Starting phenix.real_space_refine on Sun Feb 18 22:20:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2024/7svv_25454_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2024/7svv_25454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2024/7svv_25454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2024/7svv_25454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2024/7svv_25454_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7svv_25454/02_2024/7svv_25454_updated.pdb" } resolution = 3.54 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= 0.004 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 P 68 5.49 5 Mg 10 5.21 5 S 80 5.16 5 C 14367 2.51 5 N 4153 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 574": "OD1" <-> "OD2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 574": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 574": "OD1" <-> "OD2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 574": "OD1" <-> "OD2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 574": "OD1" <-> "OD2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 574": "OD1" <-> "OD2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 574": "OD1" <-> "OD2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 574": "OD1" <-> "OD2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 574": "OD1" <-> "OD2" Residue "J PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 574": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23046 Number of models: 1 Model: "" Number of chains: 32 Chain: "1" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 380 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "2" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 2 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "a" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "b" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "c" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "d" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "e" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "f" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "g" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "h" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 126 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "i" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "j" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.42, per 1000 atoms: 0.50 Number of scatterers: 23046 At special positions: 0 Unit cell: (142.31, 136.99, 135.66, 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) S 80 16.00 P 68 15.00 Mg 10 11.99 O 4368 8.00 N 4153 7.00 C 14367 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.29 Conformation dependent library (CDL) restraints added in 4.3 seconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 10 sheets defined 54.6% alpha, 7.4% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 9.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA A 155 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 160 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.144A pdb=" N ARG A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'a' and resid 575 through 580 Processing helix chain 'B' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.656A pdb=" N ARG B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 removed outlier: 4.163A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA B 155 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 158 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 160 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 575 through 580 Processing helix chain 'C' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.664A pdb=" N ALA C 155 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 160 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 274 removed outlier: 3.909A pdb=" N GLU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'c' and resid 575 through 580 Processing helix chain 'D' and resid 20 through 28 removed outlier: 3.756A pdb=" N ARG D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 removed outlier: 4.163A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 151 through 163 removed outlier: 3.664A pdb=" N ALA D 155 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 160 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 257 removed outlier: 3.547A pdb=" N GLU D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'd' and resid 575 through 580 Processing helix chain 'E' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 removed outlier: 3.567A pdb=" N LYS E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 151 through 163 removed outlier: 3.664A pdb=" N ALA E 155 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE E 160 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.144A pdb=" N ARG E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 201 through 214 Processing helix chain 'E' and resid 227 through 237 removed outlier: 3.850A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU E 246 " --> pdb=" O GLY E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 274 removed outlier: 3.909A pdb=" N GLU E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing helix chain 'e' and resid 575 through 580 Processing helix chain 'F' and resid 20 through 28 removed outlier: 3.756A pdb=" N ARG F 27 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA F 155 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG F 158 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 160 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 201 through 214 Processing helix chain 'F' and resid 227 through 237 removed outlier: 3.850A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 257 removed outlier: 3.547A pdb=" N GLU F 246 " --> pdb=" O GLY F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'f' and resid 575 through 580 Processing helix chain 'G' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS G 51 " --> pdb=" O ASP G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA G 155 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE G 160 " --> pdb=" O VAL G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 Processing helix chain 'G' and resid 201 through 214 Processing helix chain 'G' and resid 227 through 237 removed outlier: 3.850A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 257 removed outlier: 3.547A pdb=" N GLU G 246 " --> pdb=" O GLY G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'g' and resid 575 through 580 Processing helix chain 'H' and resid 20 through 28 removed outlier: 3.757A pdb=" N ARG H 27 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS H 51 " --> pdb=" O ASP H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS H 107 " --> pdb=" O LYS H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA H 155 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG H 158 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE H 160 " --> pdb=" O VAL H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 182 removed outlier: 4.144A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 Processing helix chain 'H' and resid 201 through 214 Processing helix chain 'H' and resid 227 through 237 removed outlier: 3.850A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU H 246 " --> pdb=" O GLY H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.908A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'h' and resid 575 through 580 Processing helix chain 'I' and resid 20 through 28 removed outlier: 3.756A pdb=" N ARG I 27 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 112 removed outlier: 4.163A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA I 155 " --> pdb=" O GLU I 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG I 158 " --> pdb=" O ALA I 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP I 159 " --> pdb=" O ASP I 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE I 160 " --> pdb=" O VAL I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 4.144A pdb=" N ARG I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 201 through 214 Processing helix chain 'I' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU I 246 " --> pdb=" O GLY I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 274 removed outlier: 3.909A pdb=" N GLU I 274 " --> pdb=" O GLU I 270 " (cutoff:3.500A) Processing helix chain 'i' and resid 575 through 580 Processing helix chain 'J' and resid 20 through 28 removed outlier: 3.756A pdb=" N ARG J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 52 removed outlier: 3.568A pdb=" N LYS J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 76 removed outlier: 3.657A pdb=" N ARG J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 112 removed outlier: 4.162A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS J 107 " --> pdb=" O LYS J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 151 through 163 removed outlier: 3.665A pdb=" N ALA J 155 " --> pdb=" O GLU J 152 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG J 158 " --> pdb=" O ALA J 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP J 159 " --> pdb=" O ASP J 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE J 160 " --> pdb=" O VAL J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 4.143A pdb=" N ARG J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'J' and resid 201 through 214 Processing helix chain 'J' and resid 227 through 237 removed outlier: 3.849A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 257 removed outlier: 3.546A pdb=" N GLU J 246 " --> pdb=" O GLY J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 274 removed outlier: 3.909A pdb=" N GLU J 274 " --> pdb=" O GLU J 270 " (cutoff:3.500A) Processing helix chain 'j' and resid 575 through 580 Processing sheet with id= A, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG A 57 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE A 196 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 59 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG B 57 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE B 196 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 59 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 193 through 196 removed outlier: 6.668A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE C 196 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 59 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 193 through 196 removed outlier: 6.668A pdb=" N ARG D 57 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE D 196 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL D 59 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE E 196 " --> pdb=" O ARG E 57 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL E 59 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG F 57 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE F 196 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL F 59 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE G 196 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL G 59 " --> pdb=" O PHE G 196 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 193 through 196 removed outlier: 6.668A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE H 196 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL H 59 " --> pdb=" O PHE H 196 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE I 196 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL I 59 " --> pdb=" O PHE I 196 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 193 through 196 removed outlier: 6.667A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE J 196 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL J 59 " --> pdb=" O PHE J 196 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2610 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 7.01 Time building geometry restraints manager: 10.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3736 1.28 - 1.41: 5774 1.41 - 1.55: 13745 1.55 - 1.68: 92 1.68 - 1.81: 140 Bond restraints: 23487 Sorted by residual: bond pdb=" O3A ANP F 300 " pdb=" PB ANP F 300 " ideal model delta sigma weight residual 1.700 1.506 0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" O3A ANP E 300 " pdb=" PB ANP E 300 " ideal model delta sigma weight residual 1.700 1.506 0.194 2.00e-02 2.50e+03 9.41e+01 bond pdb=" O3A ANP G 300 " pdb=" PB ANP G 300 " ideal model delta sigma weight residual 1.700 1.538 0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" O3A ANP H 300 " pdb=" PB ANP H 300 " ideal model delta sigma weight residual 1.700 1.538 0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" O3A ANP J 300 " pdb=" PB ANP J 300 " ideal model delta sigma weight residual 1.700 1.540 0.160 2.00e-02 2.50e+03 6.43e+01 ... (remaining 23482 not shown) Histogram of bond angle deviations from ideal: 86.12 - 96.36: 5 96.36 - 106.60: 1057 106.60 - 116.83: 15364 116.83 - 127.07: 15043 127.07 - 137.31: 330 Bond angle restraints: 31799 Sorted by residual: angle pdb=" N LYS I 265 " pdb=" CA LYS I 265 " pdb=" C LYS I 265 " ideal model delta sigma weight residual 111.07 120.80 -9.73 1.07e+00 8.73e-01 8.27e+01 angle pdb=" N LYS A 265 " pdb=" CA LYS A 265 " pdb=" C LYS A 265 " ideal model delta sigma weight residual 111.07 120.79 -9.72 1.07e+00 8.73e-01 8.25e+01 angle pdb=" N LYS E 265 " pdb=" CA LYS E 265 " pdb=" C LYS E 265 " ideal model delta sigma weight residual 111.07 120.79 -9.72 1.07e+00 8.73e-01 8.25e+01 angle pdb=" N LYS C 265 " pdb=" CA LYS C 265 " pdb=" C LYS C 265 " ideal model delta sigma weight residual 111.07 120.78 -9.71 1.07e+00 8.73e-01 8.23e+01 angle pdb=" N LYS G 265 " pdb=" CA LYS G 265 " pdb=" C LYS G 265 " ideal model delta sigma weight residual 111.07 120.78 -9.71 1.07e+00 8.73e-01 8.23e+01 ... (remaining 31794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 14010 34.93 - 69.85: 494 69.85 - 104.78: 75 104.78 - 139.71: 3 139.71 - 174.63: 10 Dihedral angle restraints: 14592 sinusoidal: 6732 harmonic: 7860 Sorted by residual: dihedral pdb=" C TYR h 582 " pdb=" N TYR h 582 " pdb=" CA TYR h 582 " pdb=" CB TYR h 582 " ideal model delta harmonic sigma weight residual -122.60 -137.09 14.49 0 2.50e+00 1.60e-01 3.36e+01 dihedral pdb=" C TYR a 582 " pdb=" N TYR a 582 " pdb=" CA TYR a 582 " pdb=" CB TYR a 582 " ideal model delta harmonic sigma weight residual -122.60 -137.09 14.49 0 2.50e+00 1.60e-01 3.36e+01 dihedral pdb=" C TYR e 582 " pdb=" N TYR e 582 " pdb=" CA TYR e 582 " pdb=" CB TYR e 582 " ideal model delta harmonic sigma weight residual -122.60 -137.08 14.48 0 2.50e+00 1.60e-01 3.36e+01 ... (remaining 14589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 3065 0.131 - 0.262: 409 0.262 - 0.394: 45 0.394 - 0.525: 2 0.525 - 0.656: 10 Chirality restraints: 3531 Sorted by residual: chirality pdb=" CA TYR a 582 " pdb=" N TYR a 582 " pdb=" C TYR a 582 " pdb=" CB TYR a 582 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA TYR h 582 " pdb=" N TYR h 582 " pdb=" C TYR h 582 " pdb=" CB TYR h 582 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA TYR d 582 " pdb=" N TYR d 582 " pdb=" C TYR d 582 " pdb=" CB TYR d 582 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 ... (remaining 3528 not shown) Planarity restraints: 3858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 255 " -0.030 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C SER J 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER J 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU J 256 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 255 " 0.030 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C SER A 255 " -0.103 2.00e-02 2.50e+03 pdb=" O SER A 255 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU A 256 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 255 " -0.030 2.00e-02 2.50e+03 5.94e-02 3.52e+01 pdb=" C SER B 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER B 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU B 256 " -0.036 2.00e-02 2.50e+03 ... (remaining 3855 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 15 2.04 - 2.75: 3822 2.75 - 3.47: 30987 3.47 - 4.18: 53369 4.18 - 4.90: 92165 Nonbonded interactions: 180358 Sorted by model distance: nonbonded pdb=" O1G ANP C 300 " pdb="MG MG C 301 " model vdw 1.320 2.170 nonbonded pdb=" O1G ANP G 300 " pdb="MG MG G 301 " model vdw 1.413 2.170 nonbonded pdb=" O1G ANP D 300 " pdb="MG MG D 301 " model vdw 1.557 2.170 nonbonded pdb=" O1G ANP A 300 " pdb="MG MG A 301 " model vdw 1.564 2.170 nonbonded pdb=" O1G ANP J 300 " pdb="MG MG J 301 " model vdw 1.567 2.170 ... (remaining 180353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'a' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'b' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'c' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'd' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'e' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'f' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'g' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = chain 'h' selection = (chain 'i' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) selection = (chain 'j' and ((resid 570 and (name N or name CA or name C or name O or name CB \ )) or resid 571 through 583)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.820 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 67.920 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.020 0.194 23487 Z= 1.324 Angle : 1.877 26.945 31799 Z= 1.297 Chirality : 0.100 0.656 3531 Planarity : 0.010 0.059 3858 Dihedral : 16.778 174.635 9512 Min Nonbonded Distance : 1.320 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.39 % 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: -0.21 (0.15), residues: 2670 helix: -0.55 (0.11), residues: 1560 sheet: 2.55 (0.30), residues: 230 loop : 0.25 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 45 HIS 0.001 0.000 HIS H 77 PHE 0.007 0.001 PHE E 196 TYR 0.016 0.002 TYR J 112 ARG 0.003 0.000 ARG F 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 718 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7511 (ttm110) REVERT: B 40 LYS cc_start: 0.8168 (tptp) cc_final: 0.7947 (ttmt) REVERT: B 47 ASP cc_start: 0.7479 (t70) cc_final: 0.7186 (t0) REVERT: B 54 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7566 (tttp) REVERT: B 188 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7877 (mm-30) REVERT: B 230 LEU cc_start: 0.8705 (mt) cc_final: 0.8354 (tp) REVERT: B 235 SER cc_start: 0.8612 (m) cc_final: 0.8247 (t) REVERT: B 268 LEU cc_start: 0.8973 (tp) cc_final: 0.8693 (tt) REVERT: D 159 ASP cc_start: 0.6235 (m-30) cc_final: 0.5655 (m-30) REVERT: D 229 MET cc_start: 0.8271 (mmm) cc_final: 0.7976 (mmt) REVERT: D 250 GLU cc_start: 0.7518 (tp30) cc_final: 0.7224 (tt0) REVERT: E 123 SER cc_start: 0.8818 (p) cc_final: 0.7494 (t) REVERT: F 47 ASP cc_start: 0.7945 (t70) cc_final: 0.7610 (t0) REVERT: F 54 LYS cc_start: 0.8306 (mmtm) cc_final: 0.7985 (tttm) REVERT: F 140 MET cc_start: 0.9285 (ttm) cc_final: 0.9052 (ttp) REVERT: F 159 ASP cc_start: 0.6987 (m-30) cc_final: 0.6530 (m-30) REVERT: F 163 ASP cc_start: 0.8125 (m-30) cc_final: 0.7854 (m-30) REVERT: F 229 MET cc_start: 0.8570 (mmm) cc_final: 0.8233 (mmm) REVERT: G 27 ARG cc_start: 0.7204 (ttp80) cc_final: 0.6763 (ptt90) REVERT: G 119 LYS cc_start: 0.6347 (tptp) cc_final: 0.6094 (tppt) REVERT: G 139 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8103 (mt-10) REVERT: G 162 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6054 (mm-30) REVERT: G 231 ARG cc_start: 0.7312 (ttm110) cc_final: 0.7109 (ttp80) REVERT: H 107 LYS cc_start: 0.8113 (tttm) cc_final: 0.7724 (mtmt) REVERT: H 140 MET cc_start: 0.9377 (ttm) cc_final: 0.9137 (ttm) REVERT: H 163 ASP cc_start: 0.7745 (m-30) cc_final: 0.7404 (m-30) REVERT: H 187 LEU cc_start: 0.8816 (tp) cc_final: 0.8563 (tt) REVERT: H 238 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7463 (mt-10) REVERT: h 582 TYR cc_start: 0.6758 (t80) cc_final: 0.6329 (t80) REVERT: I 76 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7395 (ttm-80) REVERT: I 238 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7806 (mt-10) REVERT: I 269 GLN cc_start: 0.7174 (mt0) cc_final: 0.6855 (tt0) REVERT: J 76 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7483 (mtt-85) REVERT: J 269 GLN cc_start: 0.7408 (mt0) cc_final: 0.7040 (mt0) outliers start: 0 outliers final: 0 residues processed: 718 average time/residue: 0.4948 time to fit residues: 489.8457 Evaluate side-chains 383 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 0.8980 chunk 198 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN I 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23487 Z= 0.185 Angle : 0.553 6.033 31799 Z= 0.292 Chirality : 0.041 0.229 3531 Planarity : 0.004 0.031 3858 Dihedral : 17.023 178.555 3794 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.11 % Allowed : 8.32 % Favored : 89.57 % 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: 1.21 (0.16), residues: 2670 helix: 1.05 (0.13), residues: 1580 sheet: 2.37 (0.31), residues: 230 loop : 0.05 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 45 HIS 0.004 0.001 HIS G 77 PHE 0.009 0.001 PHE A 106 TYR 0.013 0.001 TYR j 575 ARG 0.007 0.000 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 391 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7515 (tttm) cc_final: 0.7074 (ttpt) REVERT: A 127 ASP cc_start: 0.6955 (m-30) cc_final: 0.6539 (m-30) REVERT: A 203 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7390 (t0) REVERT: B 40 LYS cc_start: 0.7943 (tptp) cc_final: 0.7662 (ttmt) REVERT: B 230 LEU cc_start: 0.8780 (mt) cc_final: 0.8368 (tp) REVERT: C 230 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7834 (tp) REVERT: D 229 MET cc_start: 0.8025 (mmm) cc_final: 0.7728 (mmt) REVERT: D 230 LEU cc_start: 0.8589 (mt) cc_final: 0.8193 (tp) REVERT: D 231 ARG cc_start: 0.7353 (ptp90) cc_final: 0.7137 (ptp-170) REVERT: D 250 GLU cc_start: 0.7966 (tp30) cc_final: 0.7546 (tt0) REVERT: E 82 GLU cc_start: 0.5610 (pt0) cc_final: 0.5356 (pt0) REVERT: E 159 ASP cc_start: 0.6567 (m-30) cc_final: 0.6193 (m-30) REVERT: E 181 LYS cc_start: 0.8349 (mttt) cc_final: 0.7898 (mtmt) REVERT: F 54 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7864 (tttm) REVERT: G 27 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7264 (ttp80) REVERT: G 54 LYS cc_start: 0.7606 (mmtm) cc_final: 0.7329 (mtpp) REVERT: G 64 THR cc_start: 0.8656 (p) cc_final: 0.8160 (p) REVERT: G 76 ARG cc_start: 0.7524 (mtp180) cc_final: 0.6813 (mtp180) REVERT: G 119 LYS cc_start: 0.6479 (tptp) cc_final: 0.6212 (tppt) REVERT: G 123 SER cc_start: 0.7396 (OUTLIER) cc_final: 0.7065 (m) REVERT: G 162 GLU cc_start: 0.6071 (mt-10) cc_final: 0.5805 (mm-30) REVERT: H 163 ASP cc_start: 0.7987 (m-30) cc_final: 0.7429 (m-30) REVERT: I 238 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8094 (mt-10) REVERT: J 47 ASP cc_start: 0.8035 (t70) cc_final: 0.7768 (m-30) REVERT: J 76 ARG cc_start: 0.7941 (mtp180) cc_final: 0.7604 (mtt-85) REVERT: J 78 LYS cc_start: 0.8043 (mttt) cc_final: 0.7063 (mtmt) REVERT: J 114 LYS cc_start: 0.7027 (mmtt) cc_final: 0.6707 (mttm) REVERT: J 140 MET cc_start: 0.9223 (ttp) cc_final: 0.8798 (ttm) REVERT: J 163 ASP cc_start: 0.7578 (m-30) cc_final: 0.7369 (m-30) REVERT: J 269 GLN cc_start: 0.7562 (mt0) cc_final: 0.7226 (mt0) outliers start: 50 outliers final: 29 residues processed: 422 average time/residue: 0.4368 time to fit residues: 266.9214 Evaluate side-chains 351 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 319 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 158 ARG Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 269 GLN F 206 ASN H 223 ASN I 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23487 Z= 0.291 Angle : 0.591 6.625 31799 Z= 0.308 Chirality : 0.042 0.251 3531 Planarity : 0.004 0.038 3858 Dihedral : 16.645 179.321 3794 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.57 % Allowed : 9.88 % Favored : 87.55 % 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: 1.04 (0.16), residues: 2670 helix: 1.06 (0.13), residues: 1590 sheet: 1.88 (0.27), residues: 280 loop : -0.35 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 45 HIS 0.007 0.001 HIS G 77 PHE 0.012 0.002 PHE C 125 TYR 0.019 0.002 TYR a 575 ARG 0.010 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 351 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8179 (mmtm) cc_final: 0.7844 (mtpp) REVERT: A 107 LYS cc_start: 0.7902 (tttm) cc_final: 0.7230 (ttpt) REVERT: B 40 LYS cc_start: 0.8229 (tptp) cc_final: 0.7872 (mtmm) REVERT: B 230 LEU cc_start: 0.8754 (mt) cc_final: 0.8393 (tp) REVERT: B 241 ILE cc_start: 0.8895 (tp) cc_final: 0.8659 (tt) REVERT: D 203 ASP cc_start: 0.7963 (t0) cc_final: 0.7486 (t0) REVERT: D 229 MET cc_start: 0.8064 (mmm) cc_final: 0.7838 (mmt) REVERT: D 231 ARG cc_start: 0.7435 (ptp90) cc_final: 0.7036 (ptp-170) REVERT: D 250 GLU cc_start: 0.7955 (tp30) cc_final: 0.7581 (mt-10) REVERT: D 256 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8289 (mm) REVERT: E 47 ASP cc_start: 0.8046 (t0) cc_final: 0.7480 (m-30) REVERT: E 159 ASP cc_start: 0.6947 (m-30) cc_final: 0.6201 (m-30) REVERT: E 181 LYS cc_start: 0.8425 (mttt) cc_final: 0.7860 (mtmt) REVERT: F 179 VAL cc_start: 0.8178 (t) cc_final: 0.7921 (t) REVERT: F 191 ARG cc_start: 0.8271 (ttt90) cc_final: 0.8046 (ttt90) REVERT: F 229 MET cc_start: 0.8431 (mmm) cc_final: 0.7829 (mmt) REVERT: G 162 GLU cc_start: 0.6182 (mt-10) cc_final: 0.5847 (mm-30) REVERT: G 214 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7411 (mtm) REVERT: G 255 SER cc_start: 0.7605 (OUTLIER) cc_final: 0.7377 (m) REVERT: G 269 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7730 (tp-100) REVERT: H 99 LYS cc_start: 0.7248 (mttt) cc_final: 0.6957 (mttp) REVERT: H 163 ASP cc_start: 0.7796 (m-30) cc_final: 0.7197 (m-30) REVERT: H 229 MET cc_start: 0.8110 (mmm) cc_final: 0.7708 (mpp) REVERT: I 78 LYS cc_start: 0.7600 (mttt) cc_final: 0.7382 (ptpt) REVERT: I 206 ASN cc_start: 0.8206 (m-40) cc_final: 0.7916 (m-40) REVERT: I 211 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.8305 (t-100) REVERT: I 231 ARG cc_start: 0.7137 (ttm110) cc_final: 0.6793 (ttp-170) REVERT: I 238 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7967 (mt-10) REVERT: J 47 ASP cc_start: 0.8112 (t70) cc_final: 0.7881 (m-30) REVERT: J 140 MET cc_start: 0.9306 (ttp) cc_final: 0.8867 (ttm) REVERT: J 163 ASP cc_start: 0.7608 (m-30) cc_final: 0.7317 (m-30) outliers start: 61 outliers final: 40 residues processed: 392 average time/residue: 0.4275 time to fit residues: 244.3436 Evaluate side-chains 339 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 295 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain a residue 581 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 214 MET Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 211 TRP Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 235 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN G 98 GLN g 577 GLN H 213 GLN H 223 ASN I 77 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23487 Z= 0.275 Angle : 0.550 6.653 31799 Z= 0.287 Chirality : 0.041 0.239 3531 Planarity : 0.004 0.033 3858 Dihedral : 16.464 179.624 3794 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.74 % Allowed : 11.73 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.16), residues: 2670 helix: 1.02 (0.13), residues: 1570 sheet: 1.69 (0.26), residues: 280 loop : -0.51 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 45 HIS 0.006 0.001 HIS G 77 PHE 0.011 0.001 PHE J 106 TYR 0.010 0.001 TYR a 575 ARG 0.007 0.000 ARG j 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 331 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8037 (tttm) cc_final: 0.7300 (ttpt) REVERT: A 145 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7725 (mm-30) REVERT: B 40 LYS cc_start: 0.8077 (tptp) cc_final: 0.7830 (mtmm) REVERT: B 230 LEU cc_start: 0.8666 (mt) cc_final: 0.8291 (tp) REVERT: B 241 ILE cc_start: 0.8796 (tp) cc_final: 0.8566 (tt) REVERT: C 230 LEU cc_start: 0.8324 (mt) cc_final: 0.7930 (tp) REVERT: D 54 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7680 (mtpp) REVERT: D 123 SER cc_start: 0.7554 (p) cc_final: 0.7310 (m) REVERT: D 203 ASP cc_start: 0.7999 (t0) cc_final: 0.7498 (t0) REVERT: D 231 ARG cc_start: 0.7298 (ptp90) cc_final: 0.7029 (ptp-170) REVERT: D 250 GLU cc_start: 0.8020 (tp30) cc_final: 0.7597 (tt0) REVERT: E 47 ASP cc_start: 0.8012 (t0) cc_final: 0.7403 (m-30) REVERT: E 181 LYS cc_start: 0.8416 (mttt) cc_final: 0.7811 (mtmt) REVERT: E 229 MET cc_start: 0.7220 (mtt) cc_final: 0.6850 (mtt) REVERT: F 264 ASP cc_start: 0.7029 (p0) cc_final: 0.6704 (t0) REVERT: G 162 GLU cc_start: 0.6246 (mt-10) cc_final: 0.5988 (mm-30) REVERT: G 255 SER cc_start: 0.7566 (OUTLIER) cc_final: 0.7358 (m) REVERT: G 269 GLN cc_start: 0.8019 (tp-100) cc_final: 0.7687 (tp-100) REVERT: H 99 LYS cc_start: 0.7272 (mttt) cc_final: 0.7013 (mttp) REVERT: I 223 ASN cc_start: 0.7097 (p0) cc_final: 0.6629 (t0) REVERT: I 231 ARG cc_start: 0.7166 (ttm110) cc_final: 0.6769 (mtm-85) REVERT: I 238 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7934 (mt-10) REVERT: J 20 TRP cc_start: 0.7273 (t60) cc_final: 0.6963 (t60) REVERT: J 81 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6173 (mt0) REVERT: J 163 ASP cc_start: 0.7557 (m-30) cc_final: 0.7239 (m-30) outliers start: 65 outliers final: 44 residues processed: 377 average time/residue: 0.3972 time to fit residues: 222.3030 Evaluate side-chains 333 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 287 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain c residue 572 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 223 ASN Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 235 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 3 optimal weight: 0.0000 chunk 188 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 216 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 577 GLN H 223 ASN I 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23487 Z= 0.144 Angle : 0.467 6.548 31799 Z= 0.246 Chirality : 0.039 0.196 3531 Planarity : 0.003 0.029 3858 Dihedral : 15.872 179.800 3794 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.82 % Allowed : 13.68 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.16), residues: 2670 helix: 1.22 (0.13), residues: 1600 sheet: 1.63 (0.26), residues: 280 loop : -0.31 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 45 HIS 0.003 0.001 HIS G 77 PHE 0.005 0.001 PHE A 204 TYR 0.007 0.001 TYR F 93 ARG 0.005 0.000 ARG G 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 318 time to evaluate : 2.617 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8014 (tttm) cc_final: 0.7248 (ttpt) REVERT: A 127 ASP cc_start: 0.6936 (m-30) cc_final: 0.6553 (m-30) REVERT: A 145 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 40 LYS cc_start: 0.8009 (tptp) cc_final: 0.7747 (mtmm) REVERT: B 111 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7242 (mt-10) REVERT: B 230 LEU cc_start: 0.8662 (mt) cc_final: 0.8328 (tp) REVERT: C 180 ILE cc_start: 0.8040 (tt) cc_final: 0.7737 (tt) REVERT: C 230 LEU cc_start: 0.8211 (mt) cc_final: 0.7831 (tp) REVERT: D 54 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7576 (mtpp) REVERT: D 203 ASP cc_start: 0.7843 (t0) cc_final: 0.7531 (t0) REVERT: D 231 ARG cc_start: 0.7334 (ptp90) cc_final: 0.7005 (ptp-170) REVERT: D 250 GLU cc_start: 0.7943 (tp30) cc_final: 0.7578 (tt0) REVERT: D 256 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8421 (mm) REVERT: E 47 ASP cc_start: 0.7839 (t0) cc_final: 0.7317 (m-30) REVERT: E 181 LYS cc_start: 0.8273 (mttt) cc_final: 0.7571 (mtmt) REVERT: E 229 MET cc_start: 0.7191 (mtt) cc_final: 0.6901 (mtt) REVERT: F 214 MET cc_start: 0.7272 (mmp) cc_final: 0.7050 (mmp) REVERT: F 264 ASP cc_start: 0.6758 (p0) cc_final: 0.6413 (t0) REVERT: G 64 THR cc_start: 0.8730 (p) cc_final: 0.8223 (p) REVERT: G 255 SER cc_start: 0.7593 (OUTLIER) cc_final: 0.7373 (m) REVERT: G 269 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7707 (tp-100) REVERT: H 231 ARG cc_start: 0.7556 (tpp80) cc_final: 0.7343 (tpp80) REVERT: I 211 TRP cc_start: 0.8703 (OUTLIER) cc_final: 0.8425 (t-100) REVERT: I 231 ARG cc_start: 0.7082 (ttm110) cc_final: 0.6786 (mtm-85) REVERT: I 238 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8067 (mt-10) REVERT: J 20 TRP cc_start: 0.7239 (t60) cc_final: 0.6972 (t60) REVERT: J 64 THR cc_start: 0.8956 (p) cc_final: 0.8736 (p) REVERT: J 76 ARG cc_start: 0.8061 (mtm180) cc_final: 0.7683 (ttm-80) REVERT: J 81 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6038 (mt0) REVERT: J 163 ASP cc_start: 0.7593 (m-30) cc_final: 0.7368 (t0) outliers start: 43 outliers final: 27 residues processed: 348 average time/residue: 0.3954 time to fit residues: 203.5215 Evaluate side-chains 322 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 291 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 211 TRP Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 81 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 148 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 210 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN B 223 ASN g 577 GLN H 223 ASN I 206 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23487 Z= 0.182 Angle : 0.490 8.018 31799 Z= 0.255 Chirality : 0.039 0.186 3531 Planarity : 0.003 0.030 3858 Dihedral : 15.639 179.675 3794 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.11 % Allowed : 13.80 % Favored : 84.09 % 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: 1.21 (0.16), residues: 2670 helix: 1.29 (0.13), residues: 1590 sheet: 1.59 (0.26), residues: 280 loop : -0.36 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 20 HIS 0.004 0.001 HIS G 77 PHE 0.008 0.001 PHE J 106 TYR 0.008 0.001 TYR j 575 ARG 0.009 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 296 time to evaluate : 2.709 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7896 (tttm) cc_final: 0.7450 (ttpt) REVERT: A 127 ASP cc_start: 0.6961 (m-30) cc_final: 0.6599 (m-30) REVERT: A 145 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 40 LYS cc_start: 0.8097 (tptp) cc_final: 0.7790 (mtmm) REVERT: B 230 LEU cc_start: 0.8672 (mt) cc_final: 0.8300 (tp) REVERT: C 131 GLU cc_start: 0.7595 (tp30) cc_final: 0.7156 (tt0) REVERT: C 180 ILE cc_start: 0.8056 (tt) cc_final: 0.7748 (tt) REVERT: C 230 LEU cc_start: 0.8292 (mt) cc_final: 0.7924 (tp) REVERT: D 54 LYS cc_start: 0.7845 (mmtm) cc_final: 0.7604 (mtpp) REVERT: D 203 ASP cc_start: 0.7843 (t0) cc_final: 0.7529 (t0) REVERT: D 231 ARG cc_start: 0.7500 (ptp90) cc_final: 0.7056 (ptp-170) REVERT: D 250 GLU cc_start: 0.7943 (tp30) cc_final: 0.7591 (tt0) REVERT: E 47 ASP cc_start: 0.7996 (t0) cc_final: 0.7450 (m-30) REVERT: E 181 LYS cc_start: 0.8231 (mttt) cc_final: 0.7654 (mtmt) REVERT: E 229 MET cc_start: 0.7202 (mtt) cc_final: 0.6894 (mtt) REVERT: F 231 ARG cc_start: 0.7458 (mtm110) cc_final: 0.7022 (mtm180) REVERT: F 264 ASP cc_start: 0.6855 (p0) cc_final: 0.6510 (t0) REVERT: G 255 SER cc_start: 0.7562 (OUTLIER) cc_final: 0.7359 (m) REVERT: G 269 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7743 (tp-100) REVERT: H 229 MET cc_start: 0.8359 (mmm) cc_final: 0.7885 (mpp) REVERT: H 231 ARG cc_start: 0.7381 (tpp80) cc_final: 0.7113 (tpp80) REVERT: I 211 TRP cc_start: 0.8751 (OUTLIER) cc_final: 0.8503 (t-100) REVERT: I 225 LYS cc_start: 0.7172 (tptt) cc_final: 0.6741 (ptpp) REVERT: I 231 ARG cc_start: 0.7110 (ttm110) cc_final: 0.6716 (mtm-85) REVERT: I 238 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8082 (mt-10) REVERT: J 20 TRP cc_start: 0.7425 (t60) cc_final: 0.7165 (t60) REVERT: J 76 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7702 (ttm-80) REVERT: J 81 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6324 (mt0) REVERT: J 140 MET cc_start: 0.9284 (ttp) cc_final: 0.8872 (ttm) REVERT: J 163 ASP cc_start: 0.7576 (m-30) cc_final: 0.7345 (t0) outliers start: 50 outliers final: 40 residues processed: 325 average time/residue: 0.4035 time to fit residues: 194.4941 Evaluate side-chains 329 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 286 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 20 TRP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 211 TRP Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 81 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 144 optimal weight: 0.1980 chunk 185 optimal weight: 6.9990 chunk 143 optimal weight: 0.0060 chunk 213 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 252 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 577 GLN I 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23487 Z= 0.130 Angle : 0.452 7.447 31799 Z= 0.239 Chirality : 0.038 0.177 3531 Planarity : 0.003 0.029 3858 Dihedral : 15.356 178.925 3794 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.56 % Allowed : 14.69 % Favored : 83.75 % 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: 1.44 (0.16), residues: 2670 helix: 1.45 (0.13), residues: 1590 sheet: 1.68 (0.25), residues: 280 loop : -0.23 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 20 HIS 0.002 0.000 HIS G 77 PHE 0.004 0.001 PHE C 125 TYR 0.007 0.001 TYR F 93 ARG 0.007 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 314 time to evaluate : 2.913 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7833 (tttm) cc_final: 0.7338 (ttpt) REVERT: A 127 ASP cc_start: 0.6872 (m-30) cc_final: 0.6523 (m-30) REVERT: A 145 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7738 (mm-30) REVERT: B 40 LYS cc_start: 0.7841 (tptp) cc_final: 0.7631 (mtmm) REVERT: B 230 LEU cc_start: 0.8618 (mt) cc_final: 0.8221 (tp) REVERT: C 131 GLU cc_start: 0.7640 (tp30) cc_final: 0.7267 (tt0) REVERT: C 180 ILE cc_start: 0.8025 (tt) cc_final: 0.7720 (tt) REVERT: C 230 LEU cc_start: 0.8178 (mt) cc_final: 0.7811 (tp) REVERT: D 54 LYS cc_start: 0.7787 (mmtm) cc_final: 0.7545 (mtpp) REVERT: D 203 ASP cc_start: 0.7795 (t0) cc_final: 0.7508 (t0) REVERT: D 230 LEU cc_start: 0.8512 (mt) cc_final: 0.8154 (tp) REVERT: D 231 ARG cc_start: 0.7470 (ptp90) cc_final: 0.7105 (ptp-170) REVERT: D 250 GLU cc_start: 0.7920 (tp30) cc_final: 0.7541 (tt0) REVERT: E 47 ASP cc_start: 0.7864 (t0) cc_final: 0.7343 (m-30) REVERT: E 181 LYS cc_start: 0.8204 (mttt) cc_final: 0.7634 (mtmt) REVERT: E 229 MET cc_start: 0.7167 (mtt) cc_final: 0.6842 (mtt) REVERT: F 264 ASP cc_start: 0.6868 (p0) cc_final: 0.6560 (t0) REVERT: G 64 THR cc_start: 0.8627 (p) cc_final: 0.8101 (p) REVERT: G 131 GLU cc_start: 0.7590 (tp30) cc_final: 0.7363 (tt0) REVERT: G 255 SER cc_start: 0.7592 (OUTLIER) cc_final: 0.7386 (m) REVERT: G 269 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7649 (tp-100) REVERT: g 577 GLN cc_start: 0.7412 (tm130) cc_final: 0.6866 (tt0) REVERT: H 231 ARG cc_start: 0.7345 (tpp80) cc_final: 0.7066 (tpp80) REVERT: I 211 TRP cc_start: 0.8719 (OUTLIER) cc_final: 0.8435 (t-100) REVERT: I 225 LYS cc_start: 0.7040 (tptt) cc_final: 0.6629 (ptpp) REVERT: I 231 ARG cc_start: 0.7081 (ttm110) cc_final: 0.6680 (mtm-85) REVERT: I 238 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8052 (mt-10) REVERT: J 20 TRP cc_start: 0.7403 (t60) cc_final: 0.7156 (t60) REVERT: J 76 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7649 (ttm-80) REVERT: J 81 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6181 (mt0) REVERT: J 85 ARG cc_start: 0.6333 (mmt90) cc_final: 0.5979 (mtp180) REVERT: J 163 ASP cc_start: 0.7561 (m-30) cc_final: 0.7217 (t0) REVERT: J 229 MET cc_start: 0.8020 (mmt) cc_final: 0.7721 (mmm) outliers start: 37 outliers final: 29 residues processed: 340 average time/residue: 0.3940 time to fit residues: 200.0248 Evaluate side-chains 332 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 300 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 211 TRP Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 81 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 9.9990 chunk 100 optimal weight: 0.0020 chunk 150 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23487 Z= 0.279 Angle : 0.551 7.997 31799 Z= 0.285 Chirality : 0.042 0.205 3531 Planarity : 0.004 0.032 3858 Dihedral : 15.733 179.635 3794 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.57 % Allowed : 14.10 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.16), residues: 2670 helix: 1.11 (0.13), residues: 1590 sheet: 1.45 (0.26), residues: 280 loop : -0.38 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 20 HIS 0.006 0.001 HIS G 77 PHE 0.012 0.002 PHE C 125 TYR 0.011 0.001 TYR j 575 ARG 0.008 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 304 time to evaluate : 2.720 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6625 (tt) REVERT: A 107 LYS cc_start: 0.7913 (tttm) cc_final: 0.7497 (ttpt) REVERT: A 127 ASP cc_start: 0.7054 (m-30) cc_final: 0.6272 (m-30) REVERT: B 40 LYS cc_start: 0.8167 (tptp) cc_final: 0.7785 (mtmm) REVERT: B 230 LEU cc_start: 0.8601 (mt) cc_final: 0.8229 (tp) REVERT: C 230 LEU cc_start: 0.8342 (mt) cc_final: 0.7931 (tp) REVERT: D 54 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7666 (mtpp) REVERT: D 203 ASP cc_start: 0.7937 (t0) cc_final: 0.7472 (t0) REVERT: D 231 ARG cc_start: 0.7500 (ptp90) cc_final: 0.7066 (ptp-170) REVERT: D 250 GLU cc_start: 0.8009 (tp30) cc_final: 0.7636 (tt0) REVERT: E 47 ASP cc_start: 0.8060 (t0) cc_final: 0.7437 (m-30) REVERT: E 181 LYS cc_start: 0.8301 (mttt) cc_final: 0.7669 (mtmt) REVERT: E 229 MET cc_start: 0.7205 (mtt) cc_final: 0.6938 (mtt) REVERT: F 159 ASP cc_start: 0.6110 (m-30) cc_final: 0.5607 (m-30) REVERT: F 191 ARG cc_start: 0.8334 (ttt90) cc_final: 0.8080 (ttt90) REVERT: F 264 ASP cc_start: 0.7089 (p0) cc_final: 0.6884 (t0) REVERT: G 269 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7653 (tp-100) REVERT: H 231 ARG cc_start: 0.7454 (tpp80) cc_final: 0.7096 (tpp80) REVERT: I 231 ARG cc_start: 0.7154 (ttm110) cc_final: 0.6780 (mtm-85) REVERT: I 238 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8034 (mt-10) REVERT: J 20 TRP cc_start: 0.7472 (t60) cc_final: 0.7206 (t60) REVERT: J 85 ARG cc_start: 0.6242 (mmt90) cc_final: 0.5998 (mtp180) REVERT: J 163 ASP cc_start: 0.7587 (m-30) cc_final: 0.7363 (t0) outliers start: 61 outliers final: 50 residues processed: 349 average time/residue: 0.3892 time to fit residues: 203.8210 Evaluate side-chains 343 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 292 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 20 TRP Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain g residue 580 GLU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 222 SER Chi-restraints excluded: chain J residue 235 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 234 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN g 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23487 Z= 0.139 Angle : 0.467 8.207 31799 Z= 0.247 Chirality : 0.039 0.183 3531 Planarity : 0.003 0.037 3858 Dihedral : 15.416 179.221 3794 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.77 % Allowed : 15.24 % Favored : 82.99 % 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: 1.30 (0.16), residues: 2670 helix: 1.37 (0.13), residues: 1590 sheet: 1.54 (0.26), residues: 280 loop : -0.30 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 45 HIS 0.002 0.001 HIS G 77 PHE 0.005 0.001 PHE C 125 TYR 0.008 0.001 TYR I 73 ARG 0.009 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 311 time to evaluate : 2.767 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6606 (tt) REVERT: A 107 LYS cc_start: 0.7871 (tttm) cc_final: 0.7366 (ttpt) REVERT: A 127 ASP cc_start: 0.6785 (m-30) cc_final: 0.6413 (m-30) REVERT: B 40 LYS cc_start: 0.7869 (tptp) cc_final: 0.7613 (mtmm) REVERT: B 230 LEU cc_start: 0.8596 (mt) cc_final: 0.8231 (tp) REVERT: C 131 GLU cc_start: 0.7582 (tp30) cc_final: 0.7126 (tt0) REVERT: C 180 ILE cc_start: 0.8037 (tt) cc_final: 0.7722 (tt) REVERT: C 230 LEU cc_start: 0.8209 (mt) cc_final: 0.7822 (tp) REVERT: D 54 LYS cc_start: 0.7810 (mmtm) cc_final: 0.7570 (mtpp) REVERT: D 203 ASP cc_start: 0.7800 (t0) cc_final: 0.7534 (t0) REVERT: D 250 GLU cc_start: 0.7907 (tp30) cc_final: 0.7519 (tt0) REVERT: E 47 ASP cc_start: 0.7791 (t0) cc_final: 0.7284 (m-30) REVERT: E 181 LYS cc_start: 0.8161 (mttt) cc_final: 0.7605 (mtmt) REVERT: E 229 MET cc_start: 0.7169 (mtt) cc_final: 0.6837 (mtt) REVERT: F 264 ASP cc_start: 0.6918 (p0) cc_final: 0.6637 (t0) REVERT: G 62 SER cc_start: 0.8429 (t) cc_final: 0.7918 (m) REVERT: G 64 THR cc_start: 0.8736 (p) cc_final: 0.8218 (p) REVERT: G 131 GLU cc_start: 0.7712 (tp30) cc_final: 0.7450 (tt0) REVERT: G 269 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7669 (tp-100) REVERT: g 577 GLN cc_start: 0.7360 (tm130) cc_final: 0.6900 (tt0) REVERT: H 231 ARG cc_start: 0.7455 (tpp80) cc_final: 0.7094 (tpp80) REVERT: I 231 ARG cc_start: 0.7176 (ttm110) cc_final: 0.6852 (mtm-85) REVERT: I 238 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8052 (mt-10) REVERT: J 20 TRP cc_start: 0.7400 (t60) cc_final: 0.7157 (t60) REVERT: J 62 SER cc_start: 0.8498 (t) cc_final: 0.8278 (t) REVERT: J 140 MET cc_start: 0.9215 (ttp) cc_final: 0.8832 (ttm) REVERT: J 163 ASP cc_start: 0.7648 (m-30) cc_final: 0.7288 (t0) REVERT: J 229 MET cc_start: 0.8014 (mmt) cc_final: 0.7747 (mmm) outliers start: 42 outliers final: 37 residues processed: 340 average time/residue: 0.3950 time to fit residues: 200.6260 Evaluate side-chains 336 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 298 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 255 SER Chi-restraints excluded: chain J residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 151 optimal weight: 0.0370 chunk 118 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 261 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 160 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN I 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23487 Z= 0.134 Angle : 0.472 10.341 31799 Z= 0.246 Chirality : 0.038 0.186 3531 Planarity : 0.003 0.039 3858 Dihedral : 15.279 178.377 3794 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.56 % Allowed : 15.66 % Favored : 82.78 % 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: 1.44 (0.16), residues: 2670 helix: 1.46 (0.13), residues: 1590 sheet: 1.57 (0.26), residues: 280 loop : -0.19 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 45 HIS 0.002 0.000 HIS G 77 PHE 0.007 0.001 PHE A 204 TYR 0.009 0.001 TYR j 575 ARG 0.010 0.000 ARG F 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 316 time to evaluate : 2.641 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6596 (tt) REVERT: A 107 LYS cc_start: 0.7865 (tttm) cc_final: 0.7314 (ttpt) REVERT: A 127 ASP cc_start: 0.6836 (m-30) cc_final: 0.6595 (m-30) REVERT: B 40 LYS cc_start: 0.7846 (tptp) cc_final: 0.7607 (mtmm) REVERT: B 230 LEU cc_start: 0.8575 (mt) cc_final: 0.8170 (tp) REVERT: C 125 PHE cc_start: 0.6895 (m-10) cc_final: 0.6686 (m-10) REVERT: C 131 GLU cc_start: 0.7439 (tp30) cc_final: 0.7022 (tt0) REVERT: C 180 ILE cc_start: 0.8020 (tt) cc_final: 0.7709 (tt) REVERT: D 54 LYS cc_start: 0.7637 (mmtm) cc_final: 0.7399 (mtpp) REVERT: D 203 ASP cc_start: 0.7774 (t0) cc_final: 0.7511 (t0) REVERT: D 230 LEU cc_start: 0.8527 (mt) cc_final: 0.8179 (tp) REVERT: D 250 GLU cc_start: 0.7908 (tp30) cc_final: 0.7438 (mt-10) REVERT: E 47 ASP cc_start: 0.7871 (t0) cc_final: 0.7346 (m-30) REVERT: E 181 LYS cc_start: 0.8146 (mttt) cc_final: 0.7588 (mtmt) REVERT: E 229 MET cc_start: 0.7146 (mtt) cc_final: 0.6812 (mtt) REVERT: F 214 MET cc_start: 0.7334 (mmp) cc_final: 0.7119 (mmp) REVERT: F 264 ASP cc_start: 0.6880 (p0) cc_final: 0.6617 (t0) REVERT: G 62 SER cc_start: 0.8309 (t) cc_final: 0.7842 (m) REVERT: G 64 THR cc_start: 0.8747 (p) cc_final: 0.8247 (p) REVERT: G 131 GLU cc_start: 0.7680 (tp30) cc_final: 0.7461 (tt0) REVERT: G 269 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7660 (tp-100) REVERT: H 225 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7615 (ttmt) REVERT: H 231 ARG cc_start: 0.7441 (tpp80) cc_final: 0.7078 (tpp80) REVERT: I 231 ARG cc_start: 0.7050 (ttm110) cc_final: 0.6847 (ttp-110) REVERT: I 238 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8055 (mt-10) REVERT: J 20 TRP cc_start: 0.7402 (t60) cc_final: 0.7159 (t60) REVERT: J 116 ARG cc_start: 0.7373 (tpp-160) cc_final: 0.6914 (mmp-170) REVERT: J 140 MET cc_start: 0.9208 (ttp) cc_final: 0.8831 (ttm) REVERT: J 163 ASP cc_start: 0.7790 (m-30) cc_final: 0.7453 (t0) outliers start: 37 outliers final: 31 residues processed: 340 average time/residue: 0.3824 time to fit residues: 195.5801 Evaluate side-chains 338 residues out of total 2370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 306 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 20 TRP Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain J residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 0.6980 chunk 221 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 191 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 0.0970 chunk 208 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN g 577 GLN I 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.108011 restraints weight = 29759.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109432 restraints weight = 33276.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.110251 restraints weight = 26279.388| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23487 Z= 0.137 Angle : 0.474 9.049 31799 Z= 0.247 Chirality : 0.039 0.197 3531 Planarity : 0.003 0.040 3858 Dihedral : 15.219 178.120 3794 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.69 % Allowed : 15.58 % Favored : 82.74 % 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: 1.40 (0.16), residues: 2670 helix: 1.44 (0.13), residues: 1600 sheet: 1.56 (0.26), residues: 280 loop : -0.28 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 45 HIS 0.002 0.000 HIS E 193 PHE 0.005 0.001 PHE J 106 TYR 0.010 0.001 TYR j 575 ARG 0.010 0.000 ARG F 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4790.17 seconds wall clock time: 87 minutes 46.26 seconds (5266.26 seconds total)