Starting phenix.real_space_refine on Fri Oct 23 09:15:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22sk_68645/10_2026/22sk_68645.cif Found real_map, /net/cci-nas-00/data/ceres_data/22sk_68645/10_2026/22sk_68645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22sk_68645/10_2026/22sk_68645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22sk_68645/10_2026/22sk_68645.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22sk_68645/10_2026/22sk_68645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22sk_68645/10_2026/22sk_68645.map" } resolution = 3.0 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= 0.005 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 15 5.16 5 C 5691 2.51 5 N 1614 2.21 5 O 1749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9069 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2210 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain breaks: 1 Chain: "B" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2210 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain breaks: 1 Chain: "C" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 708 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "D" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 708 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "E" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2210 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain breaks: 1 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 708 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 105 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain breaks: 1 Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 105 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain breaks: 1 Chain: "I" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 105 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain breaks: 1 Time building chain proxies: 2.04, per 1000 atoms: 0.22 Number of scatterers: 9069 At special positions: 0 Unit cell: (116.4, 116.4, 115.43, 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 15 16.00 O 1749 8.00 N 1614 7.00 C 5691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.73 Conformation dependent library (CDL) restraints added in 332.9 milliseconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 21 sheets defined 19.1% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.762A pdb=" N VAL A 116 " --> pdb=" O ASN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 265 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 329 through 337 removed outlier: 4.346A pdb=" N HIS A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.761A pdb=" N VAL B 116 " --> pdb=" O ASN B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 265 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 329 through 337 removed outlier: 4.344A pdb=" N HIS B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.787A pdb=" N VAL C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 420 " --> pdb=" O PRO C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 420' Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.786A pdb=" N VAL D 419 " --> pdb=" O GLY D 415 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE D 420 " --> pdb=" O PRO D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 420' Processing helix chain 'D' and resid 438 through 448 Processing helix chain 'E' and resid 30 through 38 Processing helix chain 'E' and resid 112 through 117 removed outlier: 3.761A pdb=" N VAL E 116 " --> pdb=" O ASN E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 265 Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 329 through 337 removed outlier: 4.346A pdb=" N HIS E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 401 Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.787A pdb=" N VAL F 419 " --> pdb=" O GLY F 415 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE F 420 " --> pdb=" O PRO F 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 415 through 420' Processing helix chain 'F' and resid 438 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 48 removed outlier: 3.584A pdb=" N GLY A 100 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 44 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR A 108 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 138 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS A 149 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU A 136 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE A 122 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A 121 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 47 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 371 through 373 removed outlier: 7.076A pdb=" N PHE A 247 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE A 205 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS A 193 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN A 207 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 175 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 221 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.626A pdb=" N TRP A 271 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 278 removed outlier: 6.766A pdb=" N VAL A 275 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 278 removed outlier: 6.766A pdb=" N VAL A 275 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP A 347 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU A 320 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN A 345 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 48 removed outlier: 3.583A pdb=" N GLY B 100 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 44 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR B 108 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY B 138 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS B 149 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU B 136 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE B 122 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU B 121 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 47 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 171 through 176 removed outlier: 6.676A pdb=" N GLN B 207 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS B 193 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE B 205 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE B 247 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 221 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B 175 " --> pdb=" O PRO B 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.626A pdb=" N TRP B 271 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 274 through 278 removed outlier: 6.766A pdb=" N VAL B 275 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 274 through 278 removed outlier: 6.766A pdb=" N VAL B 275 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP B 347 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 320 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN B 345 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 381 through 383 removed outlier: 6.694A pdb=" N THR C 389 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 410 " --> pdb=" O THR C 389 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 391 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 381 through 383 removed outlier: 6.694A pdb=" N THR C 389 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 410 " --> pdb=" O THR C 389 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 391 " --> pdb=" O VAL C 408 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG C 458 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU C 431 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER C 456 " --> pdb=" O LEU C 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 381 through 383 removed outlier: 6.696A pdb=" N THR D 389 " --> pdb=" O LYS D 410 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS D 410 " --> pdb=" O THR D 389 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 391 " --> pdb=" O VAL D 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 381 through 383 removed outlier: 6.696A pdb=" N THR D 389 " --> pdb=" O LYS D 410 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS D 410 " --> pdb=" O THR D 389 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 391 " --> pdb=" O VAL D 408 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG D 458 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU D 431 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER D 456 " --> pdb=" O LEU D 431 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 41 through 48 removed outlier: 3.583A pdb=" N GLY E 100 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE E 44 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR E 108 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY E 138 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU E 136 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE E 122 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU E 121 " --> pdb=" O ARG E 47 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG E 47 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 171 through 176 removed outlier: 6.676A pdb=" N GLN E 207 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS E 193 " --> pdb=" O PHE E 205 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE E 205 " --> pdb=" O LYS E 193 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE E 247 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU E 221 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE E 175 " --> pdb=" O PRO E 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 270 through 271 removed outlier: 3.626A pdb=" N TRP E 271 " --> pdb=" O GLY E 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 274 through 278 removed outlier: 6.767A pdb=" N VAL E 275 " --> pdb=" O ALA E 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 274 through 278 removed outlier: 6.767A pdb=" N VAL E 275 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP E 347 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU E 320 " --> pdb=" O ASN E 345 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN E 345 " --> pdb=" O LEU E 320 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 381 through 383 removed outlier: 6.696A pdb=" N THR F 389 " --> pdb=" O LYS F 410 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 410 " --> pdb=" O THR F 389 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 391 " --> pdb=" O VAL F 408 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 381 through 383 removed outlier: 6.696A pdb=" N THR F 389 " --> pdb=" O LYS F 410 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 410 " --> pdb=" O THR F 389 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 391 " --> pdb=" O VAL F 408 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG F 458 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU F 431 " --> pdb=" O SER F 456 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER F 456 " --> pdb=" O LEU F 431 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 990 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: 1.33 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2961 1.33 - 1.45: 880 1.45 - 1.57: 5312 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 9183 Sorted by residual: bond pdb=" N ASN E 213 " pdb=" CA ASN E 213 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.85e+01 bond pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta sigma weight residual 1.452 1.491 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N ASN A 213 " pdb=" CA ASN A 213 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.11e-02 8.12e+03 1.06e+01 bond pdb=" N ILE E 212 " pdb=" CA ILE E 212 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.09e+00 bond pdb=" C LEU F 449 " pdb=" N PRO F 450 " ideal model delta sigma weight residual 1.326 1.369 -0.043 1.44e-02 4.82e+03 8.81e+00 ... (remaining 9178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 11879 1.77 - 3.54: 443 3.54 - 5.31: 78 5.31 - 7.09: 18 7.09 - 8.86: 2 Bond angle restraints: 12420 Sorted by residual: angle pdb=" C SER E 177 " pdb=" N PRO E 178 " pdb=" CA PRO E 178 " ideal model delta sigma weight residual 120.31 115.65 4.66 9.80e-01 1.04e+00 2.26e+01 angle pdb=" O SER B 177 " pdb=" C SER B 177 " pdb=" N PRO B 178 " ideal model delta sigma weight residual 121.37 117.50 3.87 9.00e-01 1.23e+00 1.85e+01 angle pdb=" CA LEU C 449 " pdb=" C LEU C 449 " pdb=" N PRO C 450 " ideal model delta sigma weight residual 118.23 122.12 -3.89 9.20e-01 1.18e+00 1.78e+01 angle pdb=" CA LEU F 449 " pdb=" C LEU F 449 " pdb=" N PRO F 450 " ideal model delta sigma weight residual 118.23 122.08 -3.85 9.20e-01 1.18e+00 1.75e+01 angle pdb=" CA LEU D 449 " pdb=" C LEU D 449 " pdb=" N PRO D 450 " ideal model delta sigma weight residual 118.23 122.06 -3.83 9.20e-01 1.18e+00 1.73e+01 ... (remaining 12415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.88: 4868 11.88 - 23.76: 543 23.76 - 35.65: 149 35.65 - 47.53: 41 47.53 - 59.41: 6 Dihedral angle restraints: 5607 sinusoidal: 2184 harmonic: 3423 Sorted by residual: dihedral pdb=" CA PHE A 181 " pdb=" C PHE A 181 " pdb=" N ASP A 182 " pdb=" CA ASP A 182 " ideal model delta harmonic sigma weight residual 180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA PHE B 181 " pdb=" C PHE B 181 " pdb=" N ASP B 182 " pdb=" CA ASP B 182 " ideal model delta harmonic sigma weight residual 180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA PRO B 28 " pdb=" C PRO B 28 " pdb=" N ASP B 29 " pdb=" CA ASP B 29 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 5604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1016 0.046 - 0.092: 289 0.092 - 0.138: 132 0.138 - 0.184: 34 0.184 - 0.229: 5 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA ILE A 212 " pdb=" N ILE A 212 " pdb=" C ILE A 212 " pdb=" CB ILE A 212 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LEU H 387 " pdb=" N LEU H 387 " pdb=" C LEU H 387 " pdb=" CB LEU H 387 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LEU G 387 " pdb=" N LEU G 387 " pdb=" C LEU G 387 " pdb=" CB LEU G 387 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.86e-01 ... (remaining 1473 not shown) Planarity restraints: 1629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 177 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C SER B 177 " 0.033 2.00e-02 2.50e+03 pdb=" O SER B 177 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO B 178 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 237 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C THR E 237 " -0.032 2.00e-02 2.50e+03 pdb=" O THR E 237 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG E 238 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 237 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C THR A 237 " -0.031 2.00e-02 2.50e+03 pdb=" O THR A 237 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 238 " 0.010 2.00e-02 2.50e+03 ... (remaining 1626 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1116 2.75 - 3.28: 8608 3.28 - 3.82: 13858 3.82 - 4.36: 16487 4.36 - 4.90: 29088 Nonbonded interactions: 69157 Sorted by model distance: nonbonded pdb=" O GLN F 397 " pdb=" OG SER F 400 " model vdw 2.208 3.040 nonbonded pdb=" O GLN D 397 " pdb=" OG SER D 400 " model vdw 2.208 3.040 nonbonded pdb=" O GLN C 397 " pdb=" OG SER C 400 " model vdw 2.209 3.040 nonbonded pdb=" O ASP B 282 " pdb=" OG SER B 286 " model vdw 2.221 3.040 nonbonded pdb=" O ASP A 282 " pdb=" OG SER A 286 " model vdw 2.222 3.040 ... (remaining 69152 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.090 Find NCS groups from input model: 0.160 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:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.007 0.043 9183 Z= 0.344 Angle : 0.809 8.857 12420 Z= 0.491 Chirality : 0.054 0.229 1476 Planarity : 0.004 0.032 1629 Dihedral : 11.406 59.409 3399 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.26 (0.24), residues: 1194 helix: -0.26 (0.39), residues: 192 sheet: -0.37 (0.28), residues: 336 loop : -1.25 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 461 TYR 0.002 0.001 TYR E 108 PHE 0.025 0.003 PHE E 181 TRP 0.019 0.003 TRP A 271 HIS 0.005 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.34 ( 9183) covalent geometry : angle 0.80865 / 0.49 (12420) hydrogen bonds : bond 0.24231 / 16.71 ( 355) hydrogen bonds : angle 8.52827 / 5.83 ( 990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.358 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: A 349 ILE cc_start: 0.8766 (mm) cc_final: 0.8508 (tp) REVERT: B 48 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6765 (tp40) REVERT: B 123 LEU cc_start: 0.8985 (mm) cc_final: 0.8692 (mt) REVERT: B 275 VAL cc_start: 0.8522 (t) cc_final: 0.8246 (p) REVERT: C 449 LEU cc_start: 0.8616 (mt) cc_final: 0.8411 (tm) REVERT: D 457 MET cc_start: 0.7906 (mtm) cc_final: 0.7513 (mtm) REVERT: E 144 ASP cc_start: 0.8116 (t70) cc_final: 0.7515 (t0) REVERT: E 200 GLU cc_start: 0.8425 (mp0) cc_final: 0.7612 (mp0) REVERT: E 278 GLU cc_start: 0.7581 (tp30) cc_final: 0.6537 (tp30) REVERT: F 430 HIS cc_start: 0.8923 (m90) cc_final: 0.8331 (m90) REVERT: F 440 LYS cc_start: 0.8844 (mppt) cc_final: 0.8592 (mmtm) REVERT: F 457 MET cc_start: 0.7875 (mtm) cc_final: 0.7589 (ptp) REVERT: F 468 ILE cc_start: 0.8457 (pt) cc_final: 0.7835 (pp) REVERT: H 373 ILE cc_start: 0.8794 (mm) cc_final: 0.8552 (tt) outliers start: 0 outliers final: 2 residues processed: 266 average time/residue: 0.5490 time to fit residues: 155.6180 Evaluate side-chains 169 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain E residue 349 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 100] chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 462 GLN F 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.075892 restraints weight = 16357.989| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.16 r_work: 0.2808 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9183 Z= 0.156 Angle : 0.706 9.357 12420 Z= 0.366 Chirality : 0.050 0.182 1476 Planarity : 0.005 0.043 1629 Dihedral : 4.657 30.117 1273 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.46 % Allowed : 13.82 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.83 (0.24), residues: 1194 helix: 0.11 (0.39), residues: 195 sheet: 0.09 (0.27), residues: 345 loop : -1.11 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 47 TYR 0.003 0.000 TYR B 202 PHE 0.018 0.002 PHE E 181 TRP 0.018 0.002 TRP B 271 HIS 0.003 0.001 HIS H 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 9183) covalent geometry : angle 0.70583 / 0.37 (12420) hydrogen bonds : bond 0.04806 / 3.34 ( 355) hydrogen bonds : angle 5.95118 / 4.06 ( 990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.244 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: A 47 ARG cc_start: 0.8718 (ptm160) cc_final: 0.8460 (ptm160) REVERT: A 122 ILE cc_start: 0.9017 (mm) cc_final: 0.8750 (mm) REVERT: A 349 ILE cc_start: 0.8263 (mm) cc_final: 0.7854 (tp) REVERT: A 350 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7545 (ttm-80) REVERT: B 48 GLN cc_start: 0.7182 (tm-30) cc_final: 0.6336 (tp40) REVERT: B 118 ASP cc_start: 0.8000 (t0) cc_final: 0.7571 (t0) REVERT: B 125 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7642 (ttm110) REVERT: C 401 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9146 (tm) REVERT: D 432 ASP cc_start: 0.9064 (m-30) cc_final: 0.8205 (t0) REVERT: D 457 MET cc_start: 0.8384 (mtm) cc_final: 0.8006 (mtm) REVERT: E 112 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.8825 (t0) REVERT: E 121 GLU cc_start: 0.8269 (pm20) cc_final: 0.8063 (pm20) REVERT: E 144 ASP cc_start: 0.8150 (t70) cc_final: 0.6919 (t0) REVERT: E 266 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8836 (pptt) REVERT: E 296 LEU cc_start: 0.8523 (tp) cc_final: 0.8216 (tm) REVERT: E 347 ASP cc_start: 0.7821 (m-30) cc_final: 0.7619 (m-30) REVERT: F 381 ARG cc_start: 0.6789 (mmm160) cc_final: 0.6336 (mmm-85) REVERT: F 423 ARG cc_start: 0.8429 (pmt170) cc_final: 0.8093 (pmm150) REVERT: F 433 ASN cc_start: 0.8992 (p0) cc_final: 0.8767 (p0) REVERT: F 434 LYS cc_start: 0.8979 (mmtm) cc_final: 0.8770 (mtpt) REVERT: F 440 LYS cc_start: 0.8994 (mppt) cc_final: 0.8658 (mmtm) REVERT: F 457 MET cc_start: 0.8841 (mtm) cc_final: 0.8107 (ptt) REVERT: F 468 ILE cc_start: 0.8156 (pt) cc_final: 0.7460 (pp) REVERT: G 372 LEU cc_start: 0.9163 (mp) cc_final: 0.8754 (mp) REVERT: I 374 LEU cc_start: 0.8322 (mp) cc_final: 0.8025 (mm) outliers start: 34 outliers final: 13 residues processed: 195 average time/residue: 0.5412 time to fit residues: 112.5592 Evaluate side-chains 180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 456 SER Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain I residue 377 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [22, 74, 85, 26, 50, 60, 91, 71, 2, 34, 80] chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS C 462 GLN D 462 GLN F 452 ASN F 462 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.121613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.073555 restraints weight = 16241.599| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 4.05 r_work: 0.2770 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9183 Z= 0.170 Angle : 0.674 9.068 12420 Z= 0.354 Chirality : 0.050 0.199 1476 Planarity : 0.005 0.046 1629 Dihedral : 4.382 20.363 1269 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.96 % Allowed : 18.19 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.72 (0.24), residues: 1194 helix: 0.20 (0.39), residues: 195 sheet: 0.08 (0.27), residues: 354 loop : -0.99 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 47 TYR 0.005 0.001 TYR B 202 PHE 0.017 0.002 PHE F 442 TRP 0.017 0.002 TRP B 271 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 9183) covalent geometry : angle 0.67408 / 0.35 (12420) hydrogen bonds : bond 0.04516 / 3.14 ( 355) hydrogen bonds : angle 5.53300 / 3.76 ( 990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8768 (ptm160) cc_final: 0.8390 (ptm160) REVERT: A 121 GLU cc_start: 0.8564 (pm20) cc_final: 0.8237 (pm20) REVERT: A 122 ILE cc_start: 0.9066 (mm) cc_final: 0.8798 (mm) REVERT: A 330 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7683 (t0) REVERT: A 334 LEU cc_start: 0.9333 (mm) cc_final: 0.8732 (mt) REVERT: A 338 MET cc_start: 0.8496 (ptp) cc_final: 0.8202 (ptp) REVERT: A 344 ILE cc_start: 0.9341 (pt) cc_final: 0.9083 (pp) REVERT: A 349 ILE cc_start: 0.8241 (mm) cc_final: 0.7918 (tp) REVERT: A 350 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7765 (ttm-80) REVERT: B 35 GLU cc_start: 0.8687 (pp20) cc_final: 0.8461 (pp20) REVERT: B 48 GLN cc_start: 0.7257 (tm-30) cc_final: 0.6428 (tp40) REVERT: B 118 ASP cc_start: 0.8077 (t0) cc_final: 0.7691 (t0) REVERT: B 125 ARG cc_start: 0.8193 (ttp-110) cc_final: 0.7736 (ttm110) REVERT: B 238 ARG cc_start: 0.8488 (ttm170) cc_final: 0.8212 (ttm170) REVERT: C 401 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9094 (tm) REVERT: C 434 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8496 (mmtm) REVERT: D 403 ILE cc_start: 0.8856 (mm) cc_final: 0.8653 (pp) REVERT: D 423 ARG cc_start: 0.8657 (pmm-80) cc_final: 0.8053 (pmm-80) REVERT: D 432 ASP cc_start: 0.9142 (m-30) cc_final: 0.8406 (t0) REVERT: D 457 MET cc_start: 0.8369 (mtm) cc_final: 0.8157 (mtm) REVERT: E 112 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.9023 (t0) REVERT: E 121 GLU cc_start: 0.8388 (pm20) cc_final: 0.8092 (pm20) REVERT: E 129 ARG cc_start: 0.8586 (mmm160) cc_final: 0.8186 (mmm-85) REVERT: E 144 ASP cc_start: 0.8268 (t70) cc_final: 0.6981 (t0) REVERT: E 266 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8828 (pptt) REVERT: E 296 LEU cc_start: 0.8645 (tp) cc_final: 0.8342 (tm) REVERT: F 381 ARG cc_start: 0.6795 (mmm160) cc_final: 0.6244 (mmm-85) REVERT: F 440 LYS cc_start: 0.9082 (mppt) cc_final: 0.8762 (mmtm) REVERT: F 457 MET cc_start: 0.8814 (mtm) cc_final: 0.8193 (ptp) REVERT: F 458 ARG cc_start: 0.8244 (ttt90) cc_final: 0.7805 (tpt-90) REVERT: F 468 ILE cc_start: 0.8168 (pt) cc_final: 0.7350 (pp) REVERT: F 470 PHE cc_start: 0.8125 (p90) cc_final: 0.7826 (p90) REVERT: G 372 LEU cc_start: 0.9141 (mp) cc_final: 0.8809 (mp) REVERT: I 374 LEU cc_start: 0.8509 (mp) cc_final: 0.8267 (mm) outliers start: 39 outliers final: 22 residues processed: 193 average time/residue: 0.5183 time to fit residues: 107.0740 Evaluate side-chains 193 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 456 SER Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain G residue 385 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [95, 22, 68, 93, 77, 82, 7, 96, 45, 53, 44] chunk 95 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 462 GLN E 112 ASN F 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.124476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076335 restraints weight = 16191.583| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.13 r_work: 0.2858 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9183 Z= 0.143 Angle : 0.680 10.315 12420 Z= 0.351 Chirality : 0.049 0.254 1476 Planarity : 0.004 0.049 1629 Dihedral : 4.257 19.115 1269 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.76 % Allowed : 20.02 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.62 (0.24), residues: 1194 helix: 0.06 (0.36), residues: 216 sheet: 0.19 (0.27), residues: 354 loop : -0.90 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 47 TYR 0.002 0.000 TYR B 202 PHE 0.011 0.001 PHE E 181 TRP 0.013 0.002 TRP B 271 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9183) covalent geometry : angle 0.67974 / 0.35 (12420) hydrogen bonds : bond 0.03919 / 2.74 ( 355) hydrogen bonds : angle 5.30350 / 3.59 ( 990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8759 (ptm160) cc_final: 0.8361 (ptm160) REVERT: A 121 GLU cc_start: 0.8486 (pm20) cc_final: 0.8123 (pm20) REVERT: A 122 ILE cc_start: 0.9063 (mm) cc_final: 0.8799 (mm) REVERT: A 334 LEU cc_start: 0.9330 (mm) cc_final: 0.9067 (mm) REVERT: A 344 ILE cc_start: 0.9362 (pt) cc_final: 0.9132 (pp) REVERT: A 349 ILE cc_start: 0.8231 (mm) cc_final: 0.7920 (tp) REVERT: A 350 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7727 (ttm-80) REVERT: B 118 ASP cc_start: 0.8173 (t0) cc_final: 0.7635 (t0) REVERT: B 122 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8934 (mm) REVERT: B 125 ARG cc_start: 0.8124 (ttp-110) cc_final: 0.7712 (ttm110) REVERT: B 238 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8342 (ttm170) REVERT: B 343 LYS cc_start: 0.9363 (mtpp) cc_final: 0.9161 (mppt) REVERT: C 401 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9151 (tm) REVERT: D 401 LEU cc_start: 0.9265 (tm) cc_final: 0.8934 (mm) REVERT: D 423 ARG cc_start: 0.8691 (pmm-80) cc_final: 0.8147 (pmm-80) REVERT: D 432 ASP cc_start: 0.9155 (m-30) cc_final: 0.8639 (t0) REVERT: E 121 GLU cc_start: 0.8433 (pm20) cc_final: 0.8065 (pm20) REVERT: E 129 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8229 (mmm-85) REVERT: E 144 ASP cc_start: 0.8207 (t70) cc_final: 0.7540 (t0) REVERT: E 266 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8782 (pptt) REVERT: E 296 LEU cc_start: 0.8671 (tp) cc_final: 0.8400 (tm) REVERT: E 347 ASP cc_start: 0.7717 (m-30) cc_final: 0.7366 (m-30) REVERT: F 381 ARG cc_start: 0.6615 (mmm160) cc_final: 0.5962 (mmm-85) REVERT: F 382 SER cc_start: 0.8466 (t) cc_final: 0.8131 (t) REVERT: F 434 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8593 (ptpt) REVERT: F 440 LYS cc_start: 0.9070 (mppt) cc_final: 0.8747 (mmtm) REVERT: F 457 MET cc_start: 0.8739 (mtm) cc_final: 0.8001 (ptp) REVERT: F 458 ARG cc_start: 0.8155 (ttt90) cc_final: 0.7860 (tpt-90) REVERT: F 468 ILE cc_start: 0.8070 (pt) cc_final: 0.7166 (pp) REVERT: F 470 PHE cc_start: 0.8084 (p90) cc_final: 0.7608 (p90) REVERT: G 372 LEU cc_start: 0.9074 (mp) cc_final: 0.8734 (mp) REVERT: H 372 LEU cc_start: 0.9011 (mt) cc_final: 0.8764 (mm) REVERT: I 374 LEU cc_start: 0.8492 (mp) cc_final: 0.8254 (mm) outliers start: 37 outliers final: 20 residues processed: 191 average time/residue: 0.5287 time to fit residues: 107.9728 Evaluate side-chains 185 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 454 SER Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 456 SER Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain G residue 385 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [49, 103, 9, 27, 34, 109, 80, 79, 26, 51, 99] chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 462 GLN F 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.124144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.078074 restraints weight = 15875.144| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.98 r_work: 0.2875 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9183 Z= 0.151 Angle : 0.679 10.096 12420 Z= 0.350 Chirality : 0.049 0.237 1476 Planarity : 0.004 0.061 1629 Dihedral : 4.235 19.726 1269 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.37 % Allowed : 21.14 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1194 helix: 0.02 (0.36), residues: 216 sheet: 0.25 (0.27), residues: 354 loop : -0.79 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 47 TYR 0.003 0.001 TYR B 202 PHE 0.020 0.002 PHE F 442 TRP 0.012 0.002 TRP A 271 HIS 0.002 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 9183) covalent geometry : angle 0.67934 / 0.35 (12420) hydrogen bonds : bond 0.03876 / 2.71 ( 355) hydrogen bonds : angle 5.18880 / 3.51 ( 990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8726 (ptm160) cc_final: 0.8330 (ptm160) REVERT: A 121 GLU cc_start: 0.8405 (pm20) cc_final: 0.8010 (pm20) REVERT: A 122 ILE cc_start: 0.8958 (mm) cc_final: 0.8690 (mm) REVERT: A 291 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8434 (mmmt) REVERT: A 323 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 334 LEU cc_start: 0.9292 (mm) cc_final: 0.9014 (mm) REVERT: A 344 ILE cc_start: 0.9407 (pt) cc_final: 0.9194 (pp) REVERT: A 350 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7635 (ttm-80) REVERT: B 118 ASP cc_start: 0.8197 (t0) cc_final: 0.7586 (t0) REVERT: B 122 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8833 (mm) REVERT: B 125 ARG cc_start: 0.8059 (ttp-110) cc_final: 0.7673 (mtp85) REVERT: B 238 ARG cc_start: 0.8672 (ttm170) cc_final: 0.8470 (ttm170) REVERT: B 343 LYS cc_start: 0.9383 (mtpp) cc_final: 0.9113 (mppt) REVERT: C 401 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9135 (tm) REVERT: D 432 ASP cc_start: 0.9130 (m-30) cc_final: 0.8634 (t0) REVERT: E 121 GLU cc_start: 0.8438 (pm20) cc_final: 0.8076 (pm20) REVERT: E 129 ARG cc_start: 0.8569 (mmm160) cc_final: 0.8235 (mmm-85) REVERT: E 144 ASP cc_start: 0.8062 (t70) cc_final: 0.7401 (t0) REVERT: E 238 ARG cc_start: 0.9011 (ttm170) cc_final: 0.8805 (ttm170) REVERT: E 266 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8769 (pptt) REVERT: E 296 LEU cc_start: 0.8577 (tp) cc_final: 0.8292 (tm) REVERT: E 347 ASP cc_start: 0.7663 (m-30) cc_final: 0.7276 (m-30) REVERT: F 381 ARG cc_start: 0.6357 (mmm160) cc_final: 0.5929 (mmm160) REVERT: F 382 SER cc_start: 0.8456 (t) cc_final: 0.8242 (t) REVERT: F 423 ARG cc_start: 0.8494 (pmt170) cc_final: 0.8216 (pmm150) REVERT: F 434 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8537 (ptpt) REVERT: F 440 LYS cc_start: 0.9015 (mppt) cc_final: 0.8738 (mmtm) REVERT: F 457 MET cc_start: 0.8684 (mtm) cc_final: 0.8002 (ptp) REVERT: F 468 ILE cc_start: 0.7913 (pt) cc_final: 0.7020 (pp) REVERT: F 470 PHE cc_start: 0.8089 (p90) cc_final: 0.7627 (p90) REVERT: H 372 LEU cc_start: 0.9077 (mt) cc_final: 0.8858 (mm) REVERT: I 374 LEU cc_start: 0.8403 (mp) cc_final: 0.8134 (mm) outliers start: 43 outliers final: 22 residues processed: 194 average time/residue: 0.5261 time to fit residues: 109.0942 Evaluate side-chains 188 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 456 SER Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain G residue 385 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [10, 45, 23, 70, 15, 5, 89, 116, 64, 92, 72] chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 ASN ** I 371 HIS ** 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 = 0.3667 r_free = 0.3667 target = 0.120303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.071765 restraints weight = 16258.633| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.09 r_work: 0.2823 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9183 Z= 0.147 Angle : 0.697 9.999 12420 Z= 0.356 Chirality : 0.049 0.232 1476 Planarity : 0.005 0.065 1629 Dihedral : 4.204 19.255 1269 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.96 % Allowed : 22.87 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.43 (0.24), residues: 1194 helix: -0.07 (0.35), residues: 216 sheet: 0.39 (0.27), residues: 348 loop : -0.71 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 47 TYR 0.003 0.000 TYR B 202 PHE 0.021 0.001 PHE D 442 TRP 0.012 0.002 TRP A 271 HIS 0.008 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9183) covalent geometry : angle 0.69654 / 0.36 (12420) hydrogen bonds : bond 0.03733 / 2.62 ( 355) hydrogen bonds : angle 5.10742 / 3.45 ( 990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8784 (ptm160) cc_final: 0.8447 (ptm160) REVERT: A 121 GLU cc_start: 0.8536 (pm20) cc_final: 0.8185 (pm20) REVERT: A 122 ILE cc_start: 0.9140 (mm) cc_final: 0.8876 (mm) REVERT: A 323 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8226 (tm-30) REVERT: A 326 ASN cc_start: 0.9328 (m-40) cc_final: 0.8808 (m-40) REVERT: A 327 GLU cc_start: 0.8882 (mp0) cc_final: 0.8405 (mm-30) REVERT: A 334 LEU cc_start: 0.9367 (mm) cc_final: 0.9064 (mm) REVERT: A 344 ILE cc_start: 0.9450 (pt) cc_final: 0.9198 (pp) REVERT: A 349 ILE cc_start: 0.8328 (mm) cc_final: 0.7980 (tp) REVERT: A 350 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7691 (ttm-80) REVERT: B 35 GLU cc_start: 0.8939 (pt0) cc_final: 0.8738 (pp20) REVERT: B 47 ARG cc_start: 0.8699 (ttm110) cc_final: 0.8248 (mtp-110) REVERT: B 118 ASP cc_start: 0.8239 (t0) cc_final: 0.7699 (t0) REVERT: B 125 ARG cc_start: 0.8299 (ttp-110) cc_final: 0.7934 (mtp85) REVERT: B 238 ARG cc_start: 0.8770 (ttm170) cc_final: 0.8480 (ttm170) REVERT: B 343 LYS cc_start: 0.9331 (mtpp) cc_final: 0.9115 (mppt) REVERT: C 401 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9120 (tm) REVERT: D 432 ASP cc_start: 0.9128 (m-30) cc_final: 0.8522 (t0) REVERT: D 434 LYS cc_start: 0.8930 (tptp) cc_final: 0.8596 (tptp) REVERT: E 47 ARG cc_start: 0.8619 (ttp-110) cc_final: 0.8350 (mtm110) REVERT: E 121 GLU cc_start: 0.8622 (pm20) cc_final: 0.8280 (pm20) REVERT: E 129 ARG cc_start: 0.8634 (mmm160) cc_final: 0.8337 (mmm-85) REVERT: E 144 ASP cc_start: 0.8314 (t70) cc_final: 0.7630 (t0) REVERT: E 266 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8864 (pptt) REVERT: E 296 LEU cc_start: 0.8787 (tp) cc_final: 0.8486 (tm) REVERT: E 347 ASP cc_start: 0.7843 (m-30) cc_final: 0.7523 (m-30) REVERT: F 434 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8656 (ptpt) REVERT: F 440 LYS cc_start: 0.9019 (mppt) cc_final: 0.8793 (mmtm) REVERT: F 457 MET cc_start: 0.8657 (mtm) cc_final: 0.8085 (ptp) REVERT: F 468 ILE cc_start: 0.8117 (pt) cc_final: 0.7358 (pp) REVERT: F 470 PHE cc_start: 0.8077 (p90) cc_final: 0.7741 (p90) REVERT: H 372 LEU cc_start: 0.9231 (mt) cc_final: 0.9016 (mm) outliers start: 39 outliers final: 24 residues processed: 189 average time/residue: 0.5071 time to fit residues: 102.6000 Evaluate side-chains 178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 442 PHE Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 454 SER Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 456 SER Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain G residue 385 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [28, 39, 72, 47, 62, 16, 6, 9, 74, 18, 104] chunk 28 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 0.0670 chunk 47 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 74 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 462 GLN F 452 ASN ** I 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.121688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.073362 restraints weight = 16201.794| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.17 r_work: 0.2863 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9183 Z= 0.135 Angle : 0.694 10.014 12420 Z= 0.354 Chirality : 0.049 0.223 1476 Planarity : 0.004 0.053 1629 Dihedral : 4.098 19.822 1269 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.46 % Allowed : 23.48 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.38 (0.24), residues: 1194 helix: -0.06 (0.36), residues: 216 sheet: 0.70 (0.28), residues: 321 loop : -0.79 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 47 TYR 0.002 0.000 TYR A 108 PHE 0.021 0.001 PHE F 442 TRP 0.011 0.001 TRP A 271 HIS 0.005 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 9183) covalent geometry : angle 0.69404 / 0.35 (12420) hydrogen bonds : bond 0.03553 / 2.48 ( 355) hydrogen bonds : angle 5.03090 / 3.39 ( 990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8771 (ptm160) cc_final: 0.8461 (ptm160) REVERT: A 121 GLU cc_start: 0.8494 (pm20) cc_final: 0.8163 (pm20) REVERT: A 122 ILE cc_start: 0.9104 (mm) cc_final: 0.8845 (mm) REVERT: A 323 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8173 (tm-30) REVERT: A 326 ASN cc_start: 0.9268 (m-40) cc_final: 0.9003 (m-40) REVERT: A 327 GLU cc_start: 0.8867 (mp0) cc_final: 0.8464 (mm-30) REVERT: A 334 LEU cc_start: 0.9350 (mm) cc_final: 0.9047 (mm) REVERT: A 344 ILE cc_start: 0.9443 (pt) cc_final: 0.9190 (pp) REVERT: A 349 ILE cc_start: 0.8240 (mm) cc_final: 0.7888 (tp) REVERT: B 118 ASP cc_start: 0.8186 (t0) cc_final: 0.7643 (t0) REVERT: B 238 ARG cc_start: 0.8743 (ttm170) cc_final: 0.8460 (ttm170) REVERT: B 347 ASP cc_start: 0.7783 (t0) cc_final: 0.7099 (t0) REVERT: B 354 ARG cc_start: 0.8625 (mpp80) cc_final: 0.8029 (mmm-85) REVERT: C 401 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9127 (tm) REVERT: D 385 ARG cc_start: 0.7655 (mmm160) cc_final: 0.7417 (mtp180) REVERT: D 434 LYS cc_start: 0.8909 (tptp) cc_final: 0.8603 (tptp) REVERT: E 121 GLU cc_start: 0.8637 (pm20) cc_final: 0.8233 (pm20) REVERT: E 129 ARG cc_start: 0.8617 (mmm160) cc_final: 0.8310 (mmm-85) REVERT: E 144 ASP cc_start: 0.8210 (t70) cc_final: 0.7551 (t0) REVERT: E 238 ARG cc_start: 0.9082 (ttm170) cc_final: 0.8627 (ttm110) REVERT: E 266 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8819 (pptt) REVERT: E 296 LEU cc_start: 0.8703 (tp) cc_final: 0.8389 (tm) REVERT: E 347 ASP cc_start: 0.7874 (m-30) cc_final: 0.7495 (m-30) REVERT: F 434 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8650 (ptpt) REVERT: F 440 LYS cc_start: 0.8991 (mppt) cc_final: 0.8768 (mmtm) REVERT: F 457 MET cc_start: 0.8667 (mtm) cc_final: 0.8107 (ptp) REVERT: F 468 ILE cc_start: 0.8057 (pt) cc_final: 0.7280 (pp) REVERT: F 470 PHE cc_start: 0.8032 (p90) cc_final: 0.7662 (p90) outliers start: 34 outliers final: 18 residues processed: 179 average time/residue: 0.5173 time to fit residues: 99.1541 Evaluate side-chains 173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 454 SER Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 456 SER Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain I residue 369 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [29, 86, 75, 4, 17, 9, 21, 39, 8, 20, 22] chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.122420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.075393 restraints weight = 16008.874| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.89 r_work: 0.2840 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9183 Z= 0.148 Angle : 0.719 10.795 12420 Z= 0.366 Chirality : 0.049 0.210 1476 Planarity : 0.004 0.053 1629 Dihedral : 4.113 20.043 1269 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.35 % Allowed : 24.29 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.34 (0.24), residues: 1194 helix: -0.06 (0.35), residues: 216 sheet: 0.76 (0.29), residues: 318 loop : -0.76 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 47 TYR 0.002 0.000 TYR B 202 PHE 0.019 0.001 PHE F 442 TRP 0.011 0.001 TRP A 271 HIS 0.005 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9183) covalent geometry : angle 0.71950 / 0.37 (12420) hydrogen bonds : bond 0.03641 / 2.54 ( 355) hydrogen bonds : angle 5.01194 / 3.37 ( 990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8827 (ptm160) cc_final: 0.8513 (ptm160) REVERT: A 121 GLU cc_start: 0.8527 (pm20) cc_final: 0.8185 (pm20) REVERT: A 122 ILE cc_start: 0.9110 (mm) cc_final: 0.8853 (mm) REVERT: A 323 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 326 ASN cc_start: 0.9301 (m-40) cc_final: 0.9063 (m-40) REVERT: A 327 GLU cc_start: 0.8844 (mp0) cc_final: 0.8367 (mm-30) REVERT: A 334 LEU cc_start: 0.9334 (mm) cc_final: 0.9004 (mm) REVERT: A 344 ILE cc_start: 0.9477 (pt) cc_final: 0.9200 (pp) REVERT: A 349 ILE cc_start: 0.8272 (mm) cc_final: 0.7929 (tp) REVERT: B 118 ASP cc_start: 0.8252 (t0) cc_final: 0.7772 (t0) REVERT: B 238 ARG cc_start: 0.8725 (ttm170) cc_final: 0.8463 (ttm170) REVERT: B 347 ASP cc_start: 0.7784 (t0) cc_final: 0.7053 (t0) REVERT: B 354 ARG cc_start: 0.8690 (mpp80) cc_final: 0.8047 (mmm-85) REVERT: C 382 SER cc_start: 0.8169 (p) cc_final: 0.7924 (t) REVERT: C 401 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9165 (tm) REVERT: D 423 ARG cc_start: 0.8564 (pmm-80) cc_final: 0.7838 (pmm-80) REVERT: D 432 ASP cc_start: 0.9196 (m-30) cc_final: 0.8531 (t0) REVERT: D 434 LYS cc_start: 0.8968 (tptp) cc_final: 0.8579 (tptp) REVERT: E 47 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8354 (mtm110) REVERT: E 121 GLU cc_start: 0.8651 (pm20) cc_final: 0.8280 (pm20) REVERT: E 129 ARG cc_start: 0.8641 (mmm160) cc_final: 0.8347 (mmm-85) REVERT: E 144 ASP cc_start: 0.8196 (t70) cc_final: 0.7558 (t0) REVERT: E 238 ARG cc_start: 0.9088 (ttm170) cc_final: 0.8875 (ttm170) REVERT: E 266 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8860 (pptt) REVERT: E 296 LEU cc_start: 0.8693 (tp) cc_final: 0.8374 (tm) REVERT: E 347 ASP cc_start: 0.7954 (m-30) cc_final: 0.6931 (p0) REVERT: F 423 ARG cc_start: 0.8525 (pmt170) cc_final: 0.8240 (pmm150) REVERT: F 434 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8635 (ptpt) REVERT: F 440 LYS cc_start: 0.9006 (mppt) cc_final: 0.8781 (mmtm) REVERT: F 457 MET cc_start: 0.8617 (mtm) cc_final: 0.8125 (ptt) REVERT: F 468 ILE cc_start: 0.8070 (pt) cc_final: 0.7115 (pp) REVERT: F 470 PHE cc_start: 0.8018 (p90) cc_final: 0.7637 (p90) outliers start: 33 outliers final: 23 residues processed: 177 average time/residue: 0.5122 time to fit residues: 97.2118 Evaluate side-chains 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 433 ASN Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 454 SER Chi-restraints excluded: chain F residue 456 SER Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain G residue 371 HIS Chi-restraints excluded: chain I residue 369 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [113, 93, 38, 46, 12, 47, 94, 9, 99, 77, 69] chunk 113 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 0.0010 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 9 optimal weight: 0.0270 chunk 99 optimal weight: 0.0670 chunk 77 optimal weight: 0.5980 chunk 69 optimal weight: 0.1980 overall best weight: 0.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.076794 restraints weight = 16170.476| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.13 r_work: 0.2920 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9183 Z= 0.127 Angle : 0.719 11.690 12420 Z= 0.359 Chirality : 0.048 0.202 1476 Planarity : 0.004 0.068 1629 Dihedral : 3.859 19.989 1269 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.93 % Allowed : 25.91 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.03 (0.24), residues: 1194 helix: 0.20 (0.36), residues: 219 sheet: 0.83 (0.28), residues: 333 loop : -0.44 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 47 TYR 0.001 0.000 TYR B 202 PHE 0.023 0.001 PHE F 442 TRP 0.011 0.001 TRP E 271 HIS 0.004 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9183) covalent geometry : angle 0.71890 / 0.36 (12420) hydrogen bonds : bond 0.03008 / 2.09 ( 355) hydrogen bonds : angle 4.80314 / 3.22 ( 990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8835 (ptm160) cc_final: 0.8483 (ptm160) REVERT: A 121 GLU cc_start: 0.8410 (pm20) cc_final: 0.8050 (pm20) REVERT: A 122 ILE cc_start: 0.9059 (mm) cc_final: 0.8794 (mm) REVERT: A 323 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 47 ARG cc_start: 0.8510 (ttm110) cc_final: 0.8102 (mtp-110) REVERT: B 118 ASP cc_start: 0.8325 (t0) cc_final: 0.7857 (t0) REVERT: B 238 ARG cc_start: 0.8728 (ttm170) cc_final: 0.8393 (ttm170) REVERT: B 347 ASP cc_start: 0.7762 (t0) cc_final: 0.7089 (t0) REVERT: B 354 ARG cc_start: 0.8632 (mpp80) cc_final: 0.8018 (mmm-85) REVERT: C 401 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9097 (tm) REVERT: C 461 ARG cc_start: 0.7835 (ptm-80) cc_final: 0.7578 (ptm-80) REVERT: D 432 ASP cc_start: 0.9153 (m-30) cc_final: 0.8457 (t0) REVERT: D 434 LYS cc_start: 0.8983 (tptp) cc_final: 0.8608 (tptp) REVERT: E 121 GLU cc_start: 0.8556 (pm20) cc_final: 0.8165 (pm20) REVERT: E 129 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8315 (mmm-85) REVERT: E 144 ASP cc_start: 0.7999 (t70) cc_final: 0.7529 (t0) REVERT: E 238 ARG cc_start: 0.9081 (ttm170) cc_final: 0.8631 (ttm110) REVERT: E 266 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8744 (ptmt) REVERT: E 296 LEU cc_start: 0.8668 (tp) cc_final: 0.8365 (tm) REVERT: E 347 ASP cc_start: 0.7893 (m-30) cc_final: 0.6845 (p0) REVERT: F 423 ARG cc_start: 0.8597 (pmt170) cc_final: 0.8199 (pmm150) REVERT: F 434 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8628 (ptpt) REVERT: F 440 LYS cc_start: 0.8939 (mppt) cc_final: 0.8738 (mmtm) REVERT: F 457 MET cc_start: 0.8613 (mtm) cc_final: 0.8017 (ptp) REVERT: F 468 ILE cc_start: 0.8042 (pt) cc_final: 0.7225 (pp) REVERT: F 470 PHE cc_start: 0.7962 (p90) cc_final: 0.7714 (p90) outliers start: 19 outliers final: 11 residues processed: 189 average time/residue: 0.4628 time to fit residues: 94.3093 Evaluate side-chains 175 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain I residue 369 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [7, 10, 75, 8, 42, 35, 40, 41, 91, 86, 70] chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 91 optimal weight: 0.0980 chunk 86 optimal weight: 0.5980 chunk 70 optimal weight: 0.0370 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 337 ASN ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.123531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075570 restraints weight = 15979.665| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.09 r_work: 0.2900 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9183 Z= 0.133 Angle : 0.738 12.511 12420 Z= 0.369 Chirality : 0.049 0.203 1476 Planarity : 0.005 0.079 1629 Dihedral : 3.884 18.253 1269 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.42 % Allowed : 27.24 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.04 (0.24), residues: 1194 helix: 0.22 (0.36), residues: 222 sheet: 1.07 (0.29), residues: 303 loop : -0.50 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 47 TYR 0.002 0.000 TYR A 108 PHE 0.018 0.001 PHE F 442 TRP 0.009 0.001 TRP A 271 HIS 0.005 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9183) covalent geometry : angle 0.73802 / 0.37 (12420) hydrogen bonds : bond 0.03176 / 2.21 ( 355) hydrogen bonds : angle 4.79294 / 3.19 ( 990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8845 (ptm160) cc_final: 0.8525 (ptm160) REVERT: A 121 GLU cc_start: 0.8477 (pm20) cc_final: 0.8148 (pm20) REVERT: A 122 ILE cc_start: 0.9077 (mm) cc_final: 0.8818 (mm) REVERT: A 323 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8134 (tm-30) REVERT: A 350 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7548 (ttm-80) REVERT: B 47 ARG cc_start: 0.8503 (ttm110) cc_final: 0.8043 (mtp-110) REVERT: B 118 ASP cc_start: 0.8358 (t0) cc_final: 0.7950 (t0) REVERT: B 238 ARG cc_start: 0.8719 (ttm170) cc_final: 0.8468 (ttm170) REVERT: B 347 ASP cc_start: 0.7770 (t0) cc_final: 0.7052 (t0) REVERT: B 354 ARG cc_start: 0.8667 (mpp80) cc_final: 0.8034 (mmm-85) REVERT: C 401 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9113 (tm) REVERT: D 434 LYS cc_start: 0.8980 (tptp) cc_final: 0.8647 (tptp) REVERT: D 460 LEU cc_start: 0.8364 (tt) cc_final: 0.8040 (tm) REVERT: E 47 ARG cc_start: 0.8616 (ttp-110) cc_final: 0.8359 (mtm110) REVERT: E 121 GLU cc_start: 0.8548 (pm20) cc_final: 0.8201 (pm20) REVERT: E 129 ARG cc_start: 0.8612 (mmm160) cc_final: 0.8316 (mmm-85) REVERT: E 266 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8758 (ptmt) REVERT: E 296 LEU cc_start: 0.8661 (tp) cc_final: 0.8337 (tm) REVERT: E 347 ASP cc_start: 0.7902 (m-30) cc_final: 0.6870 (p0) REVERT: F 423 ARG cc_start: 0.8621 (pmt170) cc_final: 0.8282 (pmm150) REVERT: F 434 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8626 (ptpt) REVERT: F 457 MET cc_start: 0.8595 (mtm) cc_final: 0.8029 (ptp) REVERT: F 468 ILE cc_start: 0.8032 (pt) cc_final: 0.7182 (pp) REVERT: F 470 PHE cc_start: 0.7994 (p90) cc_final: 0.7655 (p90) outliers start: 14 outliers final: 12 residues processed: 177 average time/residue: 0.4918 time to fit residues: 93.3487 Evaluate side-chains 176 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 266 LYS Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain I residue 369 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: [112, 14, 84, 89, 39, 10, 29, 81, 59, 26, 65] chunk 112 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 0.0670 chunk 89 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.0060 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 0.2312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.076596 restraints weight = 15938.041| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 4.10 r_work: 0.2922 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9183 Z= 0.130 Angle : 0.736 12.598 12420 Z= 0.368 Chirality : 0.049 0.206 1476 Planarity : 0.005 0.076 1629 Dihedral : 3.836 17.361 1269 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.32 % Allowed : 27.74 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.05 (0.24), residues: 1194 helix: 0.08 (0.36), residues: 222 sheet: 1.10 (0.29), residues: 303 loop : -0.45 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 47 TYR 0.001 0.000 TYR E 108 PHE 0.011 0.001 PHE C 467 TRP 0.009 0.001 TRP A 271 HIS 0.004 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9183) covalent geometry : angle 0.73623 / 0.37 (12420) hydrogen bonds : bond 0.02945 / 2.05 ( 355) hydrogen bonds : angle 4.73885 / 3.17 ( 990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3636.43 seconds wall clock time: 62 minutes 34.73 seconds (3754.73 seconds total)