Starting phenix.real_space_refine on Wed Sep 17 14:47:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwv_38743/09_2025/8xwv_38743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwv_38743/09_2025/8xwv_38743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xwv_38743/09_2025/8xwv_38743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwv_38743/09_2025/8xwv_38743.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwv_38743/09_2025/8xwv_38743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwv_38743/09_2025/8xwv_38743.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 1.000 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5868 2.51 5 N 1594 2.21 5 O 1691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9211 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 465 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 62} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 387 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 55} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2354 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 286} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1542 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2416 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 389 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 2.50, per 1000 atoms: 0.27 Number of scatterers: 9211 At special positions: 0 Unit cell: (87.15, 122.425, 151.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1691 8.00 N 1594 7.00 C 5868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 35 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 35 " distance=2.03 Simple disulfide: pdb=" SG CYS E 11 " - pdb=" SG CYS E 51 " distance=2.03 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 450.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 14 sheets defined 37.2% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 56 through 67 removed outlier: 3.529A pdb=" N LYS D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 21 No H-bonds generated for 'chain 'E' and resid 19 through 21' Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'R' and resid 44 through 76 removed outlier: 4.369A pdb=" N LYS R 48 " --> pdb=" O LEU R 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE R 50 " --> pdb=" O ILE R 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 99 Processing helix chain 'R' and resid 100 through 111 Processing helix chain 'R' and resid 115 through 150 removed outlier: 4.078A pdb=" N SER R 123 " --> pdb=" O CYS R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 160 removed outlier: 3.707A pdb=" N THR R 156 " --> pdb=" O ARG R 153 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.617A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 removed outlier: 3.684A pdb=" N MET R 209 " --> pdb=" O ALA R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.691A pdb=" N GLN R 216 " --> pdb=" O ARG R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 241 removed outlier: 3.785A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA R 241 " --> pdb=" O THR R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 330 removed outlier: 3.735A pdb=" N ALA R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.566A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.975A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.587A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.527A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.778A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.901A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.595A pdb=" N ASP H 223 " --> pdb=" O GLU H 220 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 220 through 224' Processing sheet with id=AA1, first strand: chain 'D' and resid 49 through 52 removed outlier: 4.189A pdb=" N VAL D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.957A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.606A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.689A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.129A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.130A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.501A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.597A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.428A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.973A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.446A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.593A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.598A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1359 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: 1.72 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2943 1.34 - 1.46: 1525 1.46 - 1.58: 4852 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9396 Sorted by residual: bond pdb=" N TYR H 235 " pdb=" CA TYR H 235 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.53e-02 4.27e+03 3.99e+00 bond pdb=" N LEU R 325 " pdb=" CA LEU R 325 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.80e+00 bond pdb=" CA SER A 6 " pdb=" CB SER A 6 " ideal model delta sigma weight residual 1.530 1.491 0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" CA ALA A 41 " pdb=" CB ALA A 41 " ideal model delta sigma weight residual 1.527 1.501 0.026 1.49e-02 4.50e+03 3.13e+00 bond pdb=" N LEU R 68 " pdb=" CA LEU R 68 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.72e+00 ... (remaining 9391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 12627 1.87 - 3.73: 152 3.73 - 5.60: 16 5.60 - 7.46: 4 7.46 - 9.33: 3 Bond angle restraints: 12802 Sorted by residual: angle pdb=" C GLY A 40 " pdb=" N ALA A 41 " pdb=" CA ALA A 41 " ideal model delta sigma weight residual 122.12 115.87 6.25 1.76e+00 3.23e-01 1.26e+01 angle pdb=" CA TYR H 235 " pdb=" C TYR H 235 " pdb=" O TYR H 235 " ideal model delta sigma weight residual 120.23 116.61 3.62 1.02e+00 9.61e-01 1.26e+01 angle pdb=" N LEU R 325 " pdb=" CA LEU R 325 " pdb=" C LEU R 325 " ideal model delta sigma weight residual 111.36 107.94 3.42 1.09e+00 8.42e-01 9.84e+00 angle pdb=" CA TYR H 235 " pdb=" C TYR H 235 " pdb=" N PRO H 236 " ideal model delta sigma weight residual 118.03 121.73 -3.70 1.19e+00 7.06e-01 9.69e+00 angle pdb=" CA GLN B 13 " pdb=" CB GLN B 13 " pdb=" CG GLN B 13 " ideal model delta sigma weight residual 114.10 119.48 -5.38 2.00e+00 2.50e-01 7.25e+00 ... (remaining 12797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4903 17.56 - 35.11: 500 35.11 - 52.67: 119 52.67 - 70.22: 22 70.22 - 87.78: 6 Dihedral angle restraints: 5550 sinusoidal: 1912 harmonic: 3638 Sorted by residual: dihedral pdb=" CB CYS D 11 " pdb=" SG CYS D 11 " pdb=" SG CYS D 51 " pdb=" CB CYS D 51 " ideal model delta sinusoidal sigma weight residual 93.00 171.62 -78.62 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual 93.00 143.19 -50.19 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" SG CYS R 119 " pdb=" CB CYS R 196 " pdb=" SG CYS R 196 " pdb=" CA CYS R 196 " ideal model delta sinusoidal sigma weight residual -73.00 -10.41 -62.59 1 2.00e+01 2.50e-03 1.30e+01 ... (remaining 5547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1092 0.041 - 0.081: 296 0.081 - 0.122: 119 0.122 - 0.162: 6 0.162 - 0.203: 2 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA LEU R 68 " pdb=" N LEU R 68 " pdb=" C LEU R 68 " pdb=" CB LEU R 68 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU R 88 " pdb=" CB LEU R 88 " pdb=" CD1 LEU R 88 " pdb=" CD2 LEU R 88 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA ILE H 189 " pdb=" N ILE H 189 " pdb=" C ILE H 189 " pdb=" CB ILE H 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 1512 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 30 " 0.035 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO E 31 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 31 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 31 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO B 194 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 193 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO R 194 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 194 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 194 " 0.022 5.00e-02 4.00e+02 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2216 2.79 - 3.32: 8271 3.32 - 3.85: 14763 3.85 - 4.37: 16682 4.37 - 4.90: 30633 Nonbonded interactions: 72565 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.265 3.040 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.292 3.040 nonbonded pdb=" O LEU R 64 " pdb=" OG SER R 67 " model vdw 2.293 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.320 3.040 ... (remaining 72560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 9 or (resid 10 and (name N or name CA or name C or name O \ or name CB )) or resid 11 or (resid 12 through 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 or (resid 15 through 16 and (name N or na \ me CA or name C or name O or name CB )) or resid 17 through 28 or (resid 29 and \ (name N or name CA or name C or name O or name CB )) or resid 30 through 33 or ( \ resid 34 and (name N or name CA or name C or name O or name CB )) or resid 35 th \ rough 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) o \ r resid 38 or (resid 39 and (name N or name CA or name C or name O or name CB )) \ or resid 40 through 51 or (resid 52 and (name N or name CA or name C or name O \ or name CB )) or resid 53 through 59 or (resid 60 through 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 66 or (resid 67 and (n \ ame N or name CA or name C or name O or name CB )) or resid 68)) selection = (chain 'E' and (resid 9 through 21 or (resid 22 and (name N or name CA or name C \ or name O or name CB )) or resid 23 through 44 or (resid 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 64 or (resid 65 and (n \ ame N or name CA or name C or name O or name CB )) or resid 66 through 68)) } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.090 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9404 Z= 0.134 Angle : 0.524 9.326 12818 Z= 0.286 Chirality : 0.042 0.203 1515 Planarity : 0.003 0.054 1630 Dihedral : 15.238 87.780 3174 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.11 % Allowed : 21.87 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.24), residues: 1235 helix: 2.06 (0.26), residues: 405 sheet: 0.50 (0.29), residues: 331 loop : -0.31 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 251 TYR 0.016 0.001 TYR A 354 PHE 0.010 0.001 PHE B 151 TRP 0.006 0.001 TRP B 211 HIS 0.002 0.001 HIS R 242 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9396) covalent geometry : angle 0.52373 (12802) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.73911 ( 16) hydrogen bonds : bond 0.17793 ( 474) hydrogen bonds : angle 6.70063 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.349 Fit side-chains REVERT: H 83 MET cc_start: 0.8881 (mtp) cc_final: 0.8680 (mtp) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.1005 time to fit residues: 18.0313 Evaluate side-chains 124 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN ** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.187124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131740 restraints weight = 11206.595| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.04 r_work: 0.3271 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9404 Z= 0.153 Angle : 0.552 12.442 12818 Z= 0.287 Chirality : 0.043 0.148 1515 Planarity : 0.004 0.054 1630 Dihedral : 3.903 16.681 1336 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.19 % Allowed : 20.22 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.24), residues: 1235 helix: 2.27 (0.26), residues: 405 sheet: 0.42 (0.29), residues: 329 loop : -0.30 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.021 0.002 TYR A 354 PHE 0.012 0.001 PHE H 29 TRP 0.013 0.002 TRP B 211 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9396) covalent geometry : angle 0.55098 (12802) SS BOND : bond 0.00322 ( 8) SS BOND : angle 0.92802 ( 16) hydrogen bonds : bond 0.04487 ( 474) hydrogen bonds : angle 4.72161 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.372 Fit side-chains REVERT: D 10 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: R 300 GLU cc_start: 0.7973 (tp30) cc_final: 0.7766 (tp30) outliers start: 29 outliers final: 14 residues processed: 155 average time/residue: 0.0941 time to fit residues: 20.8719 Evaluate side-chains 142 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 GLN Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 63 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 105 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.185988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127919 restraints weight = 11203.515| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.80 r_work: 0.3275 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9404 Z= 0.168 Angle : 0.550 13.715 12818 Z= 0.288 Chirality : 0.044 0.150 1515 Planarity : 0.004 0.055 1630 Dihedral : 3.982 17.103 1336 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.07 % Allowed : 20.33 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.24), residues: 1235 helix: 2.26 (0.26), residues: 404 sheet: 0.38 (0.28), residues: 340 loop : -0.25 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 80 TYR 0.022 0.002 TYR A 354 PHE 0.012 0.001 PHE B 151 TRP 0.012 0.002 TRP B 211 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9396) covalent geometry : angle 0.54904 (12802) SS BOND : bond 0.00268 ( 8) SS BOND : angle 0.91233 ( 16) hydrogen bonds : bond 0.04358 ( 474) hydrogen bonds : angle 4.51048 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.324 Fit side-chains REVERT: D 10 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: R 245 GLN cc_start: 0.7209 (mp10) cc_final: 0.6919 (mp10) REVERT: B 32 GLN cc_start: 0.8350 (mt0) cc_final: 0.7981 (mt0) REVERT: H 6 GLU cc_start: 0.8211 (mp0) cc_final: 0.7853 (mt-10) outliers start: 37 outliers final: 21 residues processed: 153 average time/residue: 0.0910 time to fit residues: 20.3084 Evaluate side-chains 150 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 GLN Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 61 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN H 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.184822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126505 restraints weight = 11318.510| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.89 r_work: 0.3220 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9404 Z= 0.196 Angle : 0.573 14.759 12818 Z= 0.300 Chirality : 0.044 0.147 1515 Planarity : 0.004 0.055 1630 Dihedral : 4.097 17.920 1336 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.05 % Allowed : 20.11 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.24), residues: 1235 helix: 2.20 (0.25), residues: 404 sheet: 0.27 (0.28), residues: 330 loop : -0.33 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 209 TYR 0.024 0.002 TYR A 354 PHE 0.013 0.002 PHE B 151 TRP 0.012 0.002 TRP B 211 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9396) covalent geometry : angle 0.57194 (12802) SS BOND : bond 0.00311 ( 8) SS BOND : angle 0.94689 ( 16) hydrogen bonds : bond 0.04352 ( 474) hydrogen bonds : angle 4.46398 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 0.311 Fit side-chains REVERT: D 10 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: R 245 GLN cc_start: 0.7153 (mp10) cc_final: 0.6891 (mp10) REVERT: B 32 GLN cc_start: 0.8412 (mt0) cc_final: 0.8092 (mt0) outliers start: 46 outliers final: 29 residues processed: 160 average time/residue: 0.0837 time to fit residues: 19.4706 Evaluate side-chains 156 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 GLN Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 40.0000 chunk 110 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 119 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 191 ASN ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.185932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128272 restraints weight = 11262.553| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.87 r_work: 0.3243 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9404 Z= 0.141 Angle : 0.533 15.736 12818 Z= 0.279 Chirality : 0.043 0.139 1515 Planarity : 0.004 0.054 1630 Dihedral : 3.974 17.561 1336 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.52 % Allowed : 22.42 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.24), residues: 1235 helix: 2.27 (0.25), residues: 404 sheet: 0.31 (0.28), residues: 337 loop : -0.34 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 209 TYR 0.019 0.001 TYR A 354 PHE 0.013 0.001 PHE R 59 TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9396) covalent geometry : angle 0.53221 (12802) SS BOND : bond 0.00274 ( 8) SS BOND : angle 1.14897 ( 16) hydrogen bonds : bond 0.04009 ( 474) hydrogen bonds : angle 4.35738 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.348 Fit side-chains REVERT: D 8 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7681 (mtt90) REVERT: R 245 GLN cc_start: 0.7025 (mp10) cc_final: 0.6694 (mp10) REVERT: B 59 TYR cc_start: 0.8655 (m-80) cc_final: 0.8338 (m-80) outliers start: 32 outliers final: 19 residues processed: 153 average time/residue: 0.0949 time to fit residues: 20.7378 Evaluate side-chains 148 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 39 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.186499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130391 restraints weight = 11262.473| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.88 r_work: 0.3325 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9404 Z= 0.126 Angle : 0.529 16.598 12818 Z= 0.273 Chirality : 0.042 0.138 1515 Planarity : 0.003 0.052 1630 Dihedral : 3.841 17.346 1336 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.29 % Allowed : 21.54 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.24), residues: 1235 helix: 2.25 (0.26), residues: 404 sheet: 0.24 (0.28), residues: 341 loop : -0.30 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.017 0.001 TYR A 354 PHE 0.015 0.001 PHE R 59 TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9396) covalent geometry : angle 0.52848 (12802) SS BOND : bond 0.00270 ( 8) SS BOND : angle 0.84678 ( 16) hydrogen bonds : bond 0.03821 ( 474) hydrogen bonds : angle 4.27182 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.351 Fit side-chains REVERT: D 8 ARG cc_start: 0.7867 (mtt-85) cc_final: 0.7646 (mtt90) REVERT: R 245 GLN cc_start: 0.6931 (mp10) cc_final: 0.6565 (mp10) REVERT: A 295 ASN cc_start: 0.8426 (t0) cc_final: 0.8206 (t0) REVERT: B 59 TYR cc_start: 0.8629 (m-80) cc_final: 0.8391 (m-80) REVERT: H 6 GLU cc_start: 0.8285 (mp0) cc_final: 0.7845 (mt-10) outliers start: 39 outliers final: 28 residues processed: 160 average time/residue: 0.0898 time to fit residues: 20.8626 Evaluate side-chains 163 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.182934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124983 restraints weight = 11313.641| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.79 r_work: 0.3232 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9404 Z= 0.242 Angle : 0.615 18.281 12818 Z= 0.320 Chirality : 0.046 0.168 1515 Planarity : 0.004 0.051 1630 Dihedral : 4.174 17.776 1336 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.73 % Allowed : 21.10 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.24), residues: 1235 helix: 2.19 (0.26), residues: 403 sheet: 0.16 (0.28), residues: 335 loop : -0.40 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.027 0.002 TYR A 354 PHE 0.015 0.002 PHE R 59 TRP 0.012 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 9396) covalent geometry : angle 0.61462 (12802) SS BOND : bond 0.00384 ( 8) SS BOND : angle 1.03101 ( 16) hydrogen bonds : bond 0.04503 ( 474) hydrogen bonds : angle 4.47909 ( 1359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.342 Fit side-chains REVERT: D 8 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7796 (mtt90) REVERT: R 82 VAL cc_start: 0.7124 (m) cc_final: 0.6886 (t) REVERT: R 245 GLN cc_start: 0.7224 (mp10) cc_final: 0.6787 (mp10) outliers start: 43 outliers final: 36 residues processed: 159 average time/residue: 0.0815 time to fit residues: 18.8668 Evaluate side-chains 163 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 102 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 7 optimal weight: 30.0000 chunk 121 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.186205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.129530 restraints weight = 11170.950| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.75 r_work: 0.3295 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9404 Z= 0.120 Angle : 0.525 17.254 12818 Z= 0.272 Chirality : 0.042 0.191 1515 Planarity : 0.003 0.051 1630 Dihedral : 3.889 17.986 1336 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.30 % Allowed : 22.86 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.24), residues: 1235 helix: 2.31 (0.26), residues: 404 sheet: 0.27 (0.28), residues: 332 loop : -0.36 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.017 0.001 TYR H 190 PHE 0.016 0.001 PHE R 59 TRP 0.008 0.001 TRP B 211 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9396) covalent geometry : angle 0.52416 (12802) SS BOND : bond 0.00252 ( 8) SS BOND : angle 0.87533 ( 16) hydrogen bonds : bond 0.03735 ( 474) hydrogen bonds : angle 4.29452 ( 1359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.268 Fit side-chains REVERT: D 8 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7706 (mtt90) REVERT: R 245 GLN cc_start: 0.7032 (mp10) cc_final: 0.6647 (mp10) REVERT: B 32 GLN cc_start: 0.8291 (mt0) cc_final: 0.8052 (mt0) REVERT: H 6 GLU cc_start: 0.8314 (mp0) cc_final: 0.7897 (mt-10) outliers start: 30 outliers final: 24 residues processed: 149 average time/residue: 0.0817 time to fit residues: 17.4198 Evaluate side-chains 152 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 95 optimal weight: 8.9990 chunk 113 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.185963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131954 restraints weight = 11076.790| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.87 r_work: 0.3340 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9404 Z= 0.127 Angle : 0.527 16.753 12818 Z= 0.273 Chirality : 0.042 0.171 1515 Planarity : 0.003 0.051 1630 Dihedral : 3.834 17.175 1336 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.41 % Allowed : 22.75 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.24), residues: 1235 helix: 2.38 (0.25), residues: 404 sheet: 0.21 (0.28), residues: 342 loop : -0.33 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.017 0.001 TYR A 354 PHE 0.018 0.001 PHE R 59 TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9396) covalent geometry : angle 0.52688 (12802) SS BOND : bond 0.00255 ( 8) SS BOND : angle 0.83918 ( 16) hydrogen bonds : bond 0.03708 ( 474) hydrogen bonds : angle 4.23249 ( 1359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.363 Fit side-chains REVERT: D 8 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.7751 (mtt90) REVERT: R 245 GLN cc_start: 0.6951 (mp10) cc_final: 0.6573 (mp10) REVERT: B 32 GLN cc_start: 0.8233 (mt0) cc_final: 0.7996 (mt0) REVERT: H 6 GLU cc_start: 0.8309 (mp0) cc_final: 0.7851 (mt-10) outliers start: 31 outliers final: 29 residues processed: 147 average time/residue: 0.0919 time to fit residues: 19.5127 Evaluate side-chains 155 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 chunk 84 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 54 optimal weight: 0.0370 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 5 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 GLN A 194 ASN B 176 GLN B 268 ASN G 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.189418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.138645 restraints weight = 11129.271| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.77 r_work: 0.3443 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9404 Z= 0.091 Angle : 0.504 16.287 12818 Z= 0.258 Chirality : 0.041 0.143 1515 Planarity : 0.003 0.051 1630 Dihedral : 3.602 17.477 1336 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.76 % Allowed : 24.62 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.24), residues: 1235 helix: 2.44 (0.26), residues: 404 sheet: 0.36 (0.28), residues: 330 loop : -0.21 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.018 0.001 TYR H 190 PHE 0.018 0.001 PHE R 59 TRP 0.009 0.001 TRP B 63 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 9396) covalent geometry : angle 0.50356 (12802) SS BOND : bond 0.00168 ( 8) SS BOND : angle 0.78252 ( 16) hydrogen bonds : bond 0.03321 ( 474) hydrogen bonds : angle 4.12521 ( 1359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: D 8 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.7653 (mtt90) REVERT: D 66 MET cc_start: 0.7182 (mpp) cc_final: 0.6571 (pmm) REVERT: R 325 LEU cc_start: 0.6479 (pp) cc_final: 0.6221 (pp) REVERT: A 295 ASN cc_start: 0.8340 (t0) cc_final: 0.8076 (t0) REVERT: B 32 GLN cc_start: 0.8082 (mt0) cc_final: 0.7871 (mt0) outliers start: 16 outliers final: 12 residues processed: 146 average time/residue: 0.0917 time to fit residues: 19.2223 Evaluate side-chains 143 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 44 optimal weight: 0.0770 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 103 optimal weight: 0.0000 chunk 12 optimal weight: 8.9990 overall best weight: 1.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN B 259 GLN B 268 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.194987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133570 restraints weight = 10778.624| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.65 r_work: 0.3438 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9404 Z= 0.151 Angle : 0.556 18.848 12818 Z= 0.284 Chirality : 0.043 0.135 1515 Planarity : 0.004 0.051 1630 Dihedral : 3.788 17.193 1336 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.98 % Allowed : 23.96 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.24), residues: 1235 helix: 2.48 (0.25), residues: 404 sheet: 0.30 (0.28), residues: 331 loop : -0.24 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.019 0.001 TYR A 354 PHE 0.012 0.001 PHE H 29 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9396) covalent geometry : angle 0.55540 (12802) SS BOND : bond 0.00263 ( 8) SS BOND : angle 0.79651 ( 16) hydrogen bonds : bond 0.03809 ( 474) hydrogen bonds : angle 4.21713 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3279.55 seconds wall clock time: 56 minutes 43.72 seconds (3403.72 seconds total)