285 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 148 through 152 Processing sheet with id=AC9, first strand: chain 'M' and resid 93 through 95 removed outlier: 3.584A pdb=" N ASP M 302 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL M 84 " --> pdb=" O ARG M 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG M 300 " --> pdb=" O VAL M 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY M 272 " --> pdb=" O VAL M 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU M 315 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL M 270 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE M 271 " --> pdb=" O VAL N 180 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 148 through 152 Processing sheet with id=AD2, first strand: chain 'N' and resid 93 through 95 removed outlier: 3.581A pdb=" N ASP N 302 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL N 84 " --> pdb=" O ARG N 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG N 300 " --> pdb=" O VAL N 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY N 272 " --> pdb=" O VAL N 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU N 315 " --> pdb=" O VAL N 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL N 270 " --> pdb=" O LEU N 315 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE N 271 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 166 " --> pdb=" O LYS N 285 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 117 through 119 Processing sheet with id=AD4, first strand: chain 'A' and resid 187 through 201 removed outlier: 3.869A pdb=" N ARG A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 228 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG D 228 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG E 228 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG F 228 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG G 228 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG H 228 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG I 228 " --> pdb=" O THR I 224 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG J 228 " --> pdb=" O THR J 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG K 228 " --> pdb=" O THR K 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG L 228 " --> pdb=" O THR L 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG M 228 " --> pdb=" O THR M 224 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG N 228 " --> pdb=" O THR N 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AD6, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AD7, first strand: chain 'C' and resid 2 through 7 Processing sheet with id=AD8, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AD9, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AE1, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AE2, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=AE3, first strand: chain 'E' and resid 117 through 119 Processing sheet with id=AE4, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AE5, first strand: chain 'F' and resid 117 through 119 Processing sheet with id=AE6, first strand: chain 'G' and resid 2 through 7 Processing sheet with id=AE7, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AE8, first strand: chain 'H' and resid 2 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 117 through 119 Processing sheet with id=AF1, first strand: chain 'I' and resid 2 through 7 Processing sheet with id=AF2, first strand: chain 'I' and resid 117 through 119 Processing sheet with id=AF3, first strand: chain 'J' and resid 2 through 7 Processing sheet with id=AF4, first strand: chain 'J' and resid 117 through 119 Processing sheet with id=AF5, first strand: chain 'K' and resid 2 through 7 Processing sheet with id=AF6, first strand: chain 'K' and resid 117 through 119 Processing sheet with id=AF7, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 117 through 119 Processing sheet with id=AF9, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AG1, first strand: chain 'M' and resid 117 through 119 Processing sheet with id=AG2, first strand: chain 'N' and resid 2 through 7 Processing sheet with id=AG3, first strand: chain 'N' and resid 117 through 119 2750 hydrogen bonds defined for protein. 7620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.73 Time building geometry restraints manager: 9.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 4578 1.29 - 1.35: 4550 1.35 - 1.42: 0 1.42 - 1.49: 4578 1.49 - 1.56: 8750 Bond restraints: 22456 Sorted by residual: bond pdb=" CA SER J 203 " pdb=" CB SER J 203 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.33e-02 5.65e+03 3.68e+00 bond pdb=" CA SER G 203 " pdb=" CB SER G 203 " ideal model delta sigma weight residual 1.524 1.498 0.025 1.33e-02 5.65e+03 3.57e+00 bond pdb=" CA SER C 203 " pdb=" CB SER C 203 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.33e-02 5.65e+03 3.56e+00 bond pdb=" CA SER K 203 " pdb=" CB SER K 203 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.33e-02 5.65e+03 3.52e+00 bond pdb=" C SER G 209 " pdb=" N PHE G 210 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.30e-02 5.92e+03 3.42e+00 ... (remaining 22451 not shown) Histogram of bond angle deviations from ideal: 101.35 - 106.42: 529 106.42 - 111.48: 9376 111.48 - 116.55: 5365 116.55 - 121.62: 9136 121.62 - 126.69: 6744 Bond angle restraints: 31150 Sorted by residual: angle pdb=" N SER D 203 " pdb=" CA SER D 203 " pdb=" C SER D 203 " ideal model delta sigma weight residual 108.56 118.41 -9.85 1.74e+00 3.30e-01 3.21e+01 angle pdb=" N SER F 203 " pdb=" CA SER F 203 " pdb=" C SER F 203 " ideal model delta sigma weight residual 108.56 118.40 -9.84 1.74e+00 3.30e-01 3.20e+01 angle pdb=" N SER L 203 " pdb=" CA SER L 203 " pdb=" C SER L 203 " ideal model delta sigma weight residual 108.56 118.39 -9.83 1.74e+00 3.30e-01 3.19e+01 angle pdb=" N SER H 203 " pdb=" CA SER H 203 " pdb=" C SER H 203 " ideal model delta sigma weight residual 108.56 118.39 -9.83 1.74e+00 3.30e-01 3.19e+01 angle pdb=" N SER A 203 " pdb=" CA SER A 203 " pdb=" C SER A 203 " ideal model delta sigma weight residual 108.56 118.35 -9.79 1.74e+00 3.30e-01 3.17e+01 ... (remaining 31145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.74: 9907 3.74 - 7.48: 2160 7.48 - 11.22: 589 11.22 - 14.96: 210 14.96 - 18.70: 28 Dihedral angle restraints: 12894 sinusoidal: 0 harmonic: 12894 Sorted by residual: dihedral pdb=" C SER D 203 " pdb=" N SER D 203 " pdb=" CA SER D 203 " pdb=" CB SER D 203 " ideal model delta harmonic sigma weight residual -122.60 -133.37 10.77 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C SER H 203 " pdb=" N SER H 203 " pdb=" CA SER H 203 " pdb=" CB SER H 203 " ideal model delta harmonic sigma weight residual -122.60 -133.34 10.74 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C SER J 203 " pdb=" N SER J 203 " pdb=" CA SER J 203 " pdb=" CB SER J 203 " ideal model delta harmonic sigma weight residual -122.60 -133.27 10.67 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 12891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3696 0.106 - 0.212: 448 0.212 - 0.318: 14 0.318 - 0.424: 0 0.424 - 0.530: 14 Chirality restraints: 4172 Sorted by residual: chirality pdb=" CA SER D 203 " pdb=" N SER D 203 " pdb=" C SER D 203 " pdb=" CB SER D 203 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" CA SER H 203 " pdb=" N SER H 203 " pdb=" C SER H 203 " pdb=" CB SER H 203 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CA SER F 203 " pdb=" N SER F 203 " pdb=" C SER F 203 " pdb=" CB SER F 203 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.90e+00 ... (remaining 4169 not shown) Planarity restraints: 4550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 201 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C SER A 201 " -0.077 2.00e-02 2.50e+03 pdb=" O SER A 201 " 0.029 2.00e-02 2.50e+03 pdb=" N SER A 202 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 201 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C SER C 201 " -0.077 2.00e-02 2.50e+03 pdb=" O SER C 201 " 0.029 2.00e-02 2.50e+03 pdb=" N SER C 202 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 135 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C PHE L 135 " 0.077 2.00e-02 2.50e+03 pdb=" O PHE L 135 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL L 136 " -0.026 2.00e-02 2.50e+03 ... (remaining 4547 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3707 2.77 - 3.30: 20769 3.30 - 3.83: 34554 3.83 - 4.37: 36610 4.37 - 4.90: 61221 Nonbonded interactions: 156861 Sorted by model distance: nonbonded pdb=" O SER E 203 " pdb=" N GLY F 204 " model vdw 2.233 2.520 nonbonded pdb=" O SER L 203 " pdb=" N GLY M 204 " model vdw 2.234 2.520 nonbonded pdb=" N GLY A 204 " pdb=" O SER N 203 " model vdw 2.239 2.520 nonbonded pdb=" O SER G 203 " pdb=" N GLY H 204 " model vdw 2.242 2.520 nonbonded pdb=" O SER I 203 " pdb=" N GLY J 204 " model vdw 2.264 2.520 ... (remaining 156856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.970 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 66.420 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 22456 Z= 0.380 Angle : 1.167 9.861 31150 Z= 0.742 Chirality : 0.071 0.530 4172 Planarity : 0.007 0.045 4550 Dihedral : 5.955 18.704 4550 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.41 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4522 helix: 0.88 (0.17), residues: 854 sheet: 1.02 (0.11), residues: 1946 loop : -2.32 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.389 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1946 time to fit residues: 29.0687 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 378 optimal weight: 40.0000 chunk 339 optimal weight: 5.9990 chunk 188 optimal weight: 50.0000 chunk 115 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 181 optimal weight: 30.0000 chunk 351 optimal weight: 9.9990 chunk 135 optimal weight: 50.0000 chunk 213 optimal weight: 30.0000 chunk 261 optimal weight: 20.0000 chunk 406 optimal weight: 20.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22456 Z= 0.365 Angle : 0.805 7.023 31150 Z= 0.500 Chirality : 0.055 0.146 4172 Planarity : 0.005 0.026 4550 Dihedral : 7.813 26.790 4550 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 4522 helix: 0.34 (0.17), residues: 910 sheet: 0.99 (0.10), residues: 2184 loop : -2.40 (0.14), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.523 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2316 time to fit residues: 34.6006 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 226 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 338 optimal weight: 20.0000 chunk 277 optimal weight: 40.0000 chunk 112 optimal weight: 40.0000 chunk 407 optimal weight: 50.0000 chunk 440 optimal weight: 10.0000 chunk 362 optimal weight: 8.9990 chunk 404 optimal weight: 50.0000 chunk 138 optimal weight: 8.9990 chunk 326 optimal weight: 30.0000 overall best weight: 13.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.7896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 22456 Z= 0.430 Angle : 0.839 8.197 31150 Z= 0.533 Chirality : 0.055 0.163 4172 Planarity : 0.005 0.026 4550 Dihedral : 8.697 31.665 4550 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.08 % Favored : 89.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.42 (0.12), residues: 4522 helix: -0.92 (0.16), residues: 896 sheet: 0.37 (0.11), residues: 2212 loop : -3.09 (0.13), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.537 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2086 time to fit residues: 30.7134 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 402 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 45 optimal weight: 30.0000 chunk 194 optimal weight: 4.9990 chunk 273 optimal weight: 50.0000 chunk 409 optimal weight: 50.0000 chunk 433 optimal weight: 50.0000 chunk 213 optimal weight: 40.0000 chunk 387 optimal weight: 30.0000 chunk 116 optimal weight: 30.0000 overall best weight: 10.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.8502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 22456 Z= 0.348 Angle : 0.724 7.802 31150 Z= 0.455 Chirality : 0.053 0.148 4172 Planarity : 0.004 0.020 4550 Dihedral : 8.098 32.012 4550 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.09 % 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: -1.60 (0.12), residues: 4522 helix: -0.39 (0.18), residues: 826 sheet: 0.22 (0.11), residues: 1988 loop : -3.03 (0.13), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.652 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1968 time to fit residues: 29.5342 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 360 optimal weight: 40.0000 chunk 245 optimal weight: 50.0000 chunk 6 optimal weight: 30.0000 chunk 322 optimal weight: 30.0000 chunk 178 optimal weight: 30.0000 chunk 369 optimal weight: 50.0000 chunk 299 optimal weight: 0.3980 chunk 0 optimal weight: 30.0000 chunk 221 optimal weight: 30.0000 chunk 388 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 overall best weight: 20.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.9616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 22456 Z= 0.568 Angle : 0.990 10.846 31150 Z= 0.626 Chirality : 0.054 0.157 4172 Planarity : 0.006 0.022 4550 Dihedral : 9.825 37.772 4550 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 25.52 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.64 % Favored : 85.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.67 % 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: -2.59 (0.12), residues: 4522 helix: -1.40 (0.18), residues: 728 sheet: -0.38 (0.11), residues: 1988 loop : -3.45 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.689 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1975 time to fit residues: 29.5271 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 145 optimal weight: 40.0000 chunk 389 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 254 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 433 optimal weight: 40.0000 chunk 359 optimal weight: 50.0000 chunk 200 optimal weight: 30.0000 chunk 36 optimal weight: 40.0000 chunk 143 optimal weight: 6.9990 chunk 227 optimal weight: 30.0000 overall best weight: 12.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.9733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22456 Z= 0.397 Angle : 0.783 8.162 31150 Z= 0.492 Chirality : 0.053 0.147 4172 Planarity : 0.004 0.019 4550 Dihedral : 8.703 34.267 4550 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.32 % 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: -2.67 (0.12), residues: 4522 helix: -1.13 (0.18), residues: 798 sheet: -0.54 (0.12), residues: 1918 loop : -3.49 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.901 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1806 time to fit residues: 26.5762 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 417 optimal weight: 20.0000 chunk 48 optimal weight: 50.0000 chunk 246 optimal weight: 20.0000 chunk 316 optimal weight: 30.0000 chunk 245 optimal weight: 50.0000 chunk 364 optimal weight: 30.0000 chunk 242 optimal weight: 5.9990 chunk 431 optimal weight: 7.9990 chunk 270 optimal weight: 40.0000 chunk 263 optimal weight: 50.0000 chunk 199 optimal weight: 50.0000 overall best weight: 16.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 1.0401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 22456 Z= 0.498 Angle : 0.932 9.233 31150 Z= 0.588 Chirality : 0.054 0.153 4172 Planarity : 0.005 0.020 4550 Dihedral : 9.722 39.121 4550 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.99 % Favored : 83.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.82 % Twisted General : 0.97 % 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: -3.13 (0.12), residues: 4522 helix: -1.39 (0.18), residues: 770 sheet: -1.14 (0.11), residues: 2072 loop : -3.57 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.370 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1910 time to fit residues: 28.4642 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 267 optimal weight: 20.0000 chunk 172 optimal weight: 40.0000 chunk 257 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 274 optimal weight: 20.0000 chunk 294 optimal weight: 0.5980 chunk 213 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 339 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 1.0007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 22456 Z= 0.205 Angle : 0.607 7.680 31150 Z= 0.376 Chirality : 0.053 0.144 4172 Planarity : 0.003 0.017 4550 Dihedral : 7.419 32.490 4550 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.49 (0.12), residues: 4522 helix: 0.10 (0.18), residues: 812 sheet: -0.92 (0.12), residues: 1820 loop : -3.22 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.458 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1973 time to fit residues: 29.2157 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 392 optimal weight: 50.0000 chunk 413 optimal weight: 40.0000 chunk 377 optimal weight: 0.7980 chunk 402 optimal weight: 20.0000 chunk 242 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 315 optimal weight: 50.0000 chunk 123 optimal weight: 50.0000 chunk 363 optimal weight: 50.0000 chunk 380 optimal weight: 40.0000 chunk 400 optimal weight: 20.0000 overall best weight: 11.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 1.0336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22456 Z= 0.354 Angle : 0.724 7.514 31150 Z= 0.455 Chirality : 0.053 0.145 4172 Planarity : 0.004 0.019 4550 Dihedral : 8.207 35.368 4550 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.82 % Favored : 86.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.12), residues: 4522 helix: 0.08 (0.19), residues: 798 sheet: -0.91 (0.12), residues: 1820 loop : -3.41 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.663 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1969 time to fit residues: 29.4910 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 264 optimal weight: 40.0000 chunk 425 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 295 optimal weight: 50.0000 chunk 446 optimal weight: 50.0000 chunk 410 optimal weight: 0.7980 chunk 355 optimal weight: 40.0000 chunk 36 optimal weight: 40.0000 chunk 274 optimal weight: 30.0000 chunk 217 optimal weight: 50.0000 overall best weight: 16.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 1.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 22456 Z= 0.477 Angle : 0.890 7.873 31150 Z= 0.562 Chirality : 0.054 0.158 4172 Planarity : 0.005 0.021 4550 Dihedral : 9.433 40.359 4550 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.17 % Favored : 83.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.82 % Twisted General : 1.20 % 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: -3.16 (0.12), residues: 4522 helix: -0.53 (0.19), residues: 770 sheet: -1.31 (0.11), residues: 1974 loop : -3.73 (0.13), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.814 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2122 time to fit residues: 31.9336 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 282 optimal weight: 30.0000 chunk 378 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 327 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 355 optimal weight: 40.0000 chunk 148 optimal weight: 40.0000 chunk 365 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.050410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.040421 restraints weight = 220323.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.041012 restraints weight = 172618.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.041465 restraints weight = 146215.762| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 1.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22456 Z= 0.234 Angle : 0.620 7.606 31150 Z= 0.385 Chirality : 0.053 0.139 4172 Planarity : 0.003 0.017 4550 Dihedral : 7.536 32.548 4550 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.68 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.12), residues: 4522 helix: 0.59 (0.19), residues: 812 sheet: -1.03 (0.12), residues: 1778 loop : -3.41 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.11 seconds wall clock time: 47 minutes 48.68 seconds (2868.68 seconds total)