Starting phenix.real_space_refine on Tue Feb 20 08:22:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhi_16055/02_2024/8bhi_16055_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhi_16055/02_2024/8bhi_16055.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhi_16055/02_2024/8bhi_16055_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhi_16055/02_2024/8bhi_16055_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhi_16055/02_2024/8bhi_16055_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhi_16055/02_2024/8bhi_16055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhi_16055/02_2024/8bhi_16055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhi_16055/02_2024/8bhi_16055_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhi_16055/02_2024/8bhi_16055_trim_updated.pdb" } resolution = 2.67 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 90 5.16 5 C 8940 2.51 5 N 2280 2.21 5 O 2495 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27220 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'QKF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'QKF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'QKF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'QKF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'QKF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.35, per 1000 atoms: 0.53 Number of scatterers: 27220 At special positions: 0 Unit cell: (89.976, 93.236, 123.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 O 2495 8.00 N 2280 7.00 C 8940 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 22.75 Conformation dependent library (CDL) restraints added in 2.8 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 20 sheets defined 35.4% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.90 Creating SS restraints... Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 234 through 249 removed outlier: 4.146A pdb=" N SER A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TRP A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 276 Processing helix chain 'A' and resid 288 through 311 Processing helix chain 'A' and resid 318 through 417 removed outlier: 4.140A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 234 through 249 removed outlier: 4.147A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TRP B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 318 through 417 removed outlier: 4.140A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 178 through 181 No H-bonds generated for 'chain 'C' and resid 178 through 181' Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 234 through 249 removed outlier: 4.146A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 276 Processing helix chain 'C' and resid 288 through 311 Processing helix chain 'C' and resid 318 through 417 removed outlier: 4.140A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 178 through 181 No H-bonds generated for 'chain 'D' and resid 178 through 181' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 234 through 249 removed outlier: 4.147A pdb=" N SER D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 318 through 417 removed outlier: 4.140A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 178 through 181 No H-bonds generated for 'chain 'E' and resid 178 through 181' Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 234 through 249 removed outlier: 4.146A pdb=" N SER E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TRP E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 276 Processing helix chain 'E' and resid 288 through 311 Processing helix chain 'E' and resid 318 through 417 removed outlier: 4.140A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.658A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 48 through 50 Processing sheet with id= C, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.604A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 107 through 112 removed outlier: 6.936A pdb=" N SER A 139 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER A 110 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 137 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.660A pdb=" N THR B 42 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL B 173 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL B 44 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 48 through 50 Processing sheet with id= G, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.605A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 107 through 112 removed outlier: 6.936A pdb=" N SER B 139 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER B 110 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR B 137 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.659A pdb=" N THR C 42 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL C 173 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL C 44 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 48 through 50 Processing sheet with id= K, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.604A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 107 through 112 removed outlier: 6.936A pdb=" N SER C 139 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER C 110 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR C 137 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.659A pdb=" N THR D 42 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL D 173 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL D 44 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 48 through 50 Processing sheet with id= O, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.604A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 107 through 112 removed outlier: 6.936A pdb=" N SER D 139 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER D 110 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR D 137 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 170 through 174 removed outlier: 6.659A pdb=" N THR E 42 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL E 173 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL E 44 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 48 through 50 Processing sheet with id= S, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.604A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 107 through 112 removed outlier: 6.935A pdb=" N SER E 139 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER E 110 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR E 137 " --> pdb=" O SER E 110 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.74 Time building geometry restraints manager: 23.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 10 1.23 - 1.42: 6120 1.42 - 1.61: 7890 1.61 - 1.81: 160 Bond restraints: 27595 Sorted by residual: bond pdb=" C20 QKF E 502 " pdb=" N3 QKF E 502 " ideal model delta sigma weight residual 1.646 1.466 0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" C20 QKF B 502 " pdb=" N3 QKF B 502 " ideal model delta sigma weight residual 1.646 1.466 0.180 2.00e-02 2.50e+03 8.07e+01 bond pdb=" C20 QKF D 502 " pdb=" N3 QKF D 502 " ideal model delta sigma weight residual 1.646 1.467 0.179 2.00e-02 2.50e+03 8.04e+01 bond pdb=" C20 QKF A 502 " pdb=" N3 QKF A 502 " ideal model delta sigma weight residual 1.646 1.467 0.179 2.00e-02 2.50e+03 8.04e+01 bond pdb=" C20 QKF C 502 " pdb=" N3 QKF C 502 " ideal model delta sigma weight residual 1.646 1.467 0.179 2.00e-02 2.50e+03 8.02e+01 ... (remaining 27590 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.23: 369 106.23 - 113.16: 31391 113.16 - 120.10: 8549 120.10 - 127.03: 9062 127.03 - 133.97: 209 Bond angle restraints: 49580 Sorted by residual: angle pdb=" C4 QKF E 502 " pdb=" C6 QKF E 502 " pdb=" C9 QKF E 502 " ideal model delta sigma weight residual 159.63 129.23 30.40 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C4 QKF B 502 " pdb=" C6 QKF B 502 " pdb=" C9 QKF B 502 " ideal model delta sigma weight residual 159.63 129.24 30.39 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C4 QKF C 502 " pdb=" C6 QKF C 502 " pdb=" C9 QKF C 502 " ideal model delta sigma weight residual 159.63 129.30 30.33 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C4 QKF D 502 " pdb=" C6 QKF D 502 " pdb=" C9 QKF D 502 " ideal model delta sigma weight residual 159.63 129.30 30.33 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C4 QKF A 502 " pdb=" C6 QKF A 502 " pdb=" C9 QKF A 502 " ideal model delta sigma weight residual 159.63 129.32 30.31 3.00e+00 1.11e-01 1.02e+02 ... (remaining 49575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.12: 12780 23.12 - 46.25: 212 46.25 - 69.37: 118 69.37 - 92.50: 5 92.50 - 115.62: 30 Dihedral angle restraints: 13145 sinusoidal: 7015 harmonic: 6130 Sorted by residual: dihedral pdb=" C18 QKF E 502 " pdb=" C17 QKF E 502 " pdb=" N3 QKF E 502 " pdb=" C20 QKF E 502 " ideal model delta sinusoidal sigma weight residual -53.41 62.21 -115.62 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C18 QKF B 502 " pdb=" C17 QKF B 502 " pdb=" N3 QKF B 502 " pdb=" C20 QKF B 502 " ideal model delta sinusoidal sigma weight residual -53.41 62.20 -115.61 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C18 QKF D 502 " pdb=" C17 QKF D 502 " pdb=" N3 QKF D 502 " pdb=" C20 QKF D 502 " ideal model delta sinusoidal sigma weight residual -53.41 62.17 -115.58 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 13142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 986 0.022 - 0.043: 603 0.043 - 0.065: 340 0.065 - 0.086: 122 0.086 - 0.108: 109 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE E 41 " pdb=" N ILE E 41 " pdb=" C ILE E 41 " pdb=" CB ILE E 41 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.91e-01 chirality pdb=" CA ILE D 41 " pdb=" N ILE D 41 " pdb=" C ILE D 41 " pdb=" CB ILE D 41 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.89e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.87e-01 ... (remaining 2157 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 QKF D 502 " -0.017 2.00e-02 2.50e+03 6.09e-02 7.42e+01 pdb=" C12 QKF D 502 " -0.039 2.00e-02 2.50e+03 pdb=" C13 QKF D 502 " -0.041 2.00e-02 2.50e+03 pdb=" C14 QKF D 502 " -0.028 2.00e-02 2.50e+03 pdb=" C15 QKF D 502 " -0.045 2.00e-02 2.50e+03 pdb=" C16 QKF D 502 " 0.104 2.00e-02 2.50e+03 pdb=" N2 QKF D 502 " -0.039 2.00e-02 2.50e+03 pdb=" O1 QKF D 502 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QKF C 502 " -0.018 2.00e-02 2.50e+03 6.09e-02 7.41e+01 pdb=" C12 QKF C 502 " -0.038 2.00e-02 2.50e+03 pdb=" C13 QKF C 502 " -0.041 2.00e-02 2.50e+03 pdb=" C14 QKF C 502 " -0.028 2.00e-02 2.50e+03 pdb=" C15 QKF C 502 " -0.046 2.00e-02 2.50e+03 pdb=" C16 QKF C 502 " 0.104 2.00e-02 2.50e+03 pdb=" N2 QKF C 502 " -0.039 2.00e-02 2.50e+03 pdb=" O1 QKF C 502 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QKF A 502 " -0.018 2.00e-02 2.50e+03 6.09e-02 7.41e+01 pdb=" C12 QKF A 502 " -0.038 2.00e-02 2.50e+03 pdb=" C13 QKF A 502 " -0.041 2.00e-02 2.50e+03 pdb=" C14 QKF A 502 " -0.027 2.00e-02 2.50e+03 pdb=" C15 QKF A 502 " -0.045 2.00e-02 2.50e+03 pdb=" C16 QKF A 502 " 0.104 2.00e-02 2.50e+03 pdb=" N2 QKF A 502 " -0.039 2.00e-02 2.50e+03 pdb=" O1 QKF A 502 " 0.105 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 2053 2.23 - 2.82: 61235 2.82 - 3.41: 68830 3.41 - 4.01: 99690 4.01 - 4.60: 155982 Nonbonded interactions: 387790 Sorted by model distance: nonbonded pdb=" OD1 ASP A 152 " pdb=" HE ARG A 224 " model vdw 1.631 1.850 nonbonded pdb=" OD1 ASP D 152 " pdb=" HE ARG D 224 " model vdw 1.632 1.850 nonbonded pdb=" OD1 ASP E 152 " pdb=" HE ARG E 224 " model vdw 1.632 1.850 nonbonded pdb=" OD1 ASP B 152 " pdb=" HE ARG B 224 " model vdw 1.632 1.850 nonbonded pdb=" OD1 ASP C 152 " pdb=" HE ARG C 224 " model vdw 1.632 1.850 ... (remaining 387785 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' } 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 individual isotropic 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: 10.500 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: 0.410 Extract box with map and model: 35.120 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 92.090 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.010 0.180 14180 Z= 0.629 Angle : 1.014 30.400 19305 Z= 0.381 Chirality : 0.039 0.108 2160 Planarity : 0.005 0.061 2395 Dihedral : 12.044 115.624 5135 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.52 (0.21), residues: 1670 helix: 2.55 (0.22), residues: 575 sheet: -0.14 (0.25), residues: 450 loop : 0.59 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 249 HIS 0.003 0.001 HIS C 195 PHE 0.009 0.001 PHE B 104 TYR 0.006 0.001 TYR E 285 ARG 0.002 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8834 (tttt) cc_final: 0.8575 (tptm) REVERT: A 141 GLU cc_start: 0.8296 (pt0) cc_final: 0.8081 (pp20) REVERT: A 204 GLU cc_start: 0.8452 (pt0) cc_final: 0.8226 (pt0) REVERT: B 109 LYS cc_start: 0.8817 (tttt) cc_final: 0.8565 (tptt) REVERT: B 141 GLU cc_start: 0.8336 (pt0) cc_final: 0.8103 (pp20) REVERT: B 204 GLU cc_start: 0.8456 (pt0) cc_final: 0.8217 (pt0) REVERT: C 109 LYS cc_start: 0.8812 (tttt) cc_final: 0.8561 (tptt) REVERT: C 141 GLU cc_start: 0.8327 (pt0) cc_final: 0.8101 (pp20) REVERT: C 204 GLU cc_start: 0.8440 (pt0) cc_final: 0.8191 (pt0) REVERT: D 141 GLU cc_start: 0.8340 (pt0) cc_final: 0.8081 (pp20) REVERT: D 204 GLU cc_start: 0.8421 (pt0) cc_final: 0.8158 (pt0) REVERT: E 109 LYS cc_start: 0.8812 (tttt) cc_final: 0.8568 (tptt) REVERT: E 141 GLU cc_start: 0.8341 (pt0) cc_final: 0.8084 (pp20) REVERT: E 204 GLU cc_start: 0.8431 (pt0) cc_final: 0.8180 (pt0) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 3.6904 time to fit residues: 1063.5399 Evaluate side-chains 104 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14180 Z= 0.172 Angle : 0.541 5.496 19305 Z= 0.267 Chirality : 0.040 0.121 2160 Planarity : 0.005 0.056 2395 Dihedral : 12.865 102.239 2000 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.41 % Allowed : 11.14 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.41 (0.21), residues: 1670 helix: 2.43 (0.22), residues: 570 sheet: 0.02 (0.25), residues: 460 loop : 0.41 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 73 HIS 0.002 0.001 HIS C 195 PHE 0.009 0.001 PHE D 409 TYR 0.009 0.001 TYR E 413 ARG 0.005 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8839 (tttt) cc_final: 0.8581 (tptm) REVERT: A 245 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8845 (mt0) REVERT: B 109 LYS cc_start: 0.8827 (tttt) cc_final: 0.8598 (tptm) REVERT: C 109 LYS cc_start: 0.8817 (tttt) cc_final: 0.8558 (tptm) REVERT: D 245 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8919 (mt0) REVERT: E 109 LYS cc_start: 0.8801 (tttt) cc_final: 0.8572 (tptt) outliers start: 21 outliers final: 8 residues processed: 132 average time/residue: 2.7565 time to fit residues: 401.7716 Evaluate side-chains 123 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.0270 chunk 124 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 14180 Z= 0.320 Angle : 0.546 5.785 19305 Z= 0.270 Chirality : 0.040 0.123 2160 Planarity : 0.004 0.038 2395 Dihedral : 9.713 105.531 2000 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.42 % Allowed : 10.74 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.11 (0.21), residues: 1670 helix: 2.11 (0.22), residues: 570 sheet: -0.24 (0.24), residues: 465 loop : 0.41 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 249 HIS 0.002 0.001 HIS E 221 PHE 0.012 0.001 PHE C 69 TYR 0.009 0.001 TYR B 413 ARG 0.003 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8787 (tttt) cc_final: 0.8501 (tptm) REVERT: A 245 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8881 (mt0) REVERT: B 109 LYS cc_start: 0.8798 (tttt) cc_final: 0.8525 (tptm) REVERT: B 395 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8526 (m-30) REVERT: C 109 LYS cc_start: 0.8774 (tttt) cc_final: 0.8460 (tptm) REVERT: D 115 MET cc_start: 0.8984 (mmp) cc_final: 0.8628 (mmp) REVERT: D 245 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8946 (mt0) outliers start: 36 outliers final: 13 residues processed: 142 average time/residue: 2.9446 time to fit residues: 457.8985 Evaluate side-chains 125 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 14180 Z= 0.271 Angle : 0.508 6.236 19305 Z= 0.253 Chirality : 0.040 0.120 2160 Planarity : 0.004 0.039 2395 Dihedral : 9.038 92.231 2000 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.74 % Allowed : 11.14 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.08 (0.21), residues: 1670 helix: 2.17 (0.22), residues: 570 sheet: -0.29 (0.24), residues: 460 loop : 0.30 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 249 HIS 0.002 0.001 HIS E 221 PHE 0.009 0.001 PHE A 69 TYR 0.007 0.001 TYR B 413 ARG 0.008 0.000 ARG E 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7968 (p0) REVERT: B 47 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.8067 (p0) REVERT: B 60 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8315 (mp0) outliers start: 26 outliers final: 15 residues processed: 123 average time/residue: 3.3548 time to fit residues: 451.2427 Evaluate side-chains 126 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 136 optimal weight: 0.0980 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14180 Z= 0.173 Angle : 0.482 7.253 19305 Z= 0.235 Chirality : 0.039 0.121 2160 Planarity : 0.004 0.038 2395 Dihedral : 8.521 84.760 2000 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.21 % Allowed : 12.62 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 (0.21), residues: 1670 helix: 2.32 (0.22), residues: 570 sheet: -0.17 (0.24), residues: 455 loop : 0.30 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 73 HIS 0.002 0.000 HIS E 195 PHE 0.007 0.001 PHE B 409 TYR 0.006 0.001 TYR E 413 ARG 0.007 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7875 (p0) REVERT: B 47 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7908 (p0) REVERT: D 115 MET cc_start: 0.9027 (mmp) cc_final: 0.8690 (mmp) outliers start: 18 outliers final: 11 residues processed: 116 average time/residue: 3.1885 time to fit residues: 403.8550 Evaluate side-chains 123 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14180 Z= 0.210 Angle : 0.482 6.299 19305 Z= 0.237 Chirality : 0.039 0.122 2160 Planarity : 0.004 0.040 2395 Dihedral : 8.832 89.324 2000 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.34 % Allowed : 12.68 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.20 (0.21), residues: 1670 helix: 2.33 (0.23), residues: 570 sheet: -0.16 (0.24), residues: 455 loop : 0.25 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 249 HIS 0.002 0.001 HIS B 195 PHE 0.008 0.001 PHE C 69 TYR 0.006 0.001 TYR E 297 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7932 (p0) REVERT: A 62 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8330 (pt0) REVERT: B 47 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.8003 (p0) REVERT: B 60 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: D 115 MET cc_start: 0.9036 (mmp) cc_final: 0.8702 (mmp) REVERT: E 277 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7918 (mtp-110) outliers start: 20 outliers final: 13 residues processed: 118 average time/residue: 2.9714 time to fit residues: 384.4804 Evaluate side-chains 126 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 277 ARG Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 14180 Z= 0.337 Angle : 0.520 6.587 19305 Z= 0.260 Chirality : 0.040 0.120 2160 Planarity : 0.004 0.040 2395 Dihedral : 9.819 101.415 2000 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.54 % Allowed : 12.62 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.98 (0.21), residues: 1670 helix: 2.18 (0.22), residues: 570 sheet: -0.33 (0.24), residues: 460 loop : 0.14 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 249 HIS 0.002 0.001 HIS C 113 PHE 0.010 0.001 PHE A 229 TYR 0.008 0.001 TYR E 297 ARG 0.003 0.000 ARG E 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: A 277 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7763 (mtp-110) REVERT: B 60 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: C 62 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: E 277 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8000 (mtp-110) outliers start: 23 outliers final: 14 residues processed: 121 average time/residue: 3.1484 time to fit residues: 416.9543 Evaluate side-chains 129 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 277 ARG Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14180 Z= 0.272 Angle : 0.502 8.465 19305 Z= 0.249 Chirality : 0.040 0.119 2160 Planarity : 0.004 0.044 2395 Dihedral : 9.285 95.370 2000 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.41 % Allowed : 13.29 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 0.97 (0.21), residues: 1670 helix: 2.18 (0.22), residues: 570 sheet: -0.33 (0.24), residues: 455 loop : 0.13 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 249 HIS 0.002 0.001 HIS C 113 PHE 0.008 0.001 PHE A 229 TYR 0.008 0.001 TYR E 297 ARG 0.007 0.000 ARG E 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8445 (pt0) REVERT: A 277 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7762 (mtp-110) REVERT: B 60 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: B 85 GLN cc_start: 0.7134 (mm-40) cc_final: 0.6911 (tp-100) REVERT: C 62 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8318 (pt0) REVERT: D 85 GLN cc_start: 0.7090 (mm110) cc_final: 0.6842 (tp40) REVERT: E 85 GLN cc_start: 0.7177 (mm110) cc_final: 0.6927 (tp-100) REVERT: E 277 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7950 (mtp-110) outliers start: 21 outliers final: 13 residues processed: 120 average time/residue: 2.8310 time to fit residues: 374.5202 Evaluate side-chains 128 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 277 ARG Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14180 Z= 0.181 Angle : 0.483 8.839 19305 Z= 0.236 Chirality : 0.039 0.121 2160 Planarity : 0.004 0.039 2395 Dihedral : 8.772 89.123 2000 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.28 % Allowed : 13.29 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.11 (0.21), residues: 1670 helix: 2.28 (0.23), residues: 570 sheet: -0.25 (0.24), residues: 455 loop : 0.21 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 114 HIS 0.001 0.000 HIS C 113 PHE 0.008 0.001 PHE A 69 TYR 0.007 0.001 TYR E 297 ARG 0.007 0.000 ARG E 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8382 (pt0) REVERT: A 85 GLN cc_start: 0.7154 (mm110) cc_final: 0.6930 (tp40) REVERT: A 277 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7752 (mtp-110) REVERT: B 60 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: C 62 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: D 85 GLN cc_start: 0.7110 (mm110) cc_final: 0.6880 (tp40) REVERT: D 115 MET cc_start: 0.9076 (mmp) cc_final: 0.8766 (mmp) REVERT: E 85 GLN cc_start: 0.7167 (mm110) cc_final: 0.6935 (tp-100) REVERT: E 277 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7970 (mtp-110) outliers start: 19 outliers final: 13 residues processed: 122 average time/residue: 2.9889 time to fit residues: 399.3467 Evaluate side-chains 128 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 277 ARG Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 164 optimal weight: 0.0670 chunk 151 optimal weight: 0.1980 chunk 130 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN C 85 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14180 Z= 0.132 Angle : 0.484 9.366 19305 Z= 0.231 Chirality : 0.039 0.123 2160 Planarity : 0.004 0.039 2395 Dihedral : 7.403 81.139 2000 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.01 % Allowed : 13.69 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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 (0.21), residues: 1670 helix: 2.43 (0.23), residues: 570 sheet: -0.12 (0.24), residues: 455 loop : 0.30 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 114 HIS 0.001 0.000 HIS C 195 PHE 0.007 0.001 PHE A 409 TYR 0.006 0.001 TYR D 297 ARG 0.008 0.000 ARG E 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8298 (pt0) REVERT: A 277 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7695 (mtp-110) REVERT: B 85 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7610 (tp40) REVERT: D 85 GLN cc_start: 0.7121 (mm110) cc_final: 0.6908 (tp40) REVERT: E 277 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7914 (mtp-110) outliers start: 15 outliers final: 10 residues processed: 126 average time/residue: 2.7346 time to fit residues: 380.2906 Evaluate side-chains 129 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 277 ARG Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 0.0270 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.068905 restraints weight = 76185.287| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.53 r_work: 0.2793 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14180 Z= 0.183 Angle : 0.475 9.246 19305 Z= 0.234 Chirality : 0.039 0.122 2160 Planarity : 0.004 0.041 2395 Dihedral : 5.590 81.819 2000 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.87 % Allowed : 14.56 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1670 helix: 2.41 (0.23), residues: 570 sheet: -0.12 (0.24), residues: 455 loop : 0.28 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 114 HIS 0.001 0.000 HIS C 195 PHE 0.013 0.001 PHE B 18 TYR 0.009 0.001 TYR E 297 ARG 0.008 0.000 ARG E 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9285.43 seconds wall clock time: 164 minutes 42.01 seconds (9882.01 seconds total)