Starting phenix.real_space_refine on Sun Dec 10 04:14:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/12_2023/7jse_22451.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/12_2023/7jse_22451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/12_2023/7jse_22451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/12_2023/7jse_22451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/12_2023/7jse_22451.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jse_22451/12_2023/7jse_22451.pdb" } resolution = 4.6 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= 0.013 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 24 5.49 5 C 6656 2.51 5 N 3232 2.21 5 O 3376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13288 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "B" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "C" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "D" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "E" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "F" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "I" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "J" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "L" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "M" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "N" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "O" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "P" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 792 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 185} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 869 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 10, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 6, 'HIS:plan': 5, 'PHE:plan': 9, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 427 Chain: "Q" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "R" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "S" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "T" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "U" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "V" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "W" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Chain: "X" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Classifications: {'DNA': 4} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 3} Time building chain proxies: 9.07, per 1000 atoms: 0.68 Number of scatterers: 13288 At special positions: 0 Unit cell: (164.135, 160.011, 130.318, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 24 15.00 O 3376 8.00 N 3232 7.00 C 6656 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: 4.81 Conformation dependent library (CDL) restraints added in 4.1 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 32 sheets defined 36.9% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 4.424A pdb=" N VAL A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 72 removed outlier: 3.540A pdb=" N LYS A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 120 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.548A pdb=" N ARG A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 4.175A pdb=" N VAL B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 72 removed outlier: 3.515A pdb=" N LYS B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.548A pdb=" N ARG B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 32 removed outlier: 4.160A pdb=" N VAL C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 Processing helix chain 'C' and resid 104 through 120 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.548A pdb=" N ARG C 185 " --> pdb=" O ASN C 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 32 removed outlier: 4.203A pdb=" N VAL D 27 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 72 removed outlier: 3.512A pdb=" N LYS D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.544A pdb=" N ARG D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 32 removed outlier: 4.353A pdb=" N VAL E 27 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 72 Processing helix chain 'E' and resid 104 through 120 Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 181 through 197 removed outlier: 3.547A pdb=" N ARG E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 32 removed outlier: 4.166A pdb=" N VAL F 27 " --> pdb=" O SER F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 72 Processing helix chain 'F' and resid 104 through 120 Processing helix chain 'F' and resid 152 through 157 Processing helix chain 'F' and resid 181 through 197 removed outlier: 3.546A pdb=" N ARG F 185 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 32 removed outlier: 4.422A pdb=" N VAL G 27 " --> pdb=" O SER G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 3.531A pdb=" N LYS G 58 " --> pdb=" O THR G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 120 Processing helix chain 'G' and resid 152 through 157 Processing helix chain 'G' and resid 181 through 197 removed outlier: 3.548A pdb=" N ARG G 185 " --> pdb=" O ASN G 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 32 removed outlier: 4.207A pdb=" N VAL H 27 " --> pdb=" O SER H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 72 removed outlier: 3.505A pdb=" N LYS H 58 " --> pdb=" O THR H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 120 Processing helix chain 'H' and resid 152 through 157 Processing helix chain 'H' and resid 181 through 197 removed outlier: 3.544A pdb=" N ARG H 185 " --> pdb=" O ASN H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 32 removed outlier: 3.986A pdb=" N VAL I 27 " --> pdb=" O SER I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 72 Processing helix chain 'I' and resid 104 through 120 Processing helix chain 'I' and resid 152 through 157 Processing helix chain 'I' and resid 181 through 197 removed outlier: 3.543A pdb=" N ARG I 185 " --> pdb=" O ASN I 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 32 removed outlier: 3.995A pdb=" N VAL J 27 " --> pdb=" O SER J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 72 Processing helix chain 'J' and resid 104 through 120 Processing helix chain 'J' and resid 152 through 157 Processing helix chain 'J' and resid 181 through 197 removed outlier: 3.545A pdb=" N ARG J 185 " --> pdb=" O ASN J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 32 removed outlier: 3.981A pdb=" N VAL K 27 " --> pdb=" O SER K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 Processing helix chain 'K' and resid 104 through 120 Processing helix chain 'K' and resid 152 through 157 Processing helix chain 'K' and resid 181 through 197 removed outlier: 3.545A pdb=" N ARG K 185 " --> pdb=" O ASN K 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 32 removed outlier: 3.828A pdb=" N VAL L 27 " --> pdb=" O SER L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 72 Processing helix chain 'L' and resid 104 through 120 Processing helix chain 'L' and resid 152 through 157 Processing helix chain 'L' and resid 181 through 197 removed outlier: 3.545A pdb=" N ARG L 185 " --> pdb=" O ASN L 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 32 removed outlier: 3.992A pdb=" N VAL M 27 " --> pdb=" O SER M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 72 Processing helix chain 'M' and resid 104 through 120 Processing helix chain 'M' and resid 152 through 157 Processing helix chain 'M' and resid 181 through 197 removed outlier: 3.546A pdb=" N ARG M 185 " --> pdb=" O ASN M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 32 removed outlier: 3.818A pdb=" N VAL N 27 " --> pdb=" O SER N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 72 Processing helix chain 'N' and resid 104 through 120 Processing helix chain 'N' and resid 152 through 157 Processing helix chain 'N' and resid 181 through 197 removed outlier: 3.547A pdb=" N ARG N 185 " --> pdb=" O ASN N 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 32 removed outlier: 3.983A pdb=" N VAL O 27 " --> pdb=" O SER O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 72 Processing helix chain 'O' and resid 104 through 120 Processing helix chain 'O' and resid 152 through 157 Processing helix chain 'O' and resid 181 through 197 removed outlier: 3.544A pdb=" N ARG O 185 " --> pdb=" O ASN O 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 32 removed outlier: 3.989A pdb=" N VAL P 27 " --> pdb=" O SER P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 72 Processing helix chain 'P' and resid 104 through 120 Processing helix chain 'P' and resid 152 through 157 Processing helix chain 'P' and resid 181 through 197 removed outlier: 3.546A pdb=" N ARG P 185 " --> pdb=" O ASN P 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.631A pdb=" N VAL A 95 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.320A pdb=" N ALA A 133 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 8 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 89 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP A 167 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.577A pdb=" N VAL B 95 " --> pdb=" O TYR B 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 132 through 134 removed outlier: 4.309A pdb=" N ALA B 133 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 8 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE B 89 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP B 167 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.579A pdb=" N VAL C 95 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 132 through 134 removed outlier: 4.313A pdb=" N ALA C 133 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 8 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE C 89 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP C 167 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.602A pdb=" N VAL D 95 " --> pdb=" O TYR D 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 132 through 134 removed outlier: 4.315A pdb=" N ALA D 133 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 8 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE D 89 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP D 167 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.648A pdb=" N VAL E 95 " --> pdb=" O TYR E 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 132 through 134 removed outlier: 4.316A pdb=" N ALA E 133 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL E 8 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 89 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP E 167 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.638A pdb=" N VAL F 95 " --> pdb=" O TYR F 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 132 through 134 removed outlier: 4.319A pdb=" N ALA F 133 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL F 8 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE F 89 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP F 167 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.656A pdb=" N VAL G 95 " --> pdb=" O TYR G 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 132 through 134 removed outlier: 4.290A pdb=" N ALA G 133 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL G 8 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE G 89 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP G 167 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.632A pdb=" N VAL H 95 " --> pdb=" O TYR H 5 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 132 through 134 removed outlier: 4.320A pdb=" N ALA H 133 " --> pdb=" O VAL H 8 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL H 8 " --> pdb=" O ALA H 133 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE H 89 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP H 167 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 94 through 96 removed outlier: 3.601A pdb=" N VAL I 95 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 132 through 134 removed outlier: 4.328A pdb=" N ALA I 133 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL I 8 " --> pdb=" O ALA I 133 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE I 89 " --> pdb=" O VAL I 11 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP I 167 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 95 through 96 removed outlier: 3.641A pdb=" N VAL J 95 " --> pdb=" O TYR J 5 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 132 through 134 removed outlier: 4.332A pdb=" N ALA J 133 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL J 8 " --> pdb=" O ALA J 133 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE J 89 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP J 167 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 94 through 96 removed outlier: 3.606A pdb=" N VAL K 95 " --> pdb=" O TYR K 5 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 132 through 134 removed outlier: 4.324A pdb=" N ALA K 133 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL K 8 " --> pdb=" O ALA K 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE K 89 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP K 167 " --> pdb=" O PHE K 82 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 95 through 96 removed outlier: 3.622A pdb=" N VAL L 95 " --> pdb=" O TYR L 5 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 132 through 134 removed outlier: 4.337A pdb=" N ALA L 133 " --> pdb=" O VAL L 8 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL L 8 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE L 89 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP L 167 " --> pdb=" O PHE L 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 94 through 96 removed outlier: 3.632A pdb=" N VAL M 95 " --> pdb=" O TYR M 5 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 132 through 134 removed outlier: 4.333A pdb=" N ALA M 133 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL M 8 " --> pdb=" O ALA M 133 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE M 89 " --> pdb=" O VAL M 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP M 167 " --> pdb=" O PHE M 82 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.667A pdb=" N VAL N 95 " --> pdb=" O TYR N 5 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 132 through 134 removed outlier: 4.324A pdb=" N ALA N 133 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL N 8 " --> pdb=" O ALA N 133 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE N 89 " --> pdb=" O VAL N 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP N 167 " --> pdb=" O PHE N 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 94 through 96 removed outlier: 3.657A pdb=" N VAL O 95 " --> pdb=" O TYR O 5 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 132 through 134 removed outlier: 4.326A pdb=" N ALA O 133 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL O 8 " --> pdb=" O ALA O 133 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE O 89 " --> pdb=" O VAL O 11 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS O 90 " --> pdb=" O GLU O 83 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP O 167 " --> pdb=" O PHE O 82 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 94 through 96 removed outlier: 3.627A pdb=" N VAL P 95 " --> pdb=" O TYR P 5 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 132 through 134 removed outlier: 4.325A pdb=" N ALA P 133 " --> pdb=" O VAL P 8 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL P 8 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE P 89 " --> pdb=" O VAL P 11 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP P 167 " --> pdb=" O PHE P 82 " (cutoff:3.500A) 1006 hydrogen bonds defined for protein. 2940 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: 4.44 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 3232 1.30 - 1.38: 3233 1.38 - 1.45: 682 1.45 - 1.53: 6132 1.53 - 1.61: 49 Bond restraints: 13328 Sorted by residual: bond pdb=" C ASN F 139 " pdb=" O ASN F 139 " ideal model delta sigma weight residual 1.227 1.236 -0.008 7.80e-03 1.64e+04 1.14e+00 bond pdb=" C3' DT Q 7 " pdb=" O3' DT Q 7 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 8.22e-01 bond pdb=" C3' DT W 7 " pdb=" O3' DT W 7 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 8.16e-01 bond pdb=" N GLY O 85 " pdb=" CA GLY O 85 " ideal model delta sigma weight residual 1.444 1.451 -0.008 9.10e-03 1.21e+04 6.94e-01 bond pdb=" N SER O 87 " pdb=" CA SER O 87 " ideal model delta sigma weight residual 1.468 1.458 0.010 1.24e-02 6.50e+03 6.62e-01 ... (remaining 13323 not shown) Histogram of bond angle deviations from ideal: 100.87 - 106.16: 130 106.16 - 111.44: 2357 111.44 - 116.73: 2472 116.73 - 122.02: 7575 122.02 - 127.31: 4282 Bond angle restraints: 16816 Sorted by residual: angle pdb=" C GLN K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 120.09 122.78 -2.69 1.25e+00 6.40e-01 4.63e+00 angle pdb=" C GLN N 50 " pdb=" N ALA N 51 " pdb=" CA ALA N 51 " ideal model delta sigma weight residual 120.09 122.77 -2.68 1.25e+00 6.40e-01 4.61e+00 angle pdb=" C GLN P 50 " pdb=" N ALA P 51 " pdb=" CA ALA P 51 " ideal model delta sigma weight residual 120.09 122.75 -2.66 1.25e+00 6.40e-01 4.55e+00 angle pdb=" C GLN O 50 " pdb=" N ALA O 51 " pdb=" CA ALA O 51 " ideal model delta sigma weight residual 120.09 122.74 -2.65 1.25e+00 6.40e-01 4.49e+00 angle pdb=" C GLN J 50 " pdb=" N ALA J 51 " pdb=" CA ALA J 51 " ideal model delta sigma weight residual 120.09 122.74 -2.65 1.25e+00 6.40e-01 4.48e+00 ... (remaining 16811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 3355 35.55 - 71.11: 77 71.11 - 106.66: 6 106.66 - 142.21: 0 142.21 - 177.77: 2 Dihedral angle restraints: 3440 sinusoidal: 288 harmonic: 3152 Sorted by residual: dihedral pdb=" C4' DT W 7 " pdb=" C3' DT W 7 " pdb=" O3' DT W 7 " pdb=" P DT W 8 " ideal model delta sinusoidal sigma weight residual 220.00 42.23 177.77 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT Q 7 " pdb=" C3' DT Q 7 " pdb=" O3' DT Q 7 " pdb=" P DT Q 8 " ideal model delta sinusoidal sigma weight residual 220.00 43.53 176.47 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT U 7 " pdb=" C3' DT U 7 " pdb=" O3' DT U 7 " pdb=" P DT U 8 " ideal model delta sinusoidal sigma weight residual 220.00 147.58 72.42 1 3.50e+01 8.16e-04 5.47e+00 ... (remaining 3437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 100 0.020 - 0.041: 17 0.041 - 0.061: 1 0.061 - 0.081: 0 0.081 - 0.102: 2 Chirality restraints: 120 Sorted by residual: chirality pdb=" P DT Q 8 " pdb=" OP1 DT Q 8 " pdb=" OP2 DT Q 8 " pdb=" O5' DT Q 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.45 -0.10 2.00e-01 2.50e+01 2.58e-01 chirality pdb=" P DT W 8 " pdb=" OP1 DT W 8 " pdb=" OP2 DT W 8 " pdb=" O5' DT W 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.44 -0.09 2.00e-01 2.50e+01 2.06e-01 chirality pdb=" P DT U 8 " pdb=" OP1 DT U 8 " pdb=" OP2 DT U 8 " pdb=" O5' DT U 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.40 -0.06 2.00e-01 2.50e+01 8.75e-02 ... (remaining 117 not shown) Planarity restraints: 3184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 55 " 0.003 2.00e-02 2.50e+03 5.91e-03 3.49e-01 pdb=" C VAL A 55 " -0.010 2.00e-02 2.50e+03 pdb=" O VAL A 55 " 0.004 2.00e-02 2.50e+03 pdb=" N ALA A 56 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 55 " -0.003 2.00e-02 2.50e+03 5.78e-03 3.34e-01 pdb=" C VAL C 55 " 0.010 2.00e-02 2.50e+03 pdb=" O VAL C 55 " -0.004 2.00e-02 2.50e+03 pdb=" N ALA C 56 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 55 " -0.003 2.00e-02 2.50e+03 5.77e-03 3.33e-01 pdb=" C VAL L 55 " 0.010 2.00e-02 2.50e+03 pdb=" O VAL L 55 " -0.004 2.00e-02 2.50e+03 pdb=" N ALA L 56 " -0.003 2.00e-02 2.50e+03 ... (remaining 3181 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 6225 2.92 - 3.42: 8329 3.42 - 3.91: 16139 3.91 - 4.40: 12957 4.40 - 4.90: 24162 Nonbonded interactions: 67812 Sorted by model distance: nonbonded pdb=" N LYS O 84 " pdb=" O GLU O 164 " model vdw 2.425 2.520 nonbonded pdb=" N LYS G 84 " pdb=" O GLU G 164 " model vdw 2.489 2.520 nonbonded pdb=" N LYS J 84 " pdb=" O GLU J 164 " model vdw 2.490 2.520 nonbonded pdb=" N LYS N 84 " pdb=" O GLU N 164 " model vdw 2.494 2.520 nonbonded pdb=" N LYS H 84 " pdb=" O GLU H 164 " model vdw 2.498 2.520 ... (remaining 67807 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' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.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' selection = chain 'O' selection = chain 'P' } pdb_interpretation.ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. 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: 3.080 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: 0.010 Extract box with map and model: 13.700 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 41.740 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.150 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: 0.000 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: 63.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4958 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 : 0.001 0.027 13328 Z= 0.101 Angle : 0.381 3.756 16816 Z= 0.240 Chirality : 0.019 0.102 120 Planarity : 0.001 0.006 3184 Dihedral : 10.507 177.766 3440 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.35 % Favored : 88.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.68 (0.14), residues: 3136 helix: -0.12 (0.15), residues: 1248 sheet: -2.34 (0.23), residues: 496 loop : -3.19 (0.12), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.104 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0231 time to fit residues: 0.3112 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1343 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0040 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 50.0000 chunk 230 optimal weight: 20.0000 chunk 127 optimal weight: 50.0000 chunk 78 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 123 optimal weight: 50.0000 chunk 238 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 144 optimal weight: 30.0000 chunk 177 optimal weight: 30.0000 chunk 276 optimal weight: 30.0000 overall best weight: 19.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 1.0448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 13328 Z= 0.468 Angle : 0.991 9.530 16816 Z= 0.628 Chirality : 0.048 0.109 120 Planarity : 0.005 0.015 3184 Dihedral : 13.877 174.910 3440 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.96 (0.15), residues: 3136 helix: 1.16 (0.15), residues: 1264 sheet: -2.74 (0.20), residues: 480 loop : -1.52 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.100 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0107 time to fit residues: 0.2491 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1320 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0043 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 40.0000 chunk 85 optimal weight: 50.0000 chunk 229 optimal weight: 30.0000 chunk 187 optimal weight: 20.0000 chunk 76 optimal weight: 50.0000 chunk 276 optimal weight: 30.0000 chunk 298 optimal weight: 50.0000 chunk 246 optimal weight: 40.0000 chunk 274 optimal weight: 40.0000 chunk 94 optimal weight: 50.0000 chunk 221 optimal weight: 4.9990 overall best weight: 24.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 1.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 13328 Z= 0.534 Angle : 1.010 7.161 16816 Z= 0.640 Chirality : 0.055 0.113 120 Planarity : 0.006 0.016 3184 Dihedral : 14.773 179.529 3440 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -1.10 (0.15), residues: 3136 helix: 1.14 (0.14), residues: 1168 sheet: -2.51 (0.24), residues: 432 loop : -1.70 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0099 time to fit residues: 0.2292 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1234 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0042 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 40.0000 chunk 207 optimal weight: 30.0000 chunk 143 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 chunk 131 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 293 optimal weight: 50.0000 chunk 145 optimal weight: 9.9990 chunk 263 optimal weight: 40.0000 chunk 79 optimal weight: 50.0000 overall best weight: 19.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 1.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13328 Z= 0.431 Angle : 0.802 5.690 16816 Z= 0.512 Chirality : 0.060 0.134 120 Planarity : 0.004 0.011 3184 Dihedral : 14.635 178.814 3440 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -0.81 (0.15), residues: 3136 helix: 1.33 (0.15), residues: 1168 sheet: -2.39 (0.24), residues: 432 loop : -1.47 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.109 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0107 time to fit residues: 0.2568 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1404 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0045 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 20.0000 chunk 166 optimal weight: 11.9990 chunk 4 optimal weight: 40.0000 chunk 218 optimal weight: 40.0000 chunk 121 optimal weight: 20.0000 chunk 250 optimal weight: 40.0000 chunk 203 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 150 optimal weight: 30.0000 chunk 263 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 overall best weight: 22.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 1.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 13328 Z= 0.492 Angle : 0.907 5.538 16816 Z= 0.576 Chirality : 0.070 0.147 120 Planarity : 0.005 0.013 3184 Dihedral : 14.876 164.405 3440 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -1.71 (0.14), residues: 3136 helix: 0.92 (0.15), residues: 1136 sheet: -2.94 (0.24), residues: 432 loop : -2.22 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0103 time to fit residues: 0.2372 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.101 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1260 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0039 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 8.9990 chunk 264 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 172 optimal weight: 30.0000 chunk 72 optimal weight: 0.9980 chunk 294 optimal weight: 50.0000 chunk 244 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 24 optimal weight: 0.1980 chunk 97 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 overall best weight: 7.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 1.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13328 Z= 0.204 Angle : 0.529 3.714 16816 Z= 0.329 Chirality : 0.058 0.136 120 Planarity : 0.002 0.007 3184 Dihedral : 13.840 174.222 3440 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.70 (0.15), residues: 3136 helix: 2.76 (0.16), residues: 1040 sheet: -3.17 (0.25), residues: 336 loop : -2.05 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0102 time to fit residues: 0.2300 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1229 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0038 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 30.0000 chunk 33 optimal weight: 40.0000 chunk 167 optimal weight: 20.0000 chunk 214 optimal weight: 20.0000 chunk 166 optimal weight: 30.0000 chunk 247 optimal weight: 40.0000 chunk 164 optimal weight: 6.9990 chunk 293 optimal weight: 50.0000 chunk 183 optimal weight: 20.0000 chunk 178 optimal weight: 40.0000 chunk 135 optimal weight: 20.0000 overall best weight: 17.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 1.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13328 Z= 0.386 Angle : 0.733 4.881 16816 Z= 0.463 Chirality : 0.077 0.155 120 Planarity : 0.003 0.010 3184 Dihedral : 14.411 177.714 3440 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.00 (0.15), residues: 3136 helix: 1.56 (0.15), residues: 1152 sheet: -2.71 (0.24), residues: 416 loop : -1.85 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.108 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0106 time to fit residues: 0.2533 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.106 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1370 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0044 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 30.0000 chunk 117 optimal weight: 9.9990 chunk 174 optimal weight: 40.0000 chunk 88 optimal weight: 20.0000 chunk 57 optimal weight: 40.0000 chunk 56 optimal weight: 40.0000 chunk 186 optimal weight: 30.0000 chunk 199 optimal weight: 40.0000 chunk 144 optimal weight: 20.0000 chunk 27 optimal weight: 50.0000 chunk 230 optimal weight: 20.0000 overall best weight: 19.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 1.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13328 Z= 0.415 Angle : 0.769 4.419 16816 Z= 0.495 Chirality : 0.076 0.180 120 Planarity : 0.004 0.011 3184 Dihedral : 14.208 169.594 3440 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.79 (0.15), residues: 3136 helix: 1.52 (0.16), residues: 1056 sheet: -3.65 (0.21), residues: 320 loop : -2.57 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.113 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0124 time to fit residues: 0.2630 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1225 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0040 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 40.0000 chunk 280 optimal weight: 30.0000 chunk 256 optimal weight: 50.0000 chunk 273 optimal weight: 50.0000 chunk 164 optimal weight: 20.0000 chunk 118 optimal weight: 40.0000 chunk 214 optimal weight: 40.0000 chunk 83 optimal weight: 40.0000 chunk 246 optimal weight: 30.0000 chunk 258 optimal weight: 20.0000 chunk 272 optimal weight: 30.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 1.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 13328 Z= 0.526 Angle : 0.898 5.089 16816 Z= 0.576 Chirality : 0.088 0.180 120 Planarity : 0.005 0.014 3184 Dihedral : 14.797 173.112 3440 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.86 % Favored : 82.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.48 (0.15), residues: 3136 helix: 0.84 (0.15), residues: 1040 sheet: -3.44 (0.23), residues: 416 loop : -2.92 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.130 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0130 time to fit residues: 0.2996 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.122 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1577 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0048 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 50.0000 chunk 288 optimal weight: 30.0000 chunk 176 optimal weight: 30.0000 chunk 136 optimal weight: 50.0000 chunk 200 optimal weight: 30.0000 chunk 302 optimal weight: 1.9990 chunk 278 optimal weight: 20.0000 chunk 241 optimal weight: 40.0000 chunk 25 optimal weight: 30.0000 chunk 186 optimal weight: 20.0000 chunk 147 optimal weight: 30.0000 overall best weight: 20.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 1.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13328 Z= 0.415 Angle : 0.780 4.488 16816 Z= 0.497 Chirality : 0.080 0.185 120 Planarity : 0.004 0.012 3184 Dihedral : 14.499 166.661 3440 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.35 % Favored : 82.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.47 (0.15), residues: 3136 helix: 0.93 (0.15), residues: 1040 sheet: -3.60 (0.24), residues: 416 loop : -2.93 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.113 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0114 time to fit residues: 0.2722 Evaluate side-chains 5 residues out of total 178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1393 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0046 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 40.0000 chunk 256 optimal weight: 50.0000 chunk 73 optimal weight: 20.0000 chunk 222 optimal weight: 40.0000 chunk 35 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 241 optimal weight: 40.0000 chunk 101 optimal weight: 30.0000 chunk 248 optimal weight: 40.0000 chunk 30 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 overall best weight: 24.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.029018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2242 r_free = 0.2242 target = 0.024104 restraints weight = 11841.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.024643 restraints weight = 8221.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2283 r_free = 0.2283 target = 0.025004 restraints weight = 6163.213| |-----------------------------------------------------------------------------| r_work (final): 0.2071 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.056303 restraints weight = 977.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.057786 restraints weight = 366.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.058392 restraints weight = 191.694| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 1.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13328 Z= 0.484 Angle : 0.892 5.011 16816 Z= 0.565 Chirality : 0.090 0.201 120 Planarity : 0.005 0.014 3184 Dihedral : 14.856 167.269 3440 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.41 % Favored : 79.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -3.21 (0.14), residues: 3136 helix: 0.17 (0.14), residues: 1040 sheet: -3.95 (0.22), residues: 416 loop : -3.30 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.77 seconds wall clock time: 45 minutes 37.37 seconds (2737.37 seconds total)