Starting phenix.real_space_refine (version: dev) on Mon Dec 12 02:29:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/12_2022/6pqy_20456.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/12_2022/6pqy_20456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/12_2022/6pqy_20456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/12_2022/6pqy_20456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/12_2022/6pqy_20456.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqy_20456/12_2022/6pqy_20456.pdb" } resolution = 4.2 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 ------------------------------------------------------------------------------- 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 500": "OD1" <-> "OD2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 159": "OD1" <-> "OD2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 276": "NH1" <-> "NH2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 319": "OD1" <-> "OD2" Residue "D ASP 320": "OD1" <-> "OD2" Residue "D PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 416": "OD1" <-> "OD2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D ARG 437": "NH1" <-> "NH2" Residue "D PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D ARG 445": "NH1" <-> "NH2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D ASP 481": "OD1" <-> "OD2" Residue "D PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 500": "OD1" <-> "OD2" Residue "D PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8690 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3689 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 442} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3689 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 442} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "F" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 323 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 5.40, per 1000 atoms: 0.62 Number of scatterers: 8690 At special positions: 0 Unit cell: (85.05, 122.85, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 64 15.00 O 1772 8.00 N 1496 7.00 C 5324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 1.2 seconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1764 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 52.6% alpha, 14.8% beta 28 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 removed outlier: 4.031A pdb=" N GLY A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.582A pdb=" N GLU A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.722A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 106 removed outlier: 4.271A pdb=" N ILE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 4.030A pdb=" N TYR A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 275 through 289 removed outlier: 3.697A pdb=" N VAL A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 removed outlier: 3.690A pdb=" N ASN A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.504A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 374 " --> pdb=" O GLN A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 398 Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.571A pdb=" N HIS A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.512A pdb=" N GLU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 448 Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.892A pdb=" N ASN A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.554A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 37 removed outlier: 4.031A pdb=" N GLY D 31 " --> pdb=" O GLU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.582A pdb=" N GLU D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.721A pdb=" N VAL D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 106 removed outlier: 4.270A pdb=" N ILE D 105 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.031A pdb=" N TYR D 174 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 275 through 289 removed outlier: 3.698A pdb=" N VAL D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 322 removed outlier: 3.690A pdb=" N ASN D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 347 through 355 Processing helix chain 'D' and resid 358 through 374 removed outlier: 3.505A pdb=" N ILE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER D 374 " --> pdb=" O GLN D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 398 Processing helix chain 'D' and resid 404 through 412 removed outlier: 3.572A pdb=" N HIS D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 removed outlier: 3.512A pdb=" N GLU D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 448 Processing helix chain 'D' and resid 454 through 470 removed outlier: 3.892A pdb=" N ASN D 458 " --> pdb=" O ARG D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 496 removed outlier: 3.554A pdb=" N LEU D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 125 " --> pdb=" O MET A 148 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 119 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU A 156 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 117 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N LEU A 116 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 11.586A pdb=" N LEU A 218 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N LEU A 118 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N MET A 220 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 11.195A pdb=" N SER A 120 " --> pdb=" O MET A 220 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N MET A 222 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP A 122 " --> pdb=" O MET A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR D 149 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE D 180 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE D 147 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.408A pdb=" N THR D 149 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE D 180 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE D 147 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 125 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE D 119 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU D 156 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE D 117 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N LEU D 116 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N LEU D 218 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N LEU D 118 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N MET D 220 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N SER D 120 " --> pdb=" O MET D 220 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N MET D 222 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP D 122 " --> pdb=" O MET D 222 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 4.31 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: 2151 1.33 - 1.45: 1973 1.45 - 1.57: 4688 1.57 - 1.69: 124 1.69 - 1.81: 52 Bond restraints: 8988 Sorted by residual: bond pdb=" O3' DC F 12 " pdb=" P DC F 13 " ideal model delta sigma weight residual 1.607 1.647 -0.040 1.50e-02 4.44e+03 7.16e+00 bond pdb=" O3' DC C 12 " pdb=" P DC C 13 " ideal model delta sigma weight residual 1.607 1.644 -0.037 1.50e-02 4.44e+03 6.15e+00 bond pdb=" C1' DT B 22 " pdb=" N1 DT B 22 " ideal model delta sigma weight residual 1.490 1.441 0.049 3.00e-02 1.11e+03 2.67e+00 bond pdb=" C1' DT E 22 " pdb=" N1 DT E 22 " ideal model delta sigma weight residual 1.490 1.441 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CB TRP D 41 " pdb=" CG TRP D 41 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.47e+00 ... (remaining 8983 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.96: 488 105.96 - 112.97: 4873 112.97 - 119.98: 3182 119.98 - 126.99: 3642 126.99 - 134.00: 215 Bond angle restraints: 12400 Sorted by residual: angle pdb=" C4' DC F 12 " pdb=" C3' DC F 12 " pdb=" O3' DC F 12 " ideal model delta sigma weight residual 110.00 121.29 -11.29 1.50e+00 4.44e-01 5.66e+01 angle pdb=" C4' DC C 12 " pdb=" C3' DC C 12 " pdb=" O3' DC C 12 " ideal model delta sigma weight residual 110.00 120.69 -10.69 1.50e+00 4.44e-01 5.08e+01 angle pdb=" O3' DT C 15 " pdb=" C3' DT C 15 " pdb=" C2' DT C 15 " ideal model delta sigma weight residual 111.50 120.80 -9.30 1.50e+00 4.44e-01 3.84e+01 angle pdb=" C3' DC F 12 " pdb=" C2' DC F 12 " pdb=" C1' DC F 12 " ideal model delta sigma weight residual 101.60 107.16 -5.56 1.50e+00 4.44e-01 1.37e+01 angle pdb=" C3' DC C 12 " pdb=" C2' DC C 12 " pdb=" C1' DC C 12 " ideal model delta sigma weight residual 101.60 106.93 -5.33 1.50e+00 4.44e-01 1.26e+01 ... (remaining 12395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 4898 35.87 - 71.75: 318 71.75 - 107.62: 10 107.62 - 143.49: 0 143.49 - 179.36: 10 Dihedral angle restraints: 5236 sinusoidal: 2524 harmonic: 2712 Sorted by residual: dihedral pdb=" CA ASP D 161 " pdb=" C ASP D 161 " pdb=" N THR D 162 " pdb=" CA THR D 162 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ASP A 161 " pdb=" C ASP A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA SER A 453 " pdb=" C SER A 453 " pdb=" N ARG A 454 " pdb=" CA ARG A 454 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 5233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1122 0.073 - 0.146: 238 0.146 - 0.219: 31 0.219 - 0.292: 6 0.292 - 0.364: 3 Chirality restraints: 1400 Sorted by residual: chirality pdb=" C3' DC F 12 " pdb=" C4' DC F 12 " pdb=" O3' DC F 12 " pdb=" C2' DC F 12 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C3' DC C 12 " pdb=" C4' DC C 12 " pdb=" O3' DC C 12 " pdb=" C2' DC C 12 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C3' DT C 15 " pdb=" C4' DT C 15 " pdb=" O3' DT C 15 " pdb=" C2' DT C 15 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 1397 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC C 12 " 0.041 2.00e-02 2.50e+03 2.75e-02 1.71e+01 pdb=" N1 DC C 12 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DC C 12 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC C 12 " -0.033 2.00e-02 2.50e+03 pdb=" N3 DC C 12 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC C 12 " 0.047 2.00e-02 2.50e+03 pdb=" N4 DC C 12 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DC C 12 " -0.025 2.00e-02 2.50e+03 pdb=" C6 DC C 12 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 15 " -0.051 2.00e-02 2.50e+03 2.26e-02 1.28e+01 pdb=" N1 DT C 15 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT C 15 " 0.018 2.00e-02 2.50e+03 pdb=" O2 DT C 15 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DT C 15 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DT C 15 " 0.000 2.00e-02 2.50e+03 pdb=" O4 DT C 15 " -0.026 2.00e-02 2.50e+03 pdb=" C5 DT C 15 " 0.013 2.00e-02 2.50e+03 pdb=" C7 DT C 15 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT C 15 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B 30 " 0.019 2.00e-02 2.50e+03 2.07e-02 1.18e+01 pdb=" N9 DA B 30 " -0.053 2.00e-02 2.50e+03 pdb=" C8 DA B 30 " 0.037 2.00e-02 2.50e+03 pdb=" N7 DA B 30 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA B 30 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA B 30 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA B 30 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA B 30 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DA B 30 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA B 30 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA B 30 " -0.006 2.00e-02 2.50e+03 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1501 2.76 - 3.30: 9795 3.30 - 3.83: 15952 3.83 - 4.37: 17791 4.37 - 4.90: 25995 Nonbonded interactions: 71034 Sorted by model distance: nonbonded pdb=" OG1 THR A 149 " pdb=" OE1 GLN A 179 " model vdw 2.225 2.440 nonbonded pdb=" OG1 THR D 149 " pdb=" OE1 GLN D 179 " model vdw 2.226 2.440 nonbonded pdb=" N ASP D 500 " pdb=" OD1 ASP D 500 " model vdw 2.239 2.520 nonbonded pdb=" N ASP A 500 " pdb=" OD1 ASP A 500 " model vdw 2.239 2.520 nonbonded pdb=" O VAL D 81 " pdb=" NE2 GLN D 455 " model vdw 2.244 2.520 ... (remaining 71029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 34 5.16 5 C 5324 2.51 5 N 1496 2.21 5 O 1772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 4.420 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 29.190 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 0.049 8988 Z= 0.448 Angle : 0.987 11.285 12400 Z= 0.578 Chirality : 0.064 0.364 1400 Planarity : 0.007 0.066 1348 Dihedral : 21.785 179.364 3472 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.83 % Favored : 92.51 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.22), residues: 908 helix: -2.68 (0.18), residues: 438 sheet: -3.07 (0.55), residues: 60 loop : -3.19 (0.26), residues: 410 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 147 average time/residue: 0.2454 time to fit residues: 47.4169 Evaluate side-chains 88 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0783 time to fit residues: 1.4799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 0.0870 chunk 24 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8988 Z= 0.182 Angle : 0.631 6.172 12400 Z= 0.347 Chirality : 0.040 0.151 1400 Planarity : 0.004 0.034 1348 Dihedral : 25.009 178.899 1624 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.26), residues: 908 helix: -0.65 (0.23), residues: 450 sheet: -2.01 (0.61), residues: 54 loop : -2.40 (0.29), residues: 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2382 time to fit residues: 47.5669 Evaluate side-chains 108 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 8988 Z= 0.218 Angle : 0.638 6.547 12400 Z= 0.353 Chirality : 0.041 0.242 1400 Planarity : 0.004 0.056 1348 Dihedral : 24.680 178.405 1624 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.27), residues: 908 helix: -0.15 (0.24), residues: 450 sheet: -1.38 (0.66), residues: 54 loop : -2.19 (0.29), residues: 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 135 average time/residue: 0.2317 time to fit residues: 42.3406 Evaluate side-chains 97 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 8988 Z= 0.302 Angle : 0.700 7.436 12400 Z= 0.388 Chirality : 0.042 0.157 1400 Planarity : 0.005 0.062 1348 Dihedral : 24.539 179.498 1624 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.27), residues: 908 helix: -0.34 (0.23), residues: 452 sheet: -1.28 (0.66), residues: 60 loop : -2.00 (0.30), residues: 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2212 time to fit residues: 38.1007 Evaluate side-chains 91 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 8988 Z= 0.315 Angle : 0.712 7.626 12400 Z= 0.391 Chirality : 0.042 0.150 1400 Planarity : 0.005 0.040 1348 Dihedral : 24.609 179.276 1624 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.26), residues: 908 helix: -0.36 (0.23), residues: 452 sheet: -1.43 (0.64), residues: 54 loop : -2.00 (0.30), residues: 402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2286 time to fit residues: 35.7856 Evaluate side-chains 89 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8988 Z= 0.176 Angle : 0.616 5.845 12400 Z= 0.341 Chirality : 0.040 0.138 1400 Planarity : 0.004 0.041 1348 Dihedral : 24.577 178.215 1624 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.27), residues: 908 helix: 0.17 (0.24), residues: 456 sheet: -0.88 (0.75), residues: 44 loop : -1.93 (0.30), residues: 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.2141 time to fit residues: 39.5487 Evaluate side-chains 95 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 chunk 36 optimal weight: 0.0670 chunk 55 optimal weight: 0.9980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8988 Z= 0.158 Angle : 0.605 9.214 12400 Z= 0.329 Chirality : 0.040 0.164 1400 Planarity : 0.003 0.039 1348 Dihedral : 24.432 175.777 1624 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.28), residues: 908 helix: 0.26 (0.24), residues: 456 sheet: 0.25 (0.68), residues: 60 loop : -1.80 (0.32), residues: 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2189 time to fit residues: 40.7485 Evaluate side-chains 100 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.0670 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8988 Z= 0.263 Angle : 0.688 10.717 12400 Z= 0.369 Chirality : 0.041 0.197 1400 Planarity : 0.004 0.039 1348 Dihedral : 24.438 177.423 1624 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.28), residues: 908 helix: 0.09 (0.24), residues: 456 sheet: -0.78 (0.76), residues: 44 loop : -1.79 (0.31), residues: 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1965 time to fit residues: 32.3117 Evaluate side-chains 92 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 8988 Z= 0.291 Angle : 0.711 10.952 12400 Z= 0.384 Chirality : 0.042 0.176 1400 Planarity : 0.004 0.039 1348 Dihedral : 24.440 178.862 1624 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.27), residues: 908 helix: -0.13 (0.24), residues: 452 sheet: -0.98 (0.69), residues: 54 loop : -1.77 (0.31), residues: 402 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.883 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1947 time to fit residues: 31.4115 Evaluate side-chains 93 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 76 optimal weight: 0.0020 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 0.3980 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS D 408 HIS D 463 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8988 Z= 0.201 Angle : 0.651 7.707 12400 Z= 0.352 Chirality : 0.040 0.170 1400 Planarity : 0.004 0.040 1348 Dihedral : 24.426 178.019 1624 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.27), residues: 908 helix: -0.05 (0.24), residues: 464 sheet: -1.16 (0.74), residues: 44 loop : -1.74 (0.31), residues: 400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.986 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2238 time to fit residues: 36.5309 Evaluate side-chains 93 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.0000 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.8108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.134879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.099167 restraints weight = 30364.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.102945 restraints weight = 17051.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.105386 restraints weight = 11625.743| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 8988 Z= 0.228 Angle : 0.663 8.303 12400 Z= 0.357 Chirality : 0.040 0.138 1400 Planarity : 0.004 0.040 1348 Dihedral : 24.389 177.555 1624 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.28), residues: 908 helix: -0.04 (0.24), residues: 464 sheet: -0.91 (0.66), residues: 54 loop : -1.74 (0.32), residues: 390 =============================================================================== Job complete usr+sys time: 1678.61 seconds wall clock time: 31 minutes 37.98 seconds (1897.98 seconds total)