Starting phenix.real_space_refine on Sun Apr 14 10:43:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb0_36139/04_2024/8jb0_36139_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb0_36139/04_2024/8jb0_36139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb0_36139/04_2024/8jb0_36139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb0_36139/04_2024/8jb0_36139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb0_36139/04_2024/8jb0_36139_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb0_36139/04_2024/8jb0_36139_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Fe 36 7.16 5 S 96 5.16 5 C 19773 2.51 5 N 5397 2.21 5 O 6085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 121": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "R GLU 142": "OE1" <-> "OE2" Residue "S GLU 96": "OE1" <-> "OE2" Residue "S GLU 135": "OE1" <-> "OE2" Residue "S GLU 142": "OE1" <-> "OE2" Residue "T GLU 135": "OE1" <-> "OE2" Residue "T GLU 155": "OE1" <-> "OE2" Residue "V GLU 155": "OE1" <-> "OE2" Residue "X GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31387 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1316 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1293 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1305 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1299 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1310 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1305 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1296 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "X" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.38, per 1000 atoms: 0.49 Number of scatterers: 31387 At special positions: 0 Unit cell: (130.416, 131.274, 130.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 36 26.01 S 96 16.00 O 6085 8.00 N 5397 7.00 C 19773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.17 Conformation dependent library (CDL) restraints added in 5.8 seconds 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 0 sheets defined 76.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 Processing helix chain 'A' and resid 39 through 64 Processing helix chain 'A' and resid 83 through 110 Processing helix chain 'A' and resid 115 through 144 Processing helix chain 'A' and resid 146 through 153 removed outlier: 4.114A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 35 Processing helix chain 'B' and resid 38 through 65 Processing helix chain 'B' and resid 83 through 110 Processing helix chain 'B' and resid 115 through 144 Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'C' and resid 5 through 34 Processing helix chain 'C' and resid 39 through 65 removed outlier: 3.812A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 109 Processing helix chain 'C' and resid 115 through 144 Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.776A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 35 Processing helix chain 'D' and resid 38 through 64 Processing helix chain 'D' and resid 83 through 111 removed outlier: 3.885A pdb=" N LYS D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 144 Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'F' and resid 5 through 35 Processing helix chain 'F' and resid 39 through 64 Processing helix chain 'F' and resid 83 through 109 Processing helix chain 'F' and resid 115 through 144 Processing helix chain 'F' and resid 146 through 152 removed outlier: 3.905A pdb=" N THR F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 Processing helix chain 'E' and resid 38 through 64 Processing helix chain 'E' and resid 83 through 111 removed outlier: 3.954A pdb=" N LYS E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 144 Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'G' and resid 5 through 34 Processing helix chain 'G' and resid 39 through 64 Processing helix chain 'G' and resid 83 through 110 Processing helix chain 'G' and resid 115 through 144 Processing helix chain 'G' and resid 146 through 152 removed outlier: 4.059A pdb=" N THR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 35 Processing helix chain 'H' and resid 39 through 65 removed outlier: 3.584A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 111 removed outlier: 3.710A pdb=" N LYS H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 144 Processing helix chain 'H' and resid 146 through 153 Processing helix chain 'I' and resid 5 through 35 Processing helix chain 'I' and resid 38 through 64 Processing helix chain 'I' and resid 83 through 111 removed outlier: 4.072A pdb=" N LYS I 111 " --> pdb=" O VAL I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 144 Processing helix chain 'I' and resid 146 through 152 Processing helix chain 'J' and resid 5 through 34 Processing helix chain 'J' and resid 38 through 64 Processing helix chain 'J' and resid 83 through 111 removed outlier: 3.774A pdb=" N LYS J 111 " --> pdb=" O VAL J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 144 Processing helix chain 'J' and resid 146 through 153 removed outlier: 3.613A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL J 153 " --> pdb=" O TYR J 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 35 removed outlier: 3.589A pdb=" N LYS K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 65 removed outlier: 3.573A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 110 Processing helix chain 'K' and resid 115 through 144 Processing helix chain 'K' and resid 146 through 153 removed outlier: 3.795A pdb=" N VAL K 153 " --> pdb=" O TYR K 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 35 Processing helix chain 'L' and resid 38 through 64 Processing helix chain 'L' and resid 83 through 111 Processing helix chain 'L' and resid 115 through 144 Processing helix chain 'L' and resid 146 through 153 removed outlier: 3.929A pdb=" N THR L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL L 153 " --> pdb=" O TYR L 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 35 Processing helix chain 'M' and resid 38 through 64 Processing helix chain 'M' and resid 83 through 109 Processing helix chain 'M' and resid 115 through 144 Processing helix chain 'M' and resid 147 through 152 removed outlier: 3.853A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 35 Processing helix chain 'N' and resid 38 through 64 Processing helix chain 'N' and resid 83 through 111 removed outlier: 3.550A pdb=" N LYS N 111 " --> pdb=" O VAL N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 144 Processing helix chain 'N' and resid 146 through 152 removed outlier: 4.341A pdb=" N THR N 152 " --> pdb=" O LEU N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 35 Processing helix chain 'O' and resid 38 through 64 Processing helix chain 'O' and resid 83 through 111 removed outlier: 3.714A pdb=" N LYS O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 144 Processing helix chain 'O' and resid 146 through 153 Processing helix chain 'P' and resid 5 through 35 removed outlier: 3.756A pdb=" N LYS P 35 " --> pdb=" O LEU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 64 Processing helix chain 'P' and resid 83 through 110 Processing helix chain 'P' and resid 115 through 144 Processing helix chain 'P' and resid 146 through 153 Processing helix chain 'Q' and resid 5 through 35 Processing helix chain 'Q' and resid 38 through 64 Processing helix chain 'Q' and resid 83 through 111 removed outlier: 4.167A pdb=" N ALA Q 110 " --> pdb=" O GLU Q 106 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS Q 111 " --> pdb=" O VAL Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 144 Processing helix chain 'Q' and resid 146 through 152 removed outlier: 3.675A pdb=" N THR Q 152 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 35 Processing helix chain 'R' and resid 38 through 64 Processing helix chain 'R' and resid 83 through 110 Processing helix chain 'R' and resid 115 through 144 Processing helix chain 'R' and resid 146 through 152 removed outlier: 3.719A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 35 Processing helix chain 'S' and resid 38 through 65 removed outlier: 3.546A pdb=" N LEU S 65 " --> pdb=" O ARG S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 111 removed outlier: 4.165A pdb=" N ALA S 110 " --> pdb=" O GLU S 106 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS S 111 " --> pdb=" O VAL S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 144 Processing helix chain 'S' and resid 146 through 152 removed outlier: 3.655A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 35 Processing helix chain 'T' and resid 38 through 64 Processing helix chain 'T' and resid 83 through 110 Processing helix chain 'T' and resid 115 through 144 Processing helix chain 'T' and resid 146 through 151 Processing helix chain 'U' and resid 5 through 35 Processing helix chain 'U' and resid 39 through 65 removed outlier: 3.563A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 111 removed outlier: 3.929A pdb=" N LYS U 111 " --> pdb=" O VAL U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 115 through 144 Processing helix chain 'U' and resid 147 through 153 removed outlier: 3.706A pdb=" N VAL U 153 " --> pdb=" O TYR U 149 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 35 Processing helix chain 'V' and resid 38 through 64 Processing helix chain 'V' and resid 83 through 111 removed outlier: 3.781A pdb=" N LYS V 111 " --> pdb=" O VAL V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 115 through 144 Processing helix chain 'V' and resid 146 through 152 Processing helix chain 'W' and resid 5 through 35 Processing helix chain 'W' and resid 38 through 64 Processing helix chain 'W' and resid 83 through 111 removed outlier: 3.813A pdb=" N LYS W 111 " --> pdb=" O VAL W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 144 Processing helix chain 'W' and resid 146 through 153 removed outlier: 3.725A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL W 153 " --> pdb=" O TYR W 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 35 Processing helix chain 'X' and resid 38 through 65 Processing helix chain 'X' and resid 83 through 110 Processing helix chain 'X' and resid 115 through 144 Processing helix chain 'X' and resid 146 through 153 removed outlier: 3.526A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL X 153 " --> pdb=" O TYR X 149 " (cutoff:3.500A) 2446 hydrogen bonds defined for protein. 7338 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: 10.44 Time building geometry restraints manager: 14.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8003 1.33 - 1.45: 5808 1.45 - 1.57: 17864 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 31867 Sorted by residual: bond pdb=" C GLN W 158 " pdb=" O GLN W 158 " ideal model delta sigma weight residual 1.235 1.244 -0.009 4.70e-03 4.53e+04 4.08e+00 bond pdb=" CA ALA I 110 " pdb=" C ALA I 110 " ideal model delta sigma weight residual 1.522 1.554 -0.032 1.72e-02 3.38e+03 3.54e+00 bond pdb=" CD GLU H 121 " pdb=" OE1 GLU H 121 " ideal model delta sigma weight residual 1.249 1.214 0.035 1.90e-02 2.77e+03 3.47e+00 bond pdb=" CG LEU Q 27 " pdb=" CD1 LEU Q 27 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.22e+00 bond pdb=" CG GLU E 121 " pdb=" CD GLU E 121 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.73e+00 ... (remaining 31862 not shown) Histogram of bond angle deviations from ideal: 96.28 - 103.83: 240 103.83 - 111.37: 13916 111.37 - 118.92: 12433 118.92 - 126.47: 16159 126.47 - 134.01: 323 Bond angle restraints: 43071 Sorted by residual: angle pdb=" C VAL F 107 " pdb=" N MET F 108 " pdb=" CA MET F 108 " ideal model delta sigma weight residual 122.26 113.86 8.40 1.73e+00 3.34e-01 2.36e+01 angle pdb=" C VAL N 153 " pdb=" N ILE N 154 " pdb=" CA ILE N 154 " ideal model delta sigma weight residual 121.97 130.37 -8.40 1.80e+00 3.09e-01 2.18e+01 angle pdb=" N GLU D 121 " pdb=" CA GLU D 121 " pdb=" CB GLU D 121 " ideal model delta sigma weight residual 110.28 117.10 -6.82 1.55e+00 4.16e-01 1.94e+01 angle pdb=" N GLU E 121 " pdb=" CA GLU E 121 " pdb=" CB GLU E 121 " ideal model delta sigma weight residual 110.28 117.05 -6.77 1.55e+00 4.16e-01 1.91e+01 angle pdb=" N GLU H 121 " pdb=" CA GLU H 121 " pdb=" CB GLU H 121 " ideal model delta sigma weight residual 110.28 116.70 -6.42 1.55e+00 4.16e-01 1.71e+01 ... (remaining 43066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17017 17.93 - 35.85: 1869 35.85 - 53.78: 315 53.78 - 71.70: 67 71.70 - 89.63: 74 Dihedral angle restraints: 19342 sinusoidal: 7967 harmonic: 11375 Sorted by residual: dihedral pdb=" CA TRP X 37 " pdb=" C TRP X 37 " pdb=" N THR X 38 " pdb=" CA THR X 38 " ideal model delta harmonic sigma weight residual -180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LYS L 111 " pdb=" C LYS L 111 " pdb=" N HIS L 112 " pdb=" CA HIS L 112 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ASP A 113 " pdb=" C ASP A 113 " pdb=" N ILE A 114 " pdb=" CA ILE A 114 " ideal model delta harmonic sigma weight residual -180.00 -161.04 -18.96 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 19339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3801 0.040 - 0.079: 855 0.079 - 0.119: 205 0.119 - 0.159: 30 0.159 - 0.199: 4 Chirality restraints: 4895 Sorted by residual: chirality pdb=" CA GLN N 88 " pdb=" N GLN N 88 " pdb=" C GLN N 88 " pdb=" CB GLN N 88 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CA PHE H 120 " pdb=" N PHE H 120 " pdb=" C PHE H 120 " pdb=" CB PHE H 120 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA GLU H 121 " pdb=" N GLU H 121 " pdb=" C GLU H 121 " pdb=" CB GLU H 121 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 4892 not shown) Planarity restraints: 5626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA O 21 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C ALA O 21 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA O 21 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE O 22 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 66 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" CG ASP B 66 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP B 66 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 66 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 153 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C VAL N 153 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL N 153 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE N 154 " -0.012 2.00e-02 2.50e+03 ... (remaining 5623 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2904 2.74 - 3.28: 34448 3.28 - 3.82: 54653 3.82 - 4.36: 58198 4.36 - 4.90: 99808 Nonbonded interactions: 250011 Sorted by model distance: nonbonded pdb=" OE1 GLN F 137 " pdb=" OH TYR F 149 " model vdw 2.196 2.440 nonbonded pdb=" O ARG V 109 " pdb=" NE ARG V 109 " model vdw 2.199 2.520 nonbonded pdb=" O HIS F 28 " pdb=" NE2 GLN F 32 " model vdw 2.203 2.520 nonbonded pdb=" OE1 GLN C 156 " pdb=" OG1 THR F 152 " model vdw 2.211 2.440 nonbonded pdb=" OD2 ASP B 113 " pdb=" OG SER B 116 " model vdw 2.217 2.440 ... (remaining 250006 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' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 157)) selection = (chain 'C' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'E' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'F' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'G' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'H' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'I' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'J' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'K' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'L' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'M' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'N' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'O' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'Q' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'R' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'S' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'T' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'U' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'V' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'W' and (resid 1 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 157)) selection = (chain 'X' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) } 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: 0.720 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: 0.050 Extract box with map and model: 5.570 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 81.000 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.130 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.003 0.059 31867 Z= 0.226 Angle : 0.624 9.009 43071 Z= 0.355 Chirality : 0.037 0.199 4895 Planarity : 0.003 0.051 5626 Dihedral : 16.006 89.630 11920 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.81 % Favored : 97.03 % Rotamer: Outliers : 0.09 % Allowed : 0.45 % Favored : 99.46 % 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: 2.31 (0.13), residues: 3810 helix: 2.49 (0.09), residues: 3050 sheet: None (None), residues: 0 loop : -2.75 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Q 37 HIS 0.010 0.001 HIS R 28 PHE 0.031 0.002 PHE L 120 TYR 0.025 0.002 TYR R 71 ARG 0.008 0.001 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 516 time to evaluate : 4.247 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8518 (t70) cc_final: 0.8241 (t0) REVERT: A 86 MET cc_start: 0.8989 (mmp) cc_final: 0.8732 (mmp) REVERT: C 70 ASN cc_start: 0.8591 (t0) cc_final: 0.8274 (t0) REVERT: F 99 ASP cc_start: 0.8471 (t0) cc_final: 0.8234 (t0) REVERT: G 108 MET cc_start: 0.8856 (mmt) cc_final: 0.8631 (mmm) REVERT: I 123 ILE cc_start: 0.8590 (mm) cc_final: 0.8240 (mm) REVERT: J 137 GLN cc_start: 0.8695 (pt0) cc_final: 0.7985 (tt0) REVERT: K 57 VAL cc_start: 0.9189 (p) cc_final: 0.8957 (p) REVERT: K 115 THR cc_start: 0.7105 (m) cc_final: 0.6874 (m) REVERT: P 52 MET cc_start: 0.7168 (ttm) cc_final: 0.6926 (ttm) REVERT: P 90 ASP cc_start: 0.8687 (m-30) cc_final: 0.8439 (m-30) REVERT: R 53 ARG cc_start: 0.8379 (ttm110) cc_final: 0.8118 (mtm110) REVERT: R 151 SER cc_start: 0.8842 (t) cc_final: 0.8637 (p) REVERT: S 76 HIS cc_start: 0.8610 (t-90) cc_final: 0.7580 (t-90) REVERT: S 113 ASP cc_start: 0.6746 (t0) cc_final: 0.6516 (t0) REVERT: T 22 ILE cc_start: 0.9457 (pt) cc_final: 0.9245 (pt) REVERT: T 32 GLN cc_start: 0.9127 (mp10) cc_final: 0.8685 (mp10) REVERT: T 60 ASP cc_start: 0.8120 (m-30) cc_final: 0.7546 (m-30) REVERT: T 90 ASP cc_start: 0.8842 (m-30) cc_final: 0.8565 (m-30) REVERT: U 114 ILE cc_start: 0.7730 (mm) cc_final: 0.7360 (mm) REVERT: V 86 MET cc_start: 0.7927 (mtm) cc_final: 0.7072 (mtt) REVERT: V 118 ASN cc_start: 0.8923 (m110) cc_final: 0.8555 (m-40) outliers start: 3 outliers final: 2 residues processed: 518 average time/residue: 0.4047 time to fit residues: 340.9606 Evaluate side-chains 345 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 343 time to evaluate : 4.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 20.0000 chunk 288 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 345 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 HIS G 137 GLN H 137 GLN ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 HIS M 156 GLN ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 ASN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 118 ASN ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31867 Z= 0.201 Angle : 0.508 7.630 43071 Z= 0.282 Chirality : 0.034 0.127 4895 Planarity : 0.003 0.028 5626 Dihedral : 3.951 21.416 4193 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.62 % Favored : 97.22 % Rotamer: Outliers : 0.36 % Allowed : 5.05 % Favored : 94.59 % 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: 2.55 (0.13), residues: 3810 helix: 2.68 (0.09), residues: 3039 sheet: None (None), residues: 0 loop : -2.73 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 37 HIS 0.007 0.001 HIS R 28 PHE 0.020 0.001 PHE I 10 TYR 0.019 0.001 TYR R 71 ARG 0.006 0.000 ARG X 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 510 time to evaluate : 3.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8616 (ttt) cc_final: 0.8364 (ttm) REVERT: A 66 ASP cc_start: 0.8604 (t70) cc_final: 0.8322 (t0) REVERT: B 90 ASP cc_start: 0.8762 (m-30) cc_final: 0.8343 (m-30) REVERT: C 52 MET cc_start: 0.6540 (ttt) cc_final: 0.6338 (mtp) REVERT: C 70 ASN cc_start: 0.8585 (t0) cc_final: 0.8248 (t0) REVERT: C 108 MET cc_start: 0.8256 (tmm) cc_final: 0.7952 (tmm) REVERT: D 108 MET cc_start: 0.8784 (ptp) cc_final: 0.8561 (tmm) REVERT: D 121 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: F 99 ASP cc_start: 0.8432 (t0) cc_final: 0.8192 (t0) REVERT: E 121 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8751 (mp0) REVERT: H 95 LEU cc_start: 0.9140 (mt) cc_final: 0.8774 (pp) REVERT: I 123 ILE cc_start: 0.8624 (mm) cc_final: 0.8202 (mm) REVERT: J 137 GLN cc_start: 0.8684 (pt0) cc_final: 0.8117 (tt0) REVERT: K 57 VAL cc_start: 0.9211 (p) cc_final: 0.8933 (t) REVERT: K 115 THR cc_start: 0.7142 (m) cc_final: 0.6715 (m) REVERT: N 52 MET cc_start: 0.7031 (mtp) cc_final: 0.6642 (mtp) REVERT: O 56 GLU cc_start: 0.7763 (tp30) cc_final: 0.7282 (tp30) REVERT: P 52 MET cc_start: 0.7225 (ttm) cc_final: 0.6963 (ttm) REVERT: R 151 SER cc_start: 0.8879 (t) cc_final: 0.8669 (p) REVERT: S 113 ASP cc_start: 0.6624 (t0) cc_final: 0.6379 (t0) REVERT: T 22 ILE cc_start: 0.9461 (pt) cc_final: 0.9250 (pt) REVERT: T 90 ASP cc_start: 0.8944 (m-30) cc_final: 0.8674 (m-30) REVERT: U 86 MET cc_start: 0.8399 (mtm) cc_final: 0.8093 (mtt) REVERT: U 114 ILE cc_start: 0.7537 (mm) cc_final: 0.7273 (mm) REVERT: U 139 ASP cc_start: 0.7932 (m-30) cc_final: 0.7705 (m-30) REVERT: U 143 LYS cc_start: 0.8743 (tttt) cc_final: 0.8469 (tptm) REVERT: V 86 MET cc_start: 0.7899 (mtm) cc_final: 0.7315 (mtt) REVERT: V 118 ASN cc_start: 0.8954 (m110) cc_final: 0.8654 (m-40) REVERT: W 107 VAL cc_start: 0.8513 (p) cc_final: 0.8296 (p) REVERT: W 108 MET cc_start: 0.8228 (tmm) cc_final: 0.7788 (tmm) outliers start: 12 outliers final: 4 residues processed: 516 average time/residue: 0.4150 time to fit residues: 348.1739 Evaluate side-chains 337 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 331 time to evaluate : 4.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 287 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 346 optimal weight: 6.9990 chunk 374 optimal weight: 8.9990 chunk 308 optimal weight: 4.9990 chunk 343 optimal weight: 0.5980 chunk 118 optimal weight: 20.0000 chunk 278 optimal weight: 9.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 ASN M 28 HIS ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 HIS P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 ASN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31867 Z= 0.237 Angle : 0.537 7.663 43071 Z= 0.298 Chirality : 0.036 0.160 4895 Planarity : 0.003 0.033 5626 Dihedral : 3.998 24.985 4193 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.88 % Rotamer: Outliers : 0.18 % Allowed : 4.46 % Favored : 95.36 % 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: 2.45 (0.13), residues: 3810 helix: 2.57 (0.09), residues: 3052 sheet: None (None), residues: 0 loop : -2.67 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP V 37 HIS 0.010 0.001 HIS R 28 PHE 0.033 0.001 PHE W 120 TYR 0.019 0.002 TYR X 43 ARG 0.019 0.001 ARG U 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 500 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8727 (ttt) cc_final: 0.8443 (ttm) REVERT: A 66 ASP cc_start: 0.8647 (t70) cc_final: 0.8386 (t0) REVERT: A 86 MET cc_start: 0.8862 (mmp) cc_final: 0.8319 (mmm) REVERT: B 90 ASP cc_start: 0.8790 (m-30) cc_final: 0.8503 (m-30) REVERT: C 70 ASN cc_start: 0.8546 (t0) cc_final: 0.8198 (t0) REVERT: C 119 VAL cc_start: 0.9187 (m) cc_final: 0.8962 (p) REVERT: D 121 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7945 (pt0) REVERT: F 99 ASP cc_start: 0.8479 (t0) cc_final: 0.8232 (t0) REVERT: H 52 MET cc_start: 0.7895 (ttm) cc_final: 0.7667 (ttt) REVERT: H 86 MET cc_start: 0.8276 (ptp) cc_final: 0.8019 (ptp) REVERT: H 95 LEU cc_start: 0.8989 (mt) cc_final: 0.8775 (pp) REVERT: J 14 GLN cc_start: 0.8476 (tp40) cc_final: 0.7975 (tp40) REVERT: J 137 GLN cc_start: 0.8689 (pt0) cc_final: 0.8051 (tt0) REVERT: K 115 THR cc_start: 0.7027 (m) cc_final: 0.6811 (m) REVERT: N 52 MET cc_start: 0.7045 (mtp) cc_final: 0.6824 (mtp) REVERT: P 149 TYR cc_start: 0.7766 (t80) cc_final: 0.7520 (t80) REVERT: T 22 ILE cc_start: 0.9521 (pt) cc_final: 0.9291 (pt) REVERT: T 90 ASP cc_start: 0.9078 (m-30) cc_final: 0.8826 (m-30) REVERT: U 86 MET cc_start: 0.8458 (mtm) cc_final: 0.7976 (mtt) REVERT: U 114 ILE cc_start: 0.8086 (mm) cc_final: 0.7626 (mm) REVERT: U 143 LYS cc_start: 0.8790 (tttt) cc_final: 0.8514 (tptm) REVERT: V 86 MET cc_start: 0.7911 (mtm) cc_final: 0.7641 (mtt) outliers start: 6 outliers final: 5 residues processed: 504 average time/residue: 0.4544 time to fit residues: 377.6150 Evaluate side-chains 326 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 320 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 342 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 chunk 232 optimal weight: 0.9980 chunk 347 optimal weight: 0.9990 chunk 368 optimal weight: 0.9990 chunk 181 optimal weight: 0.0370 chunk 329 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 72 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN Q 130 HIS ** R 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 ASN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 14 GLN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31867 Z= 0.168 Angle : 0.502 8.663 43071 Z= 0.274 Chirality : 0.034 0.291 4895 Planarity : 0.002 0.032 5626 Dihedral : 3.908 21.621 4193 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.55 % Favored : 97.30 % Rotamer: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.62 % 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: 2.65 (0.13), residues: 3810 helix: 2.73 (0.09), residues: 3041 sheet: None (None), residues: 0 loop : -2.60 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 37 HIS 0.011 0.001 HIS D 54 PHE 0.020 0.001 PHE H 120 TYR 0.018 0.001 TYR X 25 ARG 0.009 0.000 ARG U 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 521 time to evaluate : 5.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8722 (ttt) cc_final: 0.8297 (ttt) REVERT: A 66 ASP cc_start: 0.8592 (t70) cc_final: 0.8335 (t0) REVERT: B 90 ASP cc_start: 0.8736 (m-30) cc_final: 0.8490 (m-30) REVERT: C 70 ASN cc_start: 0.8547 (t0) cc_final: 0.8168 (t0) REVERT: D 95 LEU cc_start: 0.8986 (mt) cc_final: 0.8733 (pp) REVERT: F 99 ASP cc_start: 0.8462 (t0) cc_final: 0.8211 (t0) REVERT: F 108 MET cc_start: 0.8365 (ptp) cc_final: 0.8009 (ptp) REVERT: E 121 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: H 86 MET cc_start: 0.8223 (ptp) cc_final: 0.7952 (ptp) REVERT: J 137 GLN cc_start: 0.8707 (pt0) cc_final: 0.8053 (tt0) REVERT: K 115 THR cc_start: 0.6742 (m) cc_final: 0.6509 (m) REVERT: M 95 LEU cc_start: 0.9047 (mt) cc_final: 0.8455 (mt) REVERT: P 149 TYR cc_start: 0.7915 (t80) cc_final: 0.7668 (t80) REVERT: Q 4 ASP cc_start: 0.8343 (m-30) cc_final: 0.8032 (p0) REVERT: S 78 ARG cc_start: 0.8283 (ptp-110) cc_final: 0.7878 (ptp-110) REVERT: T 90 ASP cc_start: 0.9053 (m-30) cc_final: 0.8801 (m-30) REVERT: U 86 MET cc_start: 0.8457 (mtm) cc_final: 0.7918 (mtt) REVERT: U 114 ILE cc_start: 0.8366 (mm) cc_final: 0.7944 (mm) REVERT: U 143 LYS cc_start: 0.8754 (tttt) cc_final: 0.8489 (tptm) REVERT: V 86 MET cc_start: 0.7841 (mtm) cc_final: 0.7340 (mtt) outliers start: 4 outliers final: 2 residues processed: 525 average time/residue: 0.4167 time to fit residues: 356.2501 Evaluate side-chains 341 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 338 time to evaluate : 3.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 306 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 274 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 188 optimal weight: 8.9990 chunk 330 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 GLN E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 GLN ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 GLN ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31867 Z= 0.220 Angle : 0.541 8.593 43071 Z= 0.298 Chirality : 0.035 0.142 4895 Planarity : 0.003 0.030 5626 Dihedral : 3.928 21.761 4193 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.75 % Rotamer: Outliers : 0.18 % Allowed : 2.60 % Favored : 97.22 % 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: 2.55 (0.13), residues: 3810 helix: 2.66 (0.09), residues: 3032 sheet: None (None), residues: 0 loop : -2.60 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 37 HIS 0.009 0.001 HIS D 54 PHE 0.033 0.001 PHE L 120 TYR 0.025 0.002 TYR R 71 ARG 0.007 0.000 ARG X 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 482 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8732 (ttt) cc_final: 0.8448 (ttm) REVERT: A 66 ASP cc_start: 0.8729 (t70) cc_final: 0.8464 (t0) REVERT: C 70 ASN cc_start: 0.8599 (t0) cc_final: 0.8227 (t0) REVERT: D 95 LEU cc_start: 0.9028 (mt) cc_final: 0.8774 (pp) REVERT: F 99 ASP cc_start: 0.8525 (t0) cc_final: 0.8241 (t0) REVERT: F 108 MET cc_start: 0.8305 (ptp) cc_final: 0.7812 (ptp) REVERT: H 86 MET cc_start: 0.8253 (ptp) cc_final: 0.7789 (ptp) REVERT: H 95 LEU cc_start: 0.9134 (mt) cc_final: 0.8762 (pp) REVERT: J 141 ILE cc_start: 0.8591 (pt) cc_final: 0.8286 (pt) REVERT: K 115 THR cc_start: 0.6990 (m) cc_final: 0.6779 (m) REVERT: K 128 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: L 81 GLN cc_start: 0.8928 (mp10) cc_final: 0.8695 (mp10) REVERT: N 1 MET cc_start: 0.7748 (tmm) cc_final: 0.7324 (tmm) REVERT: P 149 TYR cc_start: 0.7916 (t80) cc_final: 0.7671 (t80) REVERT: T 60 ASP cc_start: 0.7818 (m-30) cc_final: 0.7535 (m-30) REVERT: U 86 MET cc_start: 0.8495 (mtm) cc_final: 0.7884 (mtt) REVERT: U 114 ILE cc_start: 0.8268 (mm) cc_final: 0.7835 (mm) REVERT: U 143 LYS cc_start: 0.8793 (tttt) cc_final: 0.8520 (tptm) REVERT: V 86 MET cc_start: 0.7924 (mtm) cc_final: 0.7649 (mtt) outliers start: 6 outliers final: 2 residues processed: 488 average time/residue: 0.4130 time to fit residues: 328.4718 Evaluate side-chains 328 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 325 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 123 optimal weight: 8.9990 chunk 331 optimal weight: 5.9990 chunk 72 optimal weight: 0.0170 chunk 216 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 368 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 overall best weight: 3.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN D 156 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 ASN ** K 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 HIS ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31867 Z= 0.189 Angle : 0.519 8.565 43071 Z= 0.287 Chirality : 0.034 0.148 4895 Planarity : 0.003 0.028 5626 Dihedral : 3.891 20.836 4193 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.76 % Favored : 97.09 % Rotamer: Outliers : 0.12 % Allowed : 2.03 % Favored : 97.85 % 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: 2.58 (0.13), residues: 3810 helix: 2.68 (0.09), residues: 3034 sheet: None (None), residues: 0 loop : -2.60 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 37 HIS 0.008 0.001 HIS M 112 PHE 0.040 0.001 PHE A 120 TYR 0.017 0.001 TYR R 71 ARG 0.007 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 505 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8750 (ttt) cc_final: 0.8466 (ttm) REVERT: A 66 ASP cc_start: 0.8715 (t70) cc_final: 0.8473 (t0) REVERT: B 128 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7845 (mt-10) REVERT: C 70 ASN cc_start: 0.8545 (t0) cc_final: 0.8180 (t0) REVERT: D 95 LEU cc_start: 0.9041 (mt) cc_final: 0.8780 (pp) REVERT: F 99 ASP cc_start: 0.8494 (t0) cc_final: 0.8206 (t0) REVERT: G 123 ILE cc_start: 0.8359 (mm) cc_final: 0.8157 (mm) REVERT: H 86 MET cc_start: 0.8251 (ptp) cc_final: 0.7751 (ptp) REVERT: K 115 THR cc_start: 0.6941 (m) cc_final: 0.6729 (m) REVERT: L 81 GLN cc_start: 0.8916 (mp10) cc_final: 0.8677 (mp10) REVERT: M 95 LEU cc_start: 0.9030 (mt) cc_final: 0.8450 (mt) REVERT: N 1 MET cc_start: 0.7707 (tmm) cc_final: 0.7361 (tmm) REVERT: P 149 TYR cc_start: 0.7924 (t80) cc_final: 0.7680 (t80) REVERT: Q 4 ASP cc_start: 0.8496 (m-30) cc_final: 0.7954 (p0) REVERT: S 76 HIS cc_start: 0.8548 (t70) cc_final: 0.7566 (t-90) REVERT: S 78 ARG cc_start: 0.8362 (ptp-110) cc_final: 0.8022 (ptp90) REVERT: T 90 ASP cc_start: 0.9082 (m-30) cc_final: 0.8832 (m-30) REVERT: U 86 MET cc_start: 0.8451 (mtm) cc_final: 0.7816 (mtt) REVERT: U 114 ILE cc_start: 0.8388 (mm) cc_final: 0.8048 (mm) REVERT: U 143 LYS cc_start: 0.8778 (tttt) cc_final: 0.8516 (tptm) REVERT: V 86 MET cc_start: 0.7984 (mtm) cc_final: 0.7507 (mtt) outliers start: 4 outliers final: 3 residues processed: 509 average time/residue: 0.4109 time to fit residues: 340.6745 Evaluate side-chains 345 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 342 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 355 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 208 optimal weight: 20.0000 chunk 310 optimal weight: 0.0870 chunk 205 optimal weight: 3.9990 chunk 367 optimal weight: 9.9990 chunk 229 optimal weight: 0.4980 chunk 223 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 overall best weight: 3.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS ** F 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 GLN E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 HIS ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN ** X 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31867 Z= 0.184 Angle : 0.524 8.648 43071 Z= 0.289 Chirality : 0.034 0.143 4895 Planarity : 0.003 0.033 5626 Dihedral : 3.878 19.846 4193 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.04 % Favored : 96.80 % Rotamer: Outliers : 0.06 % Allowed : 1.79 % Favored : 98.15 % 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: 2.59 (0.13), residues: 3810 helix: 2.67 (0.09), residues: 3044 sheet: None (None), residues: 0 loop : -2.55 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 37 HIS 0.010 0.001 HIS M 112 PHE 0.016 0.001 PHE N 120 TYR 0.017 0.001 TYR V 43 ARG 0.018 0.000 ARG X 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 498 time to evaluate : 3.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8686 (ttt) cc_final: 0.8428 (ttm) REVERT: A 66 ASP cc_start: 0.8745 (t70) cc_final: 0.8498 (t0) REVERT: B 128 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7867 (mt-10) REVERT: C 70 ASN cc_start: 0.8528 (t0) cc_final: 0.8152 (t0) REVERT: D 95 LEU cc_start: 0.9041 (mt) cc_final: 0.8789 (pp) REVERT: F 99 ASP cc_start: 0.8502 (t0) cc_final: 0.8219 (t0) REVERT: G 108 MET cc_start: 0.8807 (tpp) cc_final: 0.8558 (mmt) REVERT: G 123 ILE cc_start: 0.8416 (mm) cc_final: 0.8161 (mm) REVERT: H 86 MET cc_start: 0.8296 (ptp) cc_final: 0.7746 (ptp) REVERT: H 95 LEU cc_start: 0.9109 (mt) cc_final: 0.8672 (pp) REVERT: I 52 MET cc_start: 0.7764 (ttm) cc_final: 0.7488 (ttm) REVERT: K 108 MET cc_start: 0.8589 (tmm) cc_final: 0.8360 (tmm) REVERT: K 115 THR cc_start: 0.6853 (m) cc_final: 0.6624 (m) REVERT: N 1 MET cc_start: 0.7745 (tmm) cc_final: 0.7271 (tmm) REVERT: O 52 MET cc_start: 0.6455 (ttm) cc_final: 0.6072 (ttm) REVERT: P 32 GLN cc_start: 0.8159 (mt0) cc_final: 0.7866 (mt0) REVERT: P 149 TYR cc_start: 0.7950 (t80) cc_final: 0.7721 (t80) REVERT: T 90 ASP cc_start: 0.9100 (m-30) cc_final: 0.8846 (m-30) REVERT: U 86 MET cc_start: 0.8450 (mtm) cc_final: 0.7810 (mtt) REVERT: U 114 ILE cc_start: 0.8379 (mm) cc_final: 0.8014 (mm) REVERT: U 143 LYS cc_start: 0.8764 (tttt) cc_final: 0.8504 (tptm) outliers start: 2 outliers final: 2 residues processed: 500 average time/residue: 0.4124 time to fit residues: 337.3522 Evaluate side-chains 347 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 345 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 233 optimal weight: 8.9990 chunk 250 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 288 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 ASN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN ** X 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31867 Z= 0.272 Angle : 0.618 9.316 43071 Z= 0.342 Chirality : 0.037 0.186 4895 Planarity : 0.003 0.035 5626 Dihedral : 4.090 24.057 4193 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.33 % Favored : 96.51 % Rotamer: Outliers : 0.06 % Allowed : 1.61 % Favored : 98.33 % 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: 2.26 (0.13), residues: 3810 helix: 2.44 (0.09), residues: 3039 sheet: None (None), residues: 0 loop : -2.64 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 37 HIS 0.011 0.001 HIS R 28 PHE 0.028 0.002 PHE M 120 TYR 0.037 0.002 TYR Q 71 ARG 0.008 0.001 ARG X 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 468 time to evaluate : 5.208 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 52 MET cc_start: 0.8655 (ttt) cc_final: 0.8357 (ttm) REVERT: A 60 ASP cc_start: 0.8336 (m-30) cc_final: 0.8017 (m-30) REVERT: A 66 ASP cc_start: 0.8852 (t70) cc_final: 0.8601 (t0) REVERT: B 128 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7828 (mt-10) REVERT: C 70 ASN cc_start: 0.8531 (t0) cc_final: 0.8060 (t0) REVERT: F 99 ASP cc_start: 0.8554 (t0) cc_final: 0.8265 (t0) REVERT: F 108 MET cc_start: 0.8288 (ptp) cc_final: 0.8039 (ptp) REVERT: G 108 MET cc_start: 0.8888 (tpp) cc_final: 0.8495 (mmt) REVERT: G 123 ILE cc_start: 0.8660 (mm) cc_final: 0.8393 (mm) REVERT: H 86 MET cc_start: 0.8386 (ptp) cc_final: 0.7782 (ptp) REVERT: H 95 LEU cc_start: 0.9192 (mt) cc_final: 0.8732 (pp) REVERT: J 114 ILE cc_start: 0.6574 (mp) cc_final: 0.6280 (mp) REVERT: K 115 THR cc_start: 0.7202 (m) cc_final: 0.6989 (m) REVERT: M 88 GLN cc_start: 0.8616 (pp30) cc_final: 0.8372 (pp30) REVERT: M 95 LEU cc_start: 0.9026 (mt) cc_final: 0.8469 (mt) REVERT: M 155 GLU cc_start: 0.8675 (tp30) cc_final: 0.8374 (tp30) REVERT: N 1 MET cc_start: 0.7622 (tmm) cc_final: 0.7339 (tmm) REVERT: N 43 TYR cc_start: 0.6710 (m-80) cc_final: 0.6452 (m-10) REVERT: O 52 MET cc_start: 0.6556 (ttm) cc_final: 0.6282 (ttm) REVERT: R 153 VAL cc_start: 0.6552 (m) cc_final: 0.6323 (t) REVERT: S 76 HIS cc_start: 0.8571 (t-90) cc_final: 0.7404 (t-90) REVERT: S 78 ARG cc_start: 0.8441 (ptp-110) cc_final: 0.7850 (ptp-110) REVERT: T 90 ASP cc_start: 0.9124 (m-30) cc_final: 0.8857 (m-30) REVERT: U 86 MET cc_start: 0.8473 (mtm) cc_final: 0.7787 (mtt) REVERT: U 114 ILE cc_start: 0.8426 (mm) cc_final: 0.8093 (mm) REVERT: V 108 MET cc_start: 0.8302 (ptp) cc_final: 0.7975 (ptp) outliers start: 2 outliers final: 2 residues processed: 470 average time/residue: 0.3930 time to fit residues: 305.2095 Evaluate side-chains 310 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 6.9990 chunk 351 optimal weight: 9.9990 chunk 320 optimal weight: 30.0000 chunk 342 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 chunk 323 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 GLN E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN X 23 ASN ** X 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31867 Z= 0.250 Angle : 0.596 9.476 43071 Z= 0.330 Chirality : 0.037 0.181 4895 Planarity : 0.003 0.036 5626 Dihedral : 4.083 20.034 4193 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.75 % Rotamer: Outliers : 0.06 % Allowed : 0.90 % Favored : 99.04 % 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: 2.20 (0.13), residues: 3810 helix: 2.40 (0.09), residues: 3043 sheet: None (None), residues: 0 loop : -2.70 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 37 HIS 0.008 0.001 HIS D 54 PHE 0.036 0.002 PHE I 10 TYR 0.031 0.002 TYR R 71 ARG 0.007 0.001 ARG V 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 461 time to evaluate : 3.961 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8800 (ttt) cc_final: 0.8508 (ttm) REVERT: A 66 ASP cc_start: 0.8764 (t70) cc_final: 0.8533 (t0) REVERT: B 128 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7917 (mt-10) REVERT: C 70 ASN cc_start: 0.8431 (t0) cc_final: 0.8087 (t0) REVERT: F 99 ASP cc_start: 0.8544 (t0) cc_final: 0.8253 (t0) REVERT: G 108 MET cc_start: 0.8869 (tpp) cc_final: 0.8478 (mmt) REVERT: G 123 ILE cc_start: 0.8630 (mm) cc_final: 0.8380 (mm) REVERT: H 86 MET cc_start: 0.8377 (ptp) cc_final: 0.7778 (ptp) REVERT: H 95 LEU cc_start: 0.9202 (mt) cc_final: 0.8768 (pp) REVERT: K 86 MET cc_start: 0.7528 (ptp) cc_final: 0.7271 (ptp) REVERT: K 115 THR cc_start: 0.7254 (m) cc_final: 0.7044 (m) REVERT: M 88 GLN cc_start: 0.8586 (pp30) cc_final: 0.8336 (pp30) REVERT: M 95 LEU cc_start: 0.8954 (mt) cc_final: 0.8490 (mt) REVERT: M 155 GLU cc_start: 0.8679 (tp30) cc_final: 0.8423 (tp30) REVERT: O 52 MET cc_start: 0.6655 (ttm) cc_final: 0.6045 (ttm) REVERT: P 86 MET cc_start: 0.8212 (mtt) cc_final: 0.7954 (mtt) REVERT: P 149 TYR cc_start: 0.8038 (t80) cc_final: 0.7796 (t80) REVERT: S 76 HIS cc_start: 0.8574 (t-90) cc_final: 0.7389 (t-90) REVERT: S 78 ARG cc_start: 0.8413 (ptp-110) cc_final: 0.7858 (ptp-110) REVERT: T 90 ASP cc_start: 0.9135 (m-30) cc_final: 0.8872 (m-30) REVERT: U 86 MET cc_start: 0.8494 (mtm) cc_final: 0.7785 (mtt) REVERT: U 114 ILE cc_start: 0.8477 (mm) cc_final: 0.8136 (mm) REVERT: V 52 MET cc_start: 0.7967 (ttt) cc_final: 0.7676 (ttm) REVERT: V 108 MET cc_start: 0.8338 (ptp) cc_final: 0.8095 (ptp) REVERT: X 130 HIS cc_start: 0.8386 (t-90) cc_final: 0.8161 (t70) outliers start: 2 outliers final: 2 residues processed: 463 average time/residue: 0.4095 time to fit residues: 312.6345 Evaluate side-chains 311 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 309 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 5.9990 chunk 361 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 379 optimal weight: 1.9990 chunk 349 optimal weight: 20.0000 chunk 302 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 233 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 GLN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31867 Z= 0.211 Angle : 0.584 9.822 43071 Z= 0.321 Chirality : 0.036 0.198 4895 Planarity : 0.003 0.089 5626 Dihedral : 4.019 19.939 4193 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.04 % Favored : 96.80 % Rotamer: Outliers : 0.06 % Allowed : 0.48 % Favored : 99.46 % 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: 2.31 (0.13), residues: 3810 helix: 2.49 (0.09), residues: 3042 sheet: None (None), residues: 0 loop : -2.72 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 37 HIS 0.009 0.001 HIS X 28 PHE 0.032 0.001 PHE M 120 TYR 0.031 0.001 TYR R 71 ARG 0.011 0.000 ARG X 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 467 time to evaluate : 3.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8799 (ttt) cc_final: 0.8504 (ttm) REVERT: A 66 ASP cc_start: 0.8776 (t70) cc_final: 0.8542 (t0) REVERT: B 128 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7957 (mt-10) REVERT: C 70 ASN cc_start: 0.8408 (t0) cc_final: 0.8080 (t0) REVERT: F 1 MET cc_start: 0.3225 (mmm) cc_final: 0.2991 (tpt) REVERT: F 56 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7844 (mm-30) REVERT: F 99 ASP cc_start: 0.8538 (t0) cc_final: 0.8255 (t0) REVERT: G 108 MET cc_start: 0.8842 (tpp) cc_final: 0.8454 (mmt) REVERT: G 123 ILE cc_start: 0.8582 (mm) cc_final: 0.8340 (mm) REVERT: G 137 GLN cc_start: 0.8662 (tp-100) cc_final: 0.8458 (tp40) REVERT: H 53 ARG cc_start: 0.8907 (ttm110) cc_final: 0.8693 (ttm110) REVERT: H 86 MET cc_start: 0.8304 (ptp) cc_final: 0.7757 (ptp) REVERT: H 95 LEU cc_start: 0.9202 (mt) cc_final: 0.8787 (pp) REVERT: K 86 MET cc_start: 0.7539 (ptp) cc_final: 0.7309 (ptp) REVERT: K 115 THR cc_start: 0.7133 (m) cc_final: 0.6921 (m) REVERT: L 56 GLU cc_start: 0.8286 (tp30) cc_final: 0.7784 (tp30) REVERT: L 111 LYS cc_start: 0.8690 (tppt) cc_final: 0.8372 (ttmt) REVERT: L 123 ILE cc_start: 0.8877 (pt) cc_final: 0.8463 (tt) REVERT: M 155 GLU cc_start: 0.8673 (tp30) cc_final: 0.8439 (tp30) REVERT: O 52 MET cc_start: 0.6393 (ttm) cc_final: 0.5869 (ttm) REVERT: P 149 TYR cc_start: 0.8019 (t80) cc_final: 0.7503 (t80) REVERT: P 154 ILE cc_start: 0.9374 (mm) cc_final: 0.9132 (mm) REVERT: S 76 HIS cc_start: 0.8583 (t-90) cc_final: 0.7349 (t-90) REVERT: S 78 ARG cc_start: 0.8400 (ptp-110) cc_final: 0.7959 (ptp-110) REVERT: T 86 MET cc_start: 0.7506 (mtm) cc_final: 0.7287 (mtm) REVERT: T 90 ASP cc_start: 0.9135 (m-30) cc_final: 0.8875 (m-30) REVERT: U 86 MET cc_start: 0.8491 (mtm) cc_final: 0.7865 (mtt) REVERT: U 90 ASP cc_start: 0.8596 (m-30) cc_final: 0.8274 (m-30) REVERT: U 114 ILE cc_start: 0.8505 (mm) cc_final: 0.8255 (mm) REVERT: U 139 ASP cc_start: 0.7973 (m-30) cc_final: 0.7716 (m-30) REVERT: V 52 MET cc_start: 0.7972 (ttt) cc_final: 0.7663 (ttm) REVERT: V 108 MET cc_start: 0.8192 (ptp) cc_final: 0.7945 (ptp) REVERT: W 1 MET cc_start: 0.8196 (pmm) cc_final: 0.7525 (pmm) REVERT: X 114 ILE cc_start: 0.8479 (mm) cc_final: 0.7232 (mm) REVERT: X 130 HIS cc_start: 0.8150 (t-90) cc_final: 0.7929 (t70) outliers start: 2 outliers final: 2 residues processed: 469 average time/residue: 0.4134 time to fit residues: 322.3460 Evaluate side-chains 318 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 316 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 240 optimal weight: 20.0000 chunk 321 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 302 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 310 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 55 optimal weight: 30.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 ASN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 HIS ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 GLN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN ** X 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.059351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051752 restraints weight = 187852.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.052967 restraints weight = 122581.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053893 restraints weight = 88835.268| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31867 Z= 0.235 Angle : 0.600 9.709 43071 Z= 0.329 Chirality : 0.037 0.186 4895 Planarity : 0.003 0.045 5626 Dihedral : 4.056 20.625 4193 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.49 % 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: 2.23 (0.13), residues: 3810 helix: 2.43 (0.09), residues: 3039 sheet: None (None), residues: 0 loop : -2.71 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 37 HIS 0.008 0.001 HIS D 54 PHE 0.028 0.002 PHE I 10 TYR 0.021 0.001 TYR R 71 ARG 0.011 0.000 ARG X 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6249.97 seconds wall clock time: 115 minutes 25.31 seconds (6925.31 seconds total)