Starting phenix.real_space_refine on Sat Mar 16 19:28:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/03_2024/6v01_20967_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/03_2024/6v01_20967.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/03_2024/6v01_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_20967/03_2024/6v01_20967_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/03_2024/6v01_20967_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/03_2024/6v01_20967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/03_2024/6v01_20967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/03_2024/6v01_20967_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v01_20967/03_2024/6v01_20967_updated.pdb" } resolution = 3.9 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= 0.003 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.03, per 1000 atoms: 0.52 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: 5.29 Conformation dependent library (CDL) restraints added in 2.9 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: 3.44 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: 3.90 Time building geometry restraints manager: 5.83 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: 8824 35.63 - 71.27: 228 71.27 - 106.90: 40 106.90 - 142.53: 20 142.53 - 178.16: 4 Dihedral angle restraints: 9116 sinusoidal: 3180 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 9113 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.200 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 41.200 Find NCS groups from input model: 1.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.750 ------------------------------------------------------------------------------- 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 : 18.922 178.163 5292 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 % Allowed : 9.65 % Favored : 88.01 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP G 305 HIS 0.007 0.002 HIS D 549 PHE 0.032 0.002 PHE D 332 TYR 0.014 0.002 TYR D 111 ARG 0.003 0.001 ARG D 561 *********************** 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 : 1.794 Fit side-chains revert: symmetry clash REVERT: C 54 ASP cc_start: 0.6924 (m-30) cc_final: 0.6479 (p0) REVERT: C 61 ILE cc_start: 0.9504 (mt) cc_final: 0.9298 (mt) REVERT: L 54 ASP cc_start: 0.6886 (m-30) cc_final: 0.6173 (p0) REVERT: A 147 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7066 (tt0) REVERT: A 159 MET cc_start: 0.7486 (ttt) cc_final: 0.7244 (ttt) REVERT: A 249 ARG cc_start: 0.7552 (mtp85) cc_final: 0.6978 (ttm-80) REVERT: A 377 THR cc_start: 0.7054 (m) cc_final: 0.6784 (m) REVERT: A 546 SER cc_start: 0.6483 (OUTLIER) cc_final: 0.6194 (m) REVERT: J 116 ARG cc_start: 0.6729 (ptt180) cc_final: 0.6295 (ptm-80) REVERT: J 120 TRP cc_start: 0.6505 (t-100) cc_final: 0.6106 (m100) REVERT: J 147 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7448 (tt0) REVERT: J 157 PHE cc_start: 0.7822 (t80) cc_final: 0.7152 (t80) REVERT: J 249 ARG cc_start: 0.7606 (mtp85) cc_final: 0.7011 (ttm-80) REVERT: J 253 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8756 (t) REVERT: J 286 ASP cc_start: 0.6345 (m-30) cc_final: 0.6085 (p0) REVERT: J 531 GLN cc_start: 0.7123 (mt0) cc_final: 0.6911 (tt0) REVERT: J 546 SER cc_start: 0.6319 (OUTLIER) cc_final: 0.5905 (m) REVERT: D 159 MET cc_start: 0.7515 (ttt) cc_final: 0.7206 (ttm) REVERT: D 249 ARG cc_start: 0.7533 (mtp85) cc_final: 0.6946 (ttm-80) REVERT: D 284 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8303 (mm-30) REVERT: D 364 PHE cc_start: 0.7768 (t80) cc_final: 0.6547 (m-10) REVERT: G 116 ARG cc_start: 0.6938 (ptt180) cc_final: 0.6279 (ptt90) REVERT: G 139 PHE cc_start: 0.7886 (m-10) cc_final: 0.7654 (m-10) REVERT: G 157 PHE cc_start: 0.8142 (t80) cc_final: 0.7786 (t80) REVERT: G 284 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8319 (mm-30) REVERT: G 286 ASP cc_start: 0.6779 (m-30) cc_final: 0.6380 (p0) REVERT: G 365 ASN cc_start: 0.7823 (m110) cc_final: 0.7460 (t0) REVERT: G 519 ARG cc_start: 0.6593 (mtm180) cc_final: 0.6362 (mtm-85) REVERT: G 546 SER cc_start: 0.6472 (OUTLIER) cc_final: 0.5795 (m) outliers start: 32 outliers final: 12 residues processed: 387 average time/residue: 0.3097 time to fit residues: 168.4075 Evaluate side-chains 261 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 245 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain J residue 253 SER Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 546 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 546 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 185 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 376 GLN ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 GLN G 365 ASN ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2180 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= 0.187 Angle : 0.582 5.730 21436 Z= 0.303 Chirality : 0.040 0.205 2460 Planarity : 0.004 0.034 2680 Dihedral : 15.781 146.773 2360 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.68 % Allowed : 18.79 % Favored : 79.53 % 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: -3.77 (0.15), residues: 2012 helix: -2.15 (0.11), residues: 1364 sheet: None (None), residues: 0 loop : -2.95 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 304 HIS 0.006 0.001 HIS G 549 PHE 0.026 0.002 PHE D 123 TYR 0.018 0.001 TYR L 79 ARG 0.005 0.000 ARG A 190 *********************** 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 278 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 255 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: C 54 ASP cc_start: 0.6759 (m-30) cc_final: 0.6344 (p0) REVERT: H 115 GLU cc_start: 0.6510 (pt0) cc_final: 0.6236 (pt0) REVERT: I 79 TYR cc_start: 0.7308 (t80) cc_final: 0.6908 (t80) REVERT: L 79 TYR cc_start: 0.6927 (t80) cc_final: 0.6716 (t80) REVERT: A 147 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7175 (tt0) REVERT: A 190 ARG cc_start: 0.6840 (tpp80) cc_final: 0.6367 (mmm-85) REVERT: A 249 ARG cc_start: 0.7713 (mtp85) cc_final: 0.7007 (ttm-80) REVERT: A 286 ASP cc_start: 0.6545 (m-30) cc_final: 0.6335 (p0) REVERT: J 146 GLU cc_start: 0.5622 (mp0) cc_final: 0.5402 (mp0) REVERT: J 249 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7022 (ttm-80) REVERT: J 354 LYS cc_start: 0.8494 (tppt) cc_final: 0.8011 (tptp) REVERT: J 553 MET cc_start: 0.6024 (tpp) cc_final: 0.5568 (tpp) REVERT: D 159 MET cc_start: 0.7290 (ttt) cc_final: 0.7069 (ttt) REVERT: D 284 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8108 (mm-30) REVERT: G 139 PHE cc_start: 0.7934 (m-10) cc_final: 0.7675 (m-10) REVERT: G 157 PHE cc_start: 0.7940 (t80) cc_final: 0.7683 (t80) REVERT: G 238 MET cc_start: 0.6782 (mmm) cc_final: 0.6531 (mmt) REVERT: G 284 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8311 (mm-30) REVERT: G 286 ASP cc_start: 0.6855 (m-30) cc_final: 0.6486 (p0) outliers start: 23 outliers final: 14 residues processed: 270 average time/residue: 0.2747 time to fit residues: 108.0000 Evaluate side-chains 238 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 224 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 531 GLN 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: 1.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15800 Z= 0.349 Angle : 0.629 5.560 21436 Z= 0.329 Chirality : 0.043 0.202 2460 Planarity : 0.004 0.039 2680 Dihedral : 15.017 128.324 2350 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.73 % Allowed : 22.73 % Favored : 73.54 % 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: -2.87 (0.17), residues: 2012 helix: -1.45 (0.13), residues: 1376 sheet: None (None), residues: 0 loop : -2.65 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 304 HIS 0.005 0.001 HIS G 258 PHE 0.031 0.002 PHE A 123 TYR 0.022 0.002 TYR J 522 ARG 0.008 0.001 ARG J 116 *********************** 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 270 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 219 time to evaluate : 1.693 Fit side-chains revert: symmetry clash REVERT: C 54 ASP cc_start: 0.6970 (m-30) cc_final: 0.6696 (p0) REVERT: A 249 ARG cc_start: 0.7834 (mtp85) cc_final: 0.7054 (ttm-80) REVERT: A 261 GLU cc_start: 0.8164 (mp0) cc_final: 0.7824 (mp0) REVERT: A 286 ASP cc_start: 0.6623 (m-30) cc_final: 0.6362 (p0) REVERT: A 364 PHE cc_start: 0.7663 (t80) cc_final: 0.6276 (m-10) REVERT: J 249 ARG cc_start: 0.7770 (mtp85) cc_final: 0.7030 (ttm-80) REVERT: J 261 GLU cc_start: 0.8248 (mp0) cc_final: 0.7911 (mp0) REVERT: J 354 LYS cc_start: 0.8530 (tppt) cc_final: 0.8015 (tptp) REVERT: J 374 LEU cc_start: 0.8719 (tp) cc_final: 0.8501 (tt) REVERT: D 190 ARG cc_start: 0.6093 (mmm-85) cc_final: 0.5848 (mtt180) REVERT: D 249 ARG cc_start: 0.7732 (mtp85) cc_final: 0.6943 (ttm-80) REVERT: D 261 GLU cc_start: 0.8231 (mp0) cc_final: 0.7820 (mp0) REVERT: D 286 ASP cc_start: 0.6602 (m-30) cc_final: 0.6352 (p0) REVERT: D 515 LYS cc_start: 0.7683 (mtmt) cc_final: 0.7322 (mtmm) REVERT: G 157 PHE cc_start: 0.7982 (t80) cc_final: 0.7760 (t80) REVERT: G 286 ASP cc_start: 0.6944 (m-30) cc_final: 0.6509 (p0) outliers start: 51 outliers final: 34 residues processed: 253 average time/residue: 0.2338 time to fit residues: 90.5977 Evaluate side-chains 235 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 375 ILE Chi-restraints excluded: chain J residue 524 VAL Chi-restraints excluded: chain J residue 554 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 531 GLN Chi-restraints excluded: chain G residue 554 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 96 optimal weight: 0.1980 chunk 20 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 186 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 365 ASN G 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15800 Z= 0.159 Angle : 0.502 6.004 21436 Z= 0.263 Chirality : 0.039 0.190 2460 Planarity : 0.003 0.028 2680 Dihedral : 14.401 121.761 2348 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.00 % Allowed : 24.42 % Favored : 72.59 % 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: -2.29 (0.18), residues: 2012 helix: -0.93 (0.14), residues: 1388 sheet: None (None), residues: 0 loop : -2.65 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 379 HIS 0.004 0.001 HIS G 549 PHE 0.026 0.001 PHE D 123 TYR 0.019 0.001 TYR J 522 ARG 0.007 0.000 ARG G 237 *********************** 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 263 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 222 time to evaluate : 1.629 Fit side-chains REVERT: C 54 ASP cc_start: 0.6936 (m-30) cc_final: 0.6723 (p0) REVERT: F 54 ASP cc_start: 0.7321 (m-30) cc_final: 0.7018 (p0) REVERT: A 157 PHE cc_start: 0.7797 (t80) cc_final: 0.7467 (t80) REVERT: A 249 ARG cc_start: 0.7787 (mtp85) cc_final: 0.7010 (ttm-80) REVERT: A 261 GLU cc_start: 0.8151 (mp0) cc_final: 0.7946 (mp0) REVERT: A 286 ASP cc_start: 0.6602 (m-30) cc_final: 0.6368 (p0) REVERT: A 354 LYS cc_start: 0.8336 (tppt) cc_final: 0.7893 (tptp) REVERT: J 157 PHE cc_start: 0.7734 (t80) cc_final: 0.7388 (t80) REVERT: J 249 ARG cc_start: 0.7687 (mtp85) cc_final: 0.6957 (ttm-80) REVERT: J 261 GLU cc_start: 0.8241 (mp0) cc_final: 0.7963 (mp0) REVERT: J 284 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8017 (mt-10) REVERT: J 354 LYS cc_start: 0.8263 (tppt) cc_final: 0.7866 (tptp) REVERT: D 249 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7002 (ttm-80) REVERT: D 261 GLU cc_start: 0.8132 (mp0) cc_final: 0.7931 (mp0) REVERT: D 286 ASP cc_start: 0.6778 (m-30) cc_final: 0.6422 (p0) REVERT: D 354 LYS cc_start: 0.8232 (tppt) cc_final: 0.7863 (tptp) REVERT: D 515 LYS cc_start: 0.7680 (mtmt) cc_final: 0.7245 (mtmm) REVERT: D 522 TYR cc_start: 0.8058 (t80) cc_final: 0.7737 (t80) REVERT: G 157 PHE cc_start: 0.8100 (t80) cc_final: 0.7829 (t80) REVERT: G 286 ASP cc_start: 0.6962 (m-30) cc_final: 0.6473 (p0) REVERT: G 546 SER cc_start: 0.6166 (p) cc_final: 0.5883 (m) outliers start: 41 outliers final: 19 residues processed: 254 average time/residue: 0.2477 time to fit residues: 95.7915 Evaluate side-chains 230 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 211 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain J residue 240 HIS Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 375 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 531 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15800 Z= 0.268 Angle : 0.557 6.240 21436 Z= 0.289 Chirality : 0.041 0.190 2460 Planarity : 0.004 0.033 2680 Dihedral : 14.355 140.336 2348 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.97 % Allowed : 23.83 % Favored : 71.20 % 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: -0.71 (0.14), residues: 1380 sheet: None (None), residues: 0 loop : -2.41 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 379 HIS 0.004 0.001 HIS G 240 PHE 0.032 0.002 PHE A 123 TYR 0.017 0.002 TYR J 522 ARG 0.007 0.000 ARG G 237 *********************** 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 276 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 208 time to evaluate : 1.464 Fit side-chains REVERT: C 54 ASP cc_start: 0.6998 (m-30) cc_final: 0.6648 (p0) REVERT: I 79 TYR cc_start: 0.7339 (t80) cc_final: 0.6742 (t80) REVERT: L 79 TYR cc_start: 0.6900 (t80) cc_final: 0.6656 (t80) REVERT: A 249 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7017 (ttm-80) REVERT: A 261 GLU cc_start: 0.8162 (mp0) cc_final: 0.7878 (mp0) REVERT: A 286 ASP cc_start: 0.6748 (m-30) cc_final: 0.6451 (p0) REVERT: A 354 LYS cc_start: 0.8501 (tppt) cc_final: 0.8045 (tptp) REVERT: J 157 PHE cc_start: 0.7820 (t80) cc_final: 0.7545 (t80) REVERT: J 249 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7025 (ttm-80) REVERT: J 261 GLU cc_start: 0.8172 (mp0) cc_final: 0.7896 (mp0) REVERT: J 354 LYS cc_start: 0.8410 (tppt) cc_final: 0.8010 (tptp) REVERT: D 184 TYR cc_start: 0.5464 (OUTLIER) cc_final: 0.4515 (p90) REVERT: D 249 ARG cc_start: 0.7739 (mtp85) cc_final: 0.6992 (ttm-80) REVERT: D 261 GLU cc_start: 0.8119 (mp0) cc_final: 0.7796 (mp0) REVERT: D 286 ASP cc_start: 0.6715 (m-30) cc_final: 0.6373 (p0) REVERT: D 354 LYS cc_start: 0.8307 (tppt) cc_final: 0.7865 (tptp) REVERT: D 515 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7157 (mtmm) REVERT: D 522 TYR cc_start: 0.8085 (t80) cc_final: 0.7723 (t80) REVERT: G 157 PHE cc_start: 0.8248 (t80) cc_final: 0.8008 (t80) REVERT: G 261 GLU cc_start: 0.7977 (mp0) cc_final: 0.7655 (mp0) REVERT: G 286 ASP cc_start: 0.6795 (m-30) cc_final: 0.6586 (p0) REVERT: G 354 LYS cc_start: 0.8431 (tppt) cc_final: 0.8002 (tptp) REVERT: G 364 PHE cc_start: 0.7684 (t80) cc_final: 0.6347 (m-10) outliers start: 68 outliers final: 41 residues processed: 268 average time/residue: 0.2390 time to fit residues: 99.3274 Evaluate side-chains 245 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 203 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 240 HIS Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 524 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 TYR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 HIS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 115 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 197 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 510 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15800 Z= 0.176 Angle : 0.501 7.543 21436 Z= 0.259 Chirality : 0.039 0.183 2460 Planarity : 0.003 0.031 2680 Dihedral : 14.311 165.750 2348 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.87 % Allowed : 25.80 % Favored : 70.32 % 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: -1.64 (0.19), residues: 2012 helix: -0.43 (0.14), residues: 1352 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 379 HIS 0.003 0.001 HIS G 240 PHE 0.030 0.001 PHE D 123 TYR 0.014 0.001 TYR J 522 ARG 0.006 0.000 ARG G 237 *********************** 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 284 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 231 time to evaluate : 1.764 Fit side-chains REVERT: I 79 TYR cc_start: 0.7287 (t80) cc_final: 0.6687 (t80) REVERT: L 79 TYR cc_start: 0.6986 (t80) cc_final: 0.6699 (t80) REVERT: A 249 ARG cc_start: 0.7719 (mtp85) cc_final: 0.6936 (ttm-80) REVERT: A 286 ASP cc_start: 0.6656 (m-30) cc_final: 0.6394 (p0) REVERT: A 354 LYS cc_start: 0.8273 (tppt) cc_final: 0.7902 (tptp) REVERT: J 157 PHE cc_start: 0.7838 (t80) cc_final: 0.7582 (t80) REVERT: J 237 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7655 (mtp180) REVERT: J 249 ARG cc_start: 0.7690 (mtp85) cc_final: 0.6866 (ttm-80) REVERT: J 284 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7766 (mt-10) REVERT: J 354 LYS cc_start: 0.8305 (tppt) cc_final: 0.7945 (tptp) REVERT: D 184 TYR cc_start: 0.5529 (OUTLIER) cc_final: 0.4638 (p90) REVERT: D 249 ARG cc_start: 0.7722 (mtp85) cc_final: 0.6972 (ttm-80) REVERT: D 286 ASP cc_start: 0.6870 (m-30) cc_final: 0.6506 (p0) REVERT: D 354 LYS cc_start: 0.8327 (tppt) cc_final: 0.7931 (tptp) REVERT: D 515 LYS cc_start: 0.7548 (mtmt) cc_final: 0.6980 (mtmm) REVERT: D 522 TYR cc_start: 0.8071 (t80) cc_final: 0.7751 (t80) REVERT: G 157 PHE cc_start: 0.8200 (t80) cc_final: 0.7997 (t80) REVERT: G 249 ARG cc_start: 0.7778 (mtp85) cc_final: 0.6945 (ttm-80) REVERT: G 286 ASP cc_start: 0.6865 (m-30) cc_final: 0.6573 (p0) REVERT: G 354 LYS cc_start: 0.8391 (tppt) cc_final: 0.8027 (tptp) REVERT: G 364 PHE cc_start: 0.7596 (t80) cc_final: 0.6274 (m-10) REVERT: G 546 SER cc_start: 0.6253 (p) cc_final: 0.5957 (m) REVERT: G 553 MET cc_start: 0.6296 (tpp) cc_final: 0.5850 (tpp) outliers start: 53 outliers final: 35 residues processed: 278 average time/residue: 0.2555 time to fit residues: 106.2755 Evaluate side-chains 248 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 212 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 240 HIS Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 361 GLN Chi-restraints excluded: chain J residue 524 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 TYR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 HIS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 365 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.3980 chunk 22 optimal weight: 0.0770 chunk 112 optimal weight: 0.3980 chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 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: 0.6914 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15800 Z= 0.139 Angle : 0.488 9.232 21436 Z= 0.251 Chirality : 0.038 0.182 2460 Planarity : 0.003 0.030 2680 Dihedral : 14.324 176.321 2348 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.36 % Allowed : 27.78 % Favored : 68.86 % 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: -1.38 (0.19), residues: 2012 helix: -0.23 (0.14), residues: 1364 sheet: None (None), residues: 0 loop : -2.29 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 379 HIS 0.003 0.001 HIS G 240 PHE 0.030 0.001 PHE D 123 TYR 0.012 0.001 TYR J 522 ARG 0.008 0.000 ARG G 237 *********************** 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 265 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 219 time to evaluate : 1.675 Fit side-chains REVERT: C 65 MET cc_start: 0.8308 (mmt) cc_final: 0.7935 (mmt) REVERT: I 79 TYR cc_start: 0.7170 (t80) cc_final: 0.6698 (t80) REVERT: L 79 TYR cc_start: 0.7068 (t80) cc_final: 0.6845 (t80) REVERT: A 237 ARG cc_start: 0.7886 (mtp180) cc_final: 0.7632 (mtp180) REVERT: A 249 ARG cc_start: 0.7700 (mtp85) cc_final: 0.6950 (ttm-80) REVERT: A 286 ASP cc_start: 0.6575 (m-30) cc_final: 0.6370 (p0) REVERT: A 354 LYS cc_start: 0.8335 (tppt) cc_final: 0.7980 (tptp) REVERT: J 192 ARG cc_start: 0.5248 (mmp-170) cc_final: 0.4154 (ptp-170) REVERT: J 237 ARG cc_start: 0.7910 (mtp180) cc_final: 0.7659 (mtp180) REVERT: J 249 ARG cc_start: 0.7735 (mtp85) cc_final: 0.6957 (ttm-80) REVERT: J 284 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7689 (mt-10) REVERT: J 354 LYS cc_start: 0.8369 (tppt) cc_final: 0.8014 (tptp) REVERT: D 184 TYR cc_start: 0.5454 (OUTLIER) cc_final: 0.4699 (p90) REVERT: D 249 ARG cc_start: 0.7713 (mtp85) cc_final: 0.6964 (ttm-80) REVERT: D 286 ASP cc_start: 0.6819 (m-30) cc_final: 0.6430 (p0) REVERT: D 354 LYS cc_start: 0.8344 (tppt) cc_final: 0.7968 (tptp) REVERT: D 522 TYR cc_start: 0.8088 (t80) cc_final: 0.7833 (t80) REVERT: G 249 ARG cc_start: 0.7792 (mtp85) cc_final: 0.6962 (ttm-80) REVERT: G 286 ASP cc_start: 0.6829 (m-30) cc_final: 0.6533 (p0) REVERT: G 354 LYS cc_start: 0.8397 (tppt) cc_final: 0.8040 (tptp) REVERT: G 546 SER cc_start: 0.6242 (p) cc_final: 0.5936 (m) REVERT: G 553 MET cc_start: 0.6411 (tpp) cc_final: 0.6016 (tpp) outliers start: 46 outliers final: 34 residues processed: 259 average time/residue: 0.2444 time to fit residues: 96.4368 Evaluate side-chains 242 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 240 HIS Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 361 GLN Chi-restraints excluded: chain J residue 382 TYR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 TYR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 HIS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 342 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15800 Z= 0.257 Angle : 0.553 10.908 21436 Z= 0.282 Chirality : 0.041 0.182 2460 Planarity : 0.004 0.032 2680 Dihedral : 14.307 173.006 2348 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.17 % Allowed : 27.12 % Favored : 68.71 % 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: -1.34 (0.19), residues: 2012 helix: -0.28 (0.14), residues: 1340 sheet: None (None), residues: 0 loop : -2.00 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 379 HIS 0.004 0.001 HIS D 240 PHE 0.043 0.002 PHE E 90 TYR 0.019 0.001 TYR E 139 ARG 0.006 0.000 ARG G 237 *********************** 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 269 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 212 time to evaluate : 1.616 Fit side-chains REVERT: I 79 TYR cc_start: 0.7323 (t80) cc_final: 0.6792 (t80) REVERT: A 249 ARG cc_start: 0.7734 (mtp85) cc_final: 0.6982 (ttm-80) REVERT: A 354 LYS cc_start: 0.8400 (tppt) cc_final: 0.8006 (tptp) REVERT: J 237 ARG cc_start: 0.7921 (mtp180) cc_final: 0.7608 (mtp180) REVERT: J 249 ARG cc_start: 0.7705 (mtp85) cc_final: 0.6936 (ttm-80) REVERT: J 354 LYS cc_start: 0.8416 (tppt) cc_final: 0.8021 (tptp) REVERT: D 184 TYR cc_start: 0.5685 (OUTLIER) cc_final: 0.4773 (p90) REVERT: D 249 ARG cc_start: 0.7696 (mtp85) cc_final: 0.6955 (ttm-80) REVERT: D 286 ASP cc_start: 0.6954 (m-30) cc_final: 0.6559 (p0) REVERT: D 354 LYS cc_start: 0.8373 (tppt) cc_final: 0.7955 (tptp) REVERT: D 522 TYR cc_start: 0.8054 (t80) cc_final: 0.7729 (t80) REVERT: G 249 ARG cc_start: 0.7789 (mtp85) cc_final: 0.6961 (ttm-80) REVERT: G 286 ASP cc_start: 0.6937 (m-30) cc_final: 0.6631 (p0) REVERT: G 354 LYS cc_start: 0.8471 (tppt) cc_final: 0.8105 (tptp) REVERT: G 553 MET cc_start: 0.6753 (tpp) cc_final: 0.6385 (tpp) outliers start: 57 outliers final: 47 residues processed: 261 average time/residue: 0.2223 time to fit residues: 90.3657 Evaluate side-chains 254 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 206 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 240 HIS Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 361 GLN Chi-restraints excluded: chain J residue 524 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 TYR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 HIS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 365 ASN Chi-restraints excluded: chain G residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 182 optimal weight: 0.1980 chunk 120 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.4254 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= 0.177 Angle : 0.531 11.652 21436 Z= 0.268 Chirality : 0.039 0.178 2460 Planarity : 0.003 0.029 2680 Dihedral : 13.793 154.634 2348 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.65 % Allowed : 27.92 % Favored : 68.42 % 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: -1.28 (0.19), residues: 2012 helix: -0.14 (0.14), residues: 1348 sheet: None (None), residues: 0 loop : -2.22 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J 379 HIS 0.005 0.001 HIS D 240 PHE 0.031 0.001 PHE D 123 TYR 0.027 0.001 TYR L 79 ARG 0.007 0.000 ARG G 237 *********************** 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 268 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 218 time to evaluate : 1.804 Fit side-chains REVERT: I 79 TYR cc_start: 0.7266 (t80) cc_final: 0.6742 (t80) REVERT: A 192 ARG cc_start: 0.5493 (mmp-170) cc_final: 0.4073 (ptm160) REVERT: A 237 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7641 (mtp180) REVERT: A 249 ARG cc_start: 0.7740 (mtp85) cc_final: 0.6963 (ttm-80) REVERT: A 354 LYS cc_start: 0.8378 (tppt) cc_final: 0.8014 (tptp) REVERT: A 522 TYR cc_start: 0.8083 (t80) cc_final: 0.7721 (t80) REVERT: J 192 ARG cc_start: 0.5485 (mmp-170) cc_final: 0.4151 (ptp-170) REVERT: J 237 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7706 (mtp180) REVERT: J 249 ARG cc_start: 0.7690 (mtp85) cc_final: 0.6892 (ttm-80) REVERT: J 284 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7671 (mt-10) REVERT: J 354 LYS cc_start: 0.8394 (tppt) cc_final: 0.8020 (tptp) REVERT: D 184 TYR cc_start: 0.5692 (OUTLIER) cc_final: 0.4987 (p90) REVERT: D 249 ARG cc_start: 0.7684 (mtp85) cc_final: 0.6943 (ttm-80) REVERT: D 286 ASP cc_start: 0.6887 (m-30) cc_final: 0.6493 (p0) REVERT: D 354 LYS cc_start: 0.8367 (tppt) cc_final: 0.7979 (tptp) REVERT: D 522 TYR cc_start: 0.8041 (t80) cc_final: 0.7806 (t80) REVERT: G 249 ARG cc_start: 0.7760 (mtp85) cc_final: 0.6934 (ttm-80) REVERT: G 286 ASP cc_start: 0.6933 (m-30) cc_final: 0.6637 (p0) REVERT: G 354 LYS cc_start: 0.8306 (tppt) cc_final: 0.8011 (tptp) REVERT: G 546 SER cc_start: 0.6422 (p) cc_final: 0.6077 (m) REVERT: G 553 MET cc_start: 0.6834 (tpp) cc_final: 0.6399 (tpp) outliers start: 50 outliers final: 43 residues processed: 260 average time/residue: 0.2407 time to fit residues: 96.3354 Evaluate side-chains 256 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 212 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 240 HIS Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 361 GLN Chi-restraints excluded: chain J residue 524 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 TYR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 HIS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 365 ASN Chi-restraints excluded: chain G residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 161 optimal weight: 0.1980 chunk 16 optimal weight: 0.1980 chunk 125 optimal weight: 0.3980 chunk 99 optimal weight: 8.9990 chunk 128 optimal weight: 0.0980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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: 0.6892 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15800 Z= 0.138 Angle : 0.525 10.697 21436 Z= 0.262 Chirality : 0.038 0.176 2460 Planarity : 0.003 0.029 2680 Dihedral : 13.149 128.220 2348 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.27 % Allowed : 28.95 % Favored : 68.79 % 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: -1.05 (0.18), residues: 2012 helix: 0.14 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : -2.49 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP J 379 HIS 0.004 0.001 HIS G 240 PHE 0.031 0.001 PHE D 123 TYR 0.016 0.001 TYR B 139 ARG 0.009 0.000 ARG G 237 ********************** 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 255 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 224 time to evaluate : 1.693 Fit side-chains REVERT: C 65 MET cc_start: 0.8329 (mmt) cc_final: 0.7968 (mmt) REVERT: F 57 SER cc_start: 0.9387 (t) cc_final: 0.9174 (t) REVERT: F 77 LEU cc_start: 0.8098 (tt) cc_final: 0.7884 (tp) REVERT: A 192 ARG cc_start: 0.5315 (mmp-170) cc_final: 0.4019 (ptm160) REVERT: A 237 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7610 (mtp180) REVERT: A 249 ARG cc_start: 0.7698 (mtp85) cc_final: 0.6927 (ttm-80) REVERT: A 354 LYS cc_start: 0.8346 (tppt) cc_final: 0.8011 (tptp) REVERT: A 522 TYR cc_start: 0.8054 (t80) cc_final: 0.7765 (t80) REVERT: J 192 ARG cc_start: 0.5453 (mmp-170) cc_final: 0.4059 (ptp-170) REVERT: J 237 ARG cc_start: 0.7898 (mtp180) cc_final: 0.7635 (mtp180) REVERT: J 249 ARG cc_start: 0.7637 (mtp85) cc_final: 0.6846 (ttm-80) REVERT: J 284 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7549 (mt-10) REVERT: J 354 LYS cc_start: 0.8351 (tppt) cc_final: 0.8020 (tptp) REVERT: D 184 TYR cc_start: 0.5639 (OUTLIER) cc_final: 0.5072 (p90) REVERT: D 249 ARG cc_start: 0.7670 (mtp85) cc_final: 0.6911 (ttm-80) REVERT: D 286 ASP cc_start: 0.6838 (m-30) cc_final: 0.6488 (p0) REVERT: D 354 LYS cc_start: 0.8346 (tppt) cc_final: 0.7992 (tptp) REVERT: G 249 ARG cc_start: 0.7758 (mtp85) cc_final: 0.6938 (ttm-80) REVERT: G 286 ASP cc_start: 0.6867 (m-30) cc_final: 0.6581 (p0) REVERT: G 354 LYS cc_start: 0.8223 (tppt) cc_final: 0.7909 (tptp) REVERT: G 546 SER cc_start: 0.6477 (p) cc_final: 0.6113 (m) REVERT: G 553 MET cc_start: 0.6889 (tpp) cc_final: 0.6498 (tpp) outliers start: 31 outliers final: 29 residues processed: 250 average time/residue: 0.2349 time to fit residues: 89.9049 Evaluate side-chains 243 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 240 HIS Chi-restraints excluded: chain J residue 308 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 361 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 184 TYR Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 HIS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 149 optimal weight: 0.0000 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 chunk 162 optimal weight: 0.2980 chunk 67 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.201285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.195935 restraints weight = 16858.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.195199 restraints weight = 33079.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.194897 restraints weight = 31995.652| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15800 Z= 0.153 Angle : 0.539 15.291 21436 Z= 0.264 Chirality : 0.038 0.184 2460 Planarity : 0.003 0.030 2680 Dihedral : 13.058 121.898 2348 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.70 % Allowed : 29.24 % Favored : 68.06 % 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: -0.84 (0.19), residues: 2012 helix: 0.31 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : -2.41 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 379 HIS 0.003 0.001 HIS G 240 PHE 0.029 0.001 PHE D 123 TYR 0.010 0.001 TYR B 139 ARG 0.008 0.000 ARG G 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2840.45 seconds wall clock time: 52 minutes 6.55 seconds (3126.55 seconds total)