Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 17:19:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/04_2023/6v01_20967_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/04_2023/6v01_20967.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/04_2023/6v01_20967_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/04_2023/6v01_20967_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/04_2023/6v01_20967_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/04_2023/6v01_20967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/04_2023/6v01_20967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/04_2023/6v01_20967_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/04_2023/6v01_20967_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 12 5.49 5 S 60 5.16 5 C 10048 2.51 5 N 2696 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "J ARG 109": "NH1" <-> "NH2" Residue "J ARG 116": "NH1" <-> "NH2" Residue "J ARG 174": "NH1" <-> "NH2" Residue "J ARG 190": "NH1" <-> "NH2" Residue "J ARG 192": "NH1" <-> "NH2" Residue "J ARG 228": "NH1" <-> "NH2" Residue "J ARG 237": "NH1" <-> "NH2" Residue "J ARG 243": "NH1" <-> "NH2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "J ARG 360": "NH1" <-> "NH2" Residue "J ARG 507": "NH1" <-> "NH2" Residue "J ARG 511": "NH1" <-> "NH2" Residue "J ARG 533": "NH1" <-> "NH2" Residue "J GLU 543": "OE1" <-> "OE2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "D ARG 360": "NH1" <-> "NH2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "D ARG 511": "NH1" <-> "NH2" Residue "D ARG 533": "NH1" <-> "NH2" Residue "D GLU 543": "OE1" <-> "OE2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G ARG 116": "NH1" <-> "NH2" Residue "G ARG 174": "NH1" <-> "NH2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "G ARG 192": "NH1" <-> "NH2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G ARG 237": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 293": "NH1" <-> "NH2" Residue "G ARG 360": "NH1" <-> "NH2" Residue "G ARG 507": "NH1" <-> "NH2" Residue "G ARG 511": "NH1" <-> "NH2" Residue "G ARG 533": "NH1" <-> "NH2" Residue "G GLU 543": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15480 Number of models: 1 Model: "" Number of chains: 20 Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 828 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "C" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 828 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "F" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 828 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "I" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 828 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "L" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2682 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 7, 'TRANS': 323} Chain breaks: 3 Chain: "J" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2682 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 7, 'TRANS': 323} Chain breaks: 3 Chain: "D" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2682 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 7, 'TRANS': 323} Chain breaks: 3 Chain: "G" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2682 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 7, 'TRANS': 323} Chain breaks: 3 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 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: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "G" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PT5': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.83 residue: pdb="CA CA E 202 " occ=0.83 residue: pdb="CA CA H 202 " occ=0.83 residue: pdb="CA CA K 202 " occ=0.83 Time building chain proxies: 8.25, per 1000 atoms: 0.53 Number of scatterers: 15480 At special positions: 0 Unit cell: (120.99, 120.99, 113.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 60 16.00 P 12 15.00 O 2656 8.00 N 2696 7.00 C 10048 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: 6.45 Conformation dependent library (CDL) restraints added in 2.6 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 0 sheets defined 60.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 30 through 40 removed outlier: 3.730A pdb=" N GLY B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 52 through 55 No H-bonds generated for 'chain 'B' and resid 52 through 55' Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.562A pdb=" N MET B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 73' Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.615A pdb=" N ALA B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 119 through 125 removed outlier: 4.262A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'C' and resid 58 through 73 removed outlier: 3.667A pdb=" N MET C 65 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 No H-bonds generated for 'chain 'C' and resid 77 through 80' Processing helix chain 'E' and resid 13 through 17 Processing helix chain 'E' and resid 30 through 40 removed outlier: 3.730A pdb=" N GLY E 34 " --> pdb=" O THR E 30 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 Processing helix chain 'E' and resid 52 through 55 No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 69 through 73 removed outlier: 3.562A pdb=" N MET E 73 " --> pdb=" O PHE E 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 69 through 73' Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.615A pdb=" N ALA E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 91 " --> pdb=" O ARG E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 110 Processing helix chain 'E' and resid 119 through 125 removed outlier: 4.262A pdb=" N GLU E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'F' and resid 58 through 73 removed outlier: 3.667A pdb=" N MET F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 80 No H-bonds generated for 'chain 'F' and resid 77 through 80' Processing helix chain 'H' and resid 13 through 17 Processing helix chain 'H' and resid 30 through 40 removed outlier: 3.729A pdb=" N GLY H 34 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 Processing helix chain 'H' and resid 52 through 55 No H-bonds generated for 'chain 'H' and resid 52 through 55' Processing helix chain 'H' and resid 69 through 73 removed outlier: 3.562A pdb=" N MET H 73 " --> pdb=" O PHE H 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 69 through 73' Processing helix chain 'H' and resid 84 through 91 removed outlier: 3.615A pdb=" N ALA H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE H 90 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 119 through 125 removed outlier: 4.261A pdb=" N GLU H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 143 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'I' and resid 58 through 73 removed outlier: 3.668A pdb=" N MET I 65 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR I 71 " --> pdb=" O LEU I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 80 No H-bonds generated for 'chain 'I' and resid 77 through 80' Processing helix chain 'K' and resid 13 through 17 Processing helix chain 'K' and resid 30 through 40 removed outlier: 3.729A pdb=" N GLY K 34 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR K 35 " --> pdb=" O LYS K 31 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG K 38 " --> pdb=" O GLY K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 50 Processing helix chain 'K' and resid 52 through 55 No H-bonds generated for 'chain 'K' and resid 52 through 55' Processing helix chain 'K' and resid 69 through 73 removed outlier: 3.562A pdb=" N MET K 73 " --> pdb=" O PHE K 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 69 through 73' Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.614A pdb=" N ALA K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE K 90 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 110 Processing helix chain 'K' and resid 119 through 125 removed outlier: 4.262A pdb=" N GLU K 124 " --> pdb=" O GLU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 143 Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'L' and resid 58 through 73 removed outlier: 3.667A pdb=" N MET L 65 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR L 71 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 80 No H-bonds generated for 'chain 'L' and resid 77 through 80' Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.577A pdb=" N ASN A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.950A pdb=" N VAL A 124 " --> pdb=" O TRP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 4.295A pdb=" N VAL A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 140 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 178 removed outlier: 4.140A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.677A pdb=" N SER A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 removed outlier: 3.642A pdb=" N PHE A 232 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 233 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU A 236 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A 237 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.524A pdb=" N SER A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 283 removed outlier: 3.896A pdb=" N TYR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 310 Processing helix chain 'A' and resid 323 through 372 removed outlier: 4.031A pdb=" N THR A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 343 - end of helix removed outlier: 3.619A pdb=" N ALA A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 355 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 375 through 382 removed outlier: 3.622A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 530 removed outlier: 3.611A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 514 " --> pdb=" O HIS A 510 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 517 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 555 No H-bonds generated for 'chain 'A' and resid 552 through 555' Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'J' and resid 105 through 113 removed outlier: 3.577A pdb=" N ASN J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 128 removed outlier: 3.951A pdb=" N VAL J 124 " --> pdb=" O TRP J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 141 removed outlier: 4.295A pdb=" N VAL J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER J 140 " --> pdb=" O CYS J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 178 removed outlier: 4.139A pdb=" N VAL J 172 " --> pdb=" O GLY J 168 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA J 178 " --> pdb=" O ARG J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 191 No H-bonds generated for 'chain 'J' and resid 189 through 191' Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' Processing helix chain 'J' and resid 197 through 217 removed outlier: 3.678A pdb=" N SER J 217 " --> pdb=" O LEU J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 238 removed outlier: 3.642A pdb=" N PHE J 232 " --> pdb=" O GLY J 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU J 233 " --> pdb=" O ILE J 230 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU J 236 " --> pdb=" O LEU J 233 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG J 237 " --> pdb=" O GLN J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 257 removed outlier: 3.524A pdb=" N SER J 253 " --> pdb=" O ARG J 249 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE J 256 " --> pdb=" O GLY J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 283 removed outlier: 3.895A pdb=" N TYR J 278 " --> pdb=" O ILE J 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE J 279 " --> pdb=" O PHE J 275 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL J 280 " --> pdb=" O SER J 276 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR J 281 " --> pdb=" O SER J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 299 through 310 Processing helix chain 'J' and resid 323 through 372 removed outlier: 4.030A pdb=" N THR J 327 " --> pdb=" O TRP J 323 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE J 328 " --> pdb=" O VAL J 324 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE J 339 " --> pdb=" O PHE J 335 " (cutoff:3.500A) Proline residue: J 343 - end of helix removed outlier: 3.619A pdb=" N ALA J 352 " --> pdb=" O GLY J 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL J 355 " --> pdb=" O PHE J 351 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN J 356 " --> pdb=" O ALA J 352 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN J 361 " --> pdb=" O GLN J 357 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS J 363 " --> pdb=" O GLN J 359 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE J 368 " --> pdb=" O PHE J 364 " (cutoff:3.500A) Proline residue: J 369 - end of helix Processing helix chain 'J' and resid 375 through 382 removed outlier: 3.622A pdb=" N ARG J 380 " --> pdb=" O GLN J 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 509 through 530 removed outlier: 3.611A pdb=" N THR J 513 " --> pdb=" O HIS J 509 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE J 514 " --> pdb=" O HIS J 510 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS J 515 " --> pdb=" O ARG J 511 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL J 516 " --> pdb=" O ALA J 512 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE J 517 " --> pdb=" O THR J 513 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG J 519 " --> pdb=" O LYS J 515 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR J 522 " --> pdb=" O ARG J 518 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE J 523 " --> pdb=" O ARG J 519 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL J 524 " --> pdb=" O MET J 520 " (cutoff:3.500A) Processing helix chain 'J' and resid 552 through 555 No H-bonds generated for 'chain 'J' and resid 552 through 555' Processing helix chain 'J' and resid 557 through 561 Processing helix chain 'D' and resid 105 through 113 removed outlier: 3.576A pdb=" N ASN D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 removed outlier: 3.950A pdb=" N VAL D 124 " --> pdb=" O TRP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 141 removed outlier: 4.295A pdb=" N VAL D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 140 " --> pdb=" O CYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 178 removed outlier: 4.140A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 197 through 217 removed outlier: 3.677A pdb=" N SER D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 238 removed outlier: 3.642A pdb=" N PHE D 232 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 233 " --> pdb=" O ILE D 230 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU D 236 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 237 " --> pdb=" O GLN D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 257 removed outlier: 3.525A pdb=" N SER D 253 " --> pdb=" O ARG D 249 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE D 256 " --> pdb=" O GLY D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 283 removed outlier: 3.895A pdb=" N TYR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 279 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 280 " --> pdb=" O SER D 276 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 310 Processing helix chain 'D' and resid 323 through 372 removed outlier: 4.031A pdb=" N THR D 327 " --> pdb=" O TRP D 323 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 328 " --> pdb=" O VAL D 324 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Proline residue: D 343 - end of helix removed outlier: 3.619A pdb=" N ALA D 352 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 355 " --> pdb=" O PHE D 351 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS D 363 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 368 " --> pdb=" O PHE D 364 " (cutoff:3.500A) Proline residue: D 369 - end of helix Processing helix chain 'D' and resid 375 through 382 removed outlier: 3.623A pdb=" N ARG D 380 " --> pdb=" O GLN D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 530 removed outlier: 3.611A pdb=" N THR D 513 " --> pdb=" O HIS D 509 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 514 " --> pdb=" O HIS D 510 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS D 515 " --> pdb=" O ARG D 511 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE D 517 " --> pdb=" O THR D 513 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 519 " --> pdb=" O LYS D 515 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR D 522 " --> pdb=" O ARG D 518 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE D 523 " --> pdb=" O ARG D 519 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 524 " --> pdb=" O MET D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 555 No H-bonds generated for 'chain 'D' and resid 552 through 555' Processing helix chain 'D' and resid 557 through 561 Processing helix chain 'G' and resid 105 through 113 removed outlier: 3.577A pdb=" N ASN G 112 " --> pdb=" O GLY G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 removed outlier: 3.950A pdb=" N VAL G 124 " --> pdb=" O TRP G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 removed outlier: 4.295A pdb=" N VAL G 135 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER G 140 " --> pdb=" O CYS G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 178 removed outlier: 4.139A pdb=" N VAL G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA G 178 " --> pdb=" O ARG G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 191 No H-bonds generated for 'chain 'G' and resid 189 through 191' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 197 through 217 removed outlier: 3.676A pdb=" N SER G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 238 removed outlier: 3.643A pdb=" N PHE G 232 " --> pdb=" O GLY G 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 233 " --> pdb=" O ILE G 230 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU G 236 " --> pdb=" O LEU G 233 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG G 237 " --> pdb=" O GLN G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 257 removed outlier: 3.525A pdb=" N SER G 253 " --> pdb=" O ARG G 249 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE G 256 " --> pdb=" O GLY G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 283 removed outlier: 3.896A pdb=" N TYR G 278 " --> pdb=" O ILE G 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE G 279 " --> pdb=" O PHE G 275 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL G 280 " --> pdb=" O SER G 276 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR G 281 " --> pdb=" O SER G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 310 Processing helix chain 'G' and resid 323 through 372 removed outlier: 4.031A pdb=" N THR G 327 " --> pdb=" O TRP G 323 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 328 " --> pdb=" O VAL G 324 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE G 339 " --> pdb=" O PHE G 335 " (cutoff:3.500A) Proline residue: G 343 - end of helix removed outlier: 3.618A pdb=" N ALA G 352 " --> pdb=" O GLY G 348 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL G 355 " --> pdb=" O PHE G 351 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN G 356 " --> pdb=" O ALA G 352 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN G 361 " --> pdb=" O GLN G 357 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS G 363 " --> pdb=" O GLN G 359 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE G 368 " --> pdb=" O PHE G 364 " (cutoff:3.500A) Proline residue: G 369 - end of helix Processing helix chain 'G' and resid 375 through 382 removed outlier: 3.622A pdb=" N ARG G 380 " --> pdb=" O GLN G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 530 removed outlier: 3.611A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE G 514 " --> pdb=" O HIS G 510 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS G 515 " --> pdb=" O ARG G 511 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE G 517 " --> pdb=" O THR G 513 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG G 519 " --> pdb=" O LYS G 515 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR G 522 " --> pdb=" O ARG G 518 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE G 523 " --> pdb=" O ARG G 519 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL G 524 " --> pdb=" O MET G 520 " (cutoff:3.500A) Processing helix chain 'G' and resid 552 through 555 No H-bonds generated for 'chain 'G' and resid 552 through 555' Processing helix chain 'G' and resid 557 through 561 600 hydrogen bonds defined for protein. 1752 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: 3.94 Time building geometry restraints manager: 6.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2336 1.29 - 1.42: 4448 1.42 - 1.55: 8897 1.55 - 1.68: 23 1.68 - 1.81: 96 Bond restraints: 15800 Sorted by residual: bond pdb=" C TRP G 305 " pdb=" O TRP G 305 " ideal model delta sigma weight residual 1.237 1.162 0.074 1.17e-02 7.31e+03 4.05e+01 bond pdb=" C TRP D 305 " pdb=" O TRP D 305 " ideal model delta sigma weight residual 1.237 1.162 0.074 1.17e-02 7.31e+03 4.04e+01 bond pdb=" C TRP A 305 " pdb=" O TRP A 305 " ideal model delta sigma weight residual 1.237 1.163 0.074 1.17e-02 7.31e+03 3.99e+01 bond pdb=" C TRP J 305 " pdb=" O TRP J 305 " ideal model delta sigma weight residual 1.237 1.163 0.074 1.17e-02 7.31e+03 3.98e+01 bond pdb=" C TRP G 304 " pdb=" O TRP G 304 " ideal model delta sigma weight residual 1.237 1.173 0.063 1.17e-02 7.31e+03 2.93e+01 ... (remaining 15795 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.92: 348 106.92 - 113.75: 8633 113.75 - 120.59: 6902 120.59 - 127.42: 5385 127.42 - 134.26: 168 Bond angle restraints: 21436 Sorted by residual: angle pdb=" C18 PT5 G 801 " pdb=" C19 PT5 G 801 " pdb=" C20 PT5 G 801 " ideal model delta sigma weight residual 85.86 125.58 -39.72 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C18 PT5 A 801 " pdb=" C19 PT5 A 801 " pdb=" C20 PT5 A 801 " ideal model delta sigma weight residual 85.86 125.57 -39.71 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C18 PT5 D 801 " pdb=" C19 PT5 D 801 " pdb=" C20 PT5 D 801 " ideal model delta sigma weight residual 85.86 125.55 -39.69 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C18 PT5 J 801 " pdb=" C19 PT5 J 801 " pdb=" C20 PT5 J 801 " ideal model delta sigma weight residual 85.86 125.54 -39.68 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C21 PT5 J 801 " pdb=" C22 PT5 J 801 " pdb=" C23 PT5 J 801 " ideal model delta sigma weight residual 152.70 125.54 27.16 3.00e+00 1.11e-01 8.19e+01 ... (remaining 21431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 8820 35.63 - 71.27: 220 71.27 - 106.90: 40 106.90 - 142.53: 0 142.53 - 178.16: 4 Dihedral angle restraints: 9084 sinusoidal: 3148 harmonic: 5936 Sorted by residual: dihedral pdb=" CA TYR K 100 " pdb=" C TYR K 100 " pdb=" N ILE K 101 " pdb=" CA ILE K 101 " ideal model delta harmonic sigma weight residual -180.00 -153.31 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA TYR H 100 " pdb=" C TYR H 100 " pdb=" N ILE H 101 " pdb=" CA ILE H 101 " ideal model delta harmonic sigma weight residual 180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA TYR E 100 " pdb=" C TYR E 100 " pdb=" N ILE E 101 " pdb=" CA ILE E 101 " ideal model delta harmonic sigma weight residual -180.00 -153.35 -26.65 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 9081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.019: 2456 1.019 - 2.038: 0 2.038 - 3.057: 0 3.057 - 4.076: 0 4.076 - 5.095: 4 Chirality restraints: 2460 Sorted by residual: chirality pdb=" C8 PT5 G 801 " pdb=" C7 PT5 G 801 " pdb=" C9 PT5 G 801 " pdb=" O16 PT5 G 801 " both_signs ideal model delta sigma weight residual False -2.54 2.56 -5.10 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C8 PT5 J 801 " pdb=" C7 PT5 J 801 " pdb=" C9 PT5 J 801 " pdb=" O16 PT5 J 801 " both_signs ideal model delta sigma weight residual False -2.54 2.55 -5.09 2.00e-01 2.50e+01 6.48e+02 chirality pdb=" C8 PT5 D 801 " pdb=" C7 PT5 D 801 " pdb=" C9 PT5 D 801 " pdb=" O16 PT5 D 801 " both_signs ideal model delta sigma weight residual False -2.54 2.55 -5.09 2.00e-01 2.50e+01 6.48e+02 ... (remaining 2457 not shown) Planarity restraints: 2680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 PT5 G 801 " 0.071 2.00e-02 2.50e+03 7.14e-02 5.10e+01 pdb=" C21 PT5 G 801 " -0.072 2.00e-02 2.50e+03 pdb=" C22 PT5 G 801 " -0.071 2.00e-02 2.50e+03 pdb=" C23 PT5 G 801 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 PT5 A 801 " -0.071 2.00e-02 2.50e+03 7.14e-02 5.09e+01 pdb=" C21 PT5 A 801 " 0.072 2.00e-02 2.50e+03 pdb=" C22 PT5 A 801 " 0.071 2.00e-02 2.50e+03 pdb=" C23 PT5 A 801 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 PT5 J 801 " 0.071 2.00e-02 2.50e+03 7.12e-02 5.07e+01 pdb=" C21 PT5 J 801 " -0.071 2.00e-02 2.50e+03 pdb=" C22 PT5 J 801 " -0.071 2.00e-02 2.50e+03 pdb=" C23 PT5 J 801 " 0.071 2.00e-02 2.50e+03 ... (remaining 2677 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4276 2.79 - 3.32: 13676 3.32 - 3.84: 24466 3.84 - 4.37: 27813 4.37 - 4.90: 46469 Nonbonded interactions: 116700 Sorted by model distance: nonbonded pdb=" OG1 THR D 144 " pdb=" OH TYR G 281 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR A 144 " pdb=" OH TYR D 281 " model vdw 2.267 2.440 nonbonded pdb=" OG SER D 277 " pdb=" O ALA D 302 " model vdw 2.302 2.440 nonbonded pdb=" OG SER G 277 " pdb=" O ALA G 302 " model vdw 2.303 2.440 nonbonded pdb=" OG SER A 277 " pdb=" O ALA A 302 " model vdw 2.303 2.440 ... (remaining 116695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.83 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.940 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 39.150 Find NCS groups from input model: 1.090 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: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 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 : 0.009 0.096 15800 Z= 0.573 Angle : 1.311 39.722 21436 Z= 0.642 Chirality : 0.216 5.095 2460 Planarity : 0.007 0.071 2680 Dihedral : 17.598 178.163 5260 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.42 % 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: -5.38 (0.12), residues: 2012 helix: -3.48 (0.09), residues: 1336 sheet: None (None), residues: 0 loop : -3.34 (0.17), residues: 676 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 363 time to evaluate : 1.613 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 12 residues processed: 387 average time/residue: 0.3187 time to fit residues: 173.2522 Evaluate side-chains 251 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 239 time to evaluate : 1.727 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1327 time to fit residues: 5.4117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 HIS A 357 GLN A 359 GLN A 376 GLN J 147 GLN J 359 GLN ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 GLN D 363 HIS G 357 GLN ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15800 Z= 0.208 Angle : 0.604 5.567 21436 Z= 0.313 Chirality : 0.040 0.201 2460 Planarity : 0.004 0.036 2680 Dihedral : 11.379 145.205 2312 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 1.61 % 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: -3.84 (0.15), residues: 2012 helix: -2.19 (0.11), residues: 1368 sheet: None (None), residues: 0 loop : -3.02 (0.20), residues: 644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 242 time to evaluate : 3.524 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 258 average time/residue: 0.2667 time to fit residues: 102.1713 Evaluate side-chains 232 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1371 time to fit residues: 6.3275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 148 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 GLN G 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 15800 Z= 0.236 Angle : 0.560 5.802 21436 Z= 0.291 Chirality : 0.040 0.192 2460 Planarity : 0.004 0.033 2680 Dihedral : 10.315 129.637 2312 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 2.41 % 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: -2.63 (0.17), residues: 2012 helix: -1.22 (0.13), residues: 1376 sheet: None (None), residues: 0 loop : -2.68 (0.22), residues: 636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 230 time to evaluate : 1.811 Fit side-chains outliers start: 33 outliers final: 13 residues processed: 252 average time/residue: 0.2543 time to fit residues: 98.0929 Evaluate side-chains 210 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 197 time to evaluate : 1.675 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1323 time to fit residues: 5.5915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.5980 chunk 139 optimal weight: 7.9990 chunk 96 optimal weight: 0.2980 chunk 20 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 186 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 15800 Z= 0.152 Angle : 0.505 6.934 21436 Z= 0.262 Chirality : 0.038 0.201 2460 Planarity : 0.003 0.029 2680 Dihedral : 9.657 121.963 2312 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 2.49 % 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: -1.95 (0.18), residues: 2012 helix: -0.70 (0.14), residues: 1364 sheet: None (None), residues: 0 loop : -2.41 (0.23), residues: 648 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 222 time to evaluate : 1.844 Fit side-chains outliers start: 34 outliers final: 17 residues processed: 250 average time/residue: 0.2263 time to fit residues: 89.4651 Evaluate side-chains 219 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 1.705 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1326 time to fit residues: 6.5382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 chunk 146 optimal weight: 0.0020 chunk 81 optimal weight: 0.6980 chunk 168 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15800 Z= 0.175 Angle : 0.506 6.538 21436 Z= 0.260 Chirality : 0.038 0.187 2460 Planarity : 0.003 0.029 2680 Dihedral : 9.322 117.420 2312 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 2.05 % 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: -1.68 (0.18), residues: 2012 helix: -0.47 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 644 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 1.991 Fit side-chains outliers start: 28 outliers final: 7 residues processed: 236 average time/residue: 0.2424 time to fit residues: 89.5379 Evaluate side-chains 208 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 201 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1505 time to fit residues: 4.3199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 38 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 363 HIS ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 510 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15800 Z= 0.204 Angle : 0.522 7.919 21436 Z= 0.267 Chirality : 0.039 0.183 2460 Planarity : 0.003 0.057 2680 Dihedral : 9.129 114.276 2312 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.83 % 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: -1.43 (0.19), residues: 2012 helix: -0.32 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : -2.18 (0.24), residues: 644 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 215 time to evaluate : 1.716 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 230 average time/residue: 0.2328 time to fit residues: 84.3904 Evaluate side-chains 211 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 200 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1446 time to fit residues: 5.4079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 112 optimal weight: 6.9990 chunk 144 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 15800 Z= 0.165 Angle : 0.506 8.659 21436 Z= 0.257 Chirality : 0.038 0.183 2460 Planarity : 0.003 0.031 2680 Dihedral : 8.931 122.591 2312 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 1.10 % 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: -1.17 (0.19), residues: 2012 helix: -0.10 (0.14), residues: 1360 sheet: None (None), residues: 0 loop : -2.13 (0.24), residues: 652 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 1.808 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 228 average time/residue: 0.2218 time to fit residues: 81.2533 Evaluate side-chains 209 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 200 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1527 time to fit residues: 4.6915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 125 optimal weight: 0.0970 chunk 133 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 GLN ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15800 Z= 0.172 Angle : 0.518 9.548 21436 Z= 0.261 Chirality : 0.038 0.183 2460 Planarity : 0.003 0.032 2680 Dihedral : 8.916 142.248 2312 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.46 % 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: -1.06 (0.19), residues: 2012 helix: 0.01 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : -2.16 (0.23), residues: 644 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 1.826 Fit side-chains outliers start: 20 outliers final: 8 residues processed: 217 average time/residue: 0.2130 time to fit residues: 75.8165 Evaluate side-chains 211 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1487 time to fit residues: 4.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 165 optimal weight: 0.0770 chunk 173 optimal weight: 0.4980 chunk 182 optimal weight: 0.1980 chunk 120 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 15800 Z= 0.152 Angle : 0.516 11.616 21436 Z= 0.257 Chirality : 0.038 0.184 2460 Planarity : 0.003 0.031 2680 Dihedral : 8.921 159.408 2312 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.19), residues: 2012 helix: 0.25 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -2.18 (0.23), residues: 668 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 207 time to evaluate : 1.943 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 211 average time/residue: 0.2213 time to fit residues: 75.9658 Evaluate side-chains 196 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 1.652 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1721 time to fit residues: 3.2453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.9990 chunk 118 optimal weight: 0.0020 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 161 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 99 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 15800 Z= 0.153 Angle : 0.525 12.232 21436 Z= 0.262 Chirality : 0.038 0.184 2460 Planarity : 0.003 0.032 2680 Dihedral : 8.940 174.112 2312 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 2012 helix: 0.41 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -2.23 (0.22), residues: 692 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 1.689 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 211 average time/residue: 0.2245 time to fit residues: 78.9195 Evaluate side-chains 195 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 1.877 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1747 time to fit residues: 3.2900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 49 optimal weight: 0.0070 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.200298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.194836 restraints weight = 16900.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.193996 restraints weight = 34620.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.178246 restraints weight = 37807.287| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 15800 Z= 0.218 Angle : 0.563 11.040 21436 Z= 0.281 Chirality : 0.039 0.182 2460 Planarity : 0.003 0.033 2680 Dihedral : 9.025 171.134 2312 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.18), residues: 2012 helix: 0.31 (0.14), residues: 1360 sheet: None (None), residues: 0 loop : -2.52 (0.21), residues: 652 =============================================================================== Job complete usr+sys time: 2640.78 seconds wall clock time: 49 minutes 9.80 seconds (2949.80 seconds total)