Starting phenix.real_space_refine on Sat Dec 9 08:02:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/12_2023/8fej_29029.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/12_2023/8fej_29029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/12_2023/8fej_29029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/12_2023/8fej_29029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/12_2023/8fej_29029.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fej_29029/12_2023/8fej_29029.pdb" } resolution = 4.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.098 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 54 5.16 5 C 6606 2.51 5 N 1743 2.21 5 O 2061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10464 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3488 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Chain: "B" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3488 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Chain: "C" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3488 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Time building chain proxies: 5.83, per 1000 atoms: 0.56 Number of scatterers: 10464 At special positions: 0 Unit cell: (105.84, 111.24, 123.12, 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 54 16.00 O 2061 8.00 N 1743 7.00 C 6606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.93 Conformation dependent library (CDL) restraints added in 1.9 seconds 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 24 sheets defined 36.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 67 through 90 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 119 through 147 removed outlier: 5.226A pdb=" N GLU A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.946A pdb=" N ASN A 175 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 removed outlier: 3.652A pdb=" N ILE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 213 removed outlier: 3.923A pdb=" N LEU A 213 " --> pdb=" O GLY A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 210 through 213' Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.585A pdb=" N LEU A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 447 through 473 removed outlier: 3.540A pdb=" N GLN A 463 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 90 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 119 through 147 removed outlier: 5.227A pdb=" N GLU B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.945A pdb=" N ASN B 175 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 209 removed outlier: 3.652A pdb=" N ILE B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 213 removed outlier: 3.922A pdb=" N LEU B 213 " --> pdb=" O GLY B 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 210 through 213' Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 234 through 242 removed outlier: 3.586A pdb=" N LEU B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 447 through 473 removed outlier: 3.541A pdb=" N GLN B 463 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 67 through 90 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 119 through 147 removed outlier: 5.226A pdb=" N GLU C 134 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 178 removed outlier: 3.945A pdb=" N ASN C 175 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 209 removed outlier: 3.652A pdb=" N ILE C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 213 removed outlier: 3.922A pdb=" N LEU C 213 " --> pdb=" O GLY C 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 210 through 213' Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 234 through 242 removed outlier: 3.585A pdb=" N LEU C 238 " --> pdb=" O PHE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 447 through 473 removed outlier: 3.540A pdb=" N GLN C 463 " --> pdb=" O ASN C 459 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 39 removed outlier: 6.135A pdb=" N GLU A 290 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR A 38 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 288 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 45 Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.700A pdb=" N ALA A 272 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP A 263 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLU A 274 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE A 261 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.536A pdb=" N ILE A 221 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA8, first strand: chain 'A' and resid 405 through 406 removed outlier: 3.890A pdb=" N ALA A 380 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 415 through 417 removed outlier: 7.972A pdb=" N LEU A 421 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 34 through 39 removed outlier: 6.135A pdb=" N GLU B 290 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR B 38 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 288 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 42 through 45 Processing sheet with id=AB3, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.700A pdb=" N ALA B 272 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP B 263 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU B 274 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE B 261 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 153 through 156 Processing sheet with id=AB5, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.536A pdb=" N ILE B 221 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 296 through 297 Processing sheet with id=AB7, first strand: chain 'B' and resid 405 through 406 removed outlier: 3.891A pdb=" N ALA B 380 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 415 through 417 removed outlier: 7.916A pdb=" N LEU B 421 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 34 through 39 removed outlier: 6.134A pdb=" N GLU C 290 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR C 38 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL C 288 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 42 through 45 Processing sheet with id=AC2, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.701A pdb=" N ALA C 272 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP C 263 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU C 274 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE C 261 " --> pdb=" O GLU C 274 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AC4, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.536A pdb=" N ILE C 221 " --> pdb=" O GLY C 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 296 through 297 Processing sheet with id=AC6, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.890A pdb=" N ALA C 380 " --> pdb=" O SER C 405 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1158 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: 3.15 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3486 1.35 - 1.46: 2114 1.46 - 1.58: 4927 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 10605 Sorted by residual: bond pdb=" N VAL C 181 " pdb=" CA VAL C 181 " ideal model delta sigma weight residual 1.459 1.467 -0.008 1.25e-02 6.40e+03 4.28e-01 bond pdb=" N VAL B 181 " pdb=" CA VAL B 181 " ideal model delta sigma weight residual 1.459 1.467 -0.008 1.25e-02 6.40e+03 3.68e-01 bond pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 1.459 1.466 -0.007 1.25e-02 6.40e+03 3.55e-01 bond pdb=" CG PRO A 216 " pdb=" CD PRO A 216 " ideal model delta sigma weight residual 1.503 1.485 0.018 3.40e-02 8.65e+02 2.67e-01 bond pdb=" CG PRO B 216 " pdb=" CD PRO B 216 " ideal model delta sigma weight residual 1.503 1.485 0.018 3.40e-02 8.65e+02 2.66e-01 ... (remaining 10600 not shown) Histogram of bond angle deviations from ideal: 100.84 - 107.46: 237 107.46 - 114.08: 6304 114.08 - 120.69: 4091 120.69 - 127.31: 3741 127.31 - 133.93: 45 Bond angle restraints: 14418 Sorted by residual: angle pdb=" C PRO B 180 " pdb=" N VAL B 181 " pdb=" CA VAL B 181 " ideal model delta sigma weight residual 121.97 126.16 -4.19 1.80e+00 3.09e-01 5.42e+00 angle pdb=" C PRO C 180 " pdb=" N VAL C 181 " pdb=" CA VAL C 181 " ideal model delta sigma weight residual 121.97 126.15 -4.18 1.80e+00 3.09e-01 5.39e+00 angle pdb=" C PRO A 180 " pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 121.97 126.15 -4.18 1.80e+00 3.09e-01 5.38e+00 angle pdb=" CA LEU C 455 " pdb=" CB LEU C 455 " pdb=" CG LEU C 455 " ideal model delta sigma weight residual 116.30 121.50 -5.20 3.50e+00 8.16e-02 2.21e+00 angle pdb=" CA LEU B 455 " pdb=" CB LEU B 455 " pdb=" CG LEU B 455 " ideal model delta sigma weight residual 116.30 121.45 -5.15 3.50e+00 8.16e-02 2.16e+00 ... (remaining 14413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 5769 16.45 - 32.90: 561 32.90 - 49.35: 159 49.35 - 65.80: 15 65.80 - 82.25: 12 Dihedral angle restraints: 6516 sinusoidal: 2538 harmonic: 3978 Sorted by residual: dihedral pdb=" CA LYS C 79 " pdb=" CB LYS C 79 " pdb=" CG LYS C 79 " pdb=" CD LYS C 79 " ideal model delta sinusoidal sigma weight residual -60.00 -116.09 56.09 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA LYS B 79 " pdb=" CB LYS B 79 " pdb=" CG LYS B 79 " pdb=" CD LYS B 79 " ideal model delta sinusoidal sigma weight residual -60.00 -116.08 56.08 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA LYS A 79 " pdb=" CB LYS A 79 " pdb=" CG LYS A 79 " pdb=" CD LYS A 79 " ideal model delta sinusoidal sigma weight residual -60.00 -116.06 56.06 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 6513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1113 0.025 - 0.050: 359 0.050 - 0.075: 136 0.075 - 0.100: 70 0.100 - 0.125: 77 Chirality restraints: 1755 Sorted by residual: chirality pdb=" CA ILE B 57 " pdb=" N ILE B 57 " pdb=" C ILE B 57 " pdb=" CB ILE B 57 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE B 275 " pdb=" N ILE B 275 " pdb=" C ILE B 275 " pdb=" CB ILE B 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA VAL A 444 " pdb=" N VAL A 444 " pdb=" C VAL A 444 " pdb=" CB VAL A 444 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1752 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 368 " -0.013 5.00e-02 4.00e+02 1.98e-02 6.30e-01 pdb=" N PRO C 369 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO C 369 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 369 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 368 " -0.013 5.00e-02 4.00e+02 1.97e-02 6.22e-01 pdb=" N PRO A 369 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 369 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 369 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 368 " -0.013 5.00e-02 4.00e+02 1.96e-02 6.15e-01 pdb=" N PRO B 369 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO B 369 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 369 " -0.011 5.00e-02 4.00e+02 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2244 2.78 - 3.31: 9986 3.31 - 3.84: 16675 3.84 - 4.37: 18175 4.37 - 4.90: 31657 Nonbonded interactions: 78737 Sorted by model distance: nonbonded pdb=" NZ LYS A 50 " pdb=" O MET A 241 " model vdw 2.253 2.520 nonbonded pdb=" NZ LYS B 50 " pdb=" O MET B 241 " model vdw 2.253 2.520 nonbonded pdb=" NZ LYS C 50 " pdb=" O MET C 241 " model vdw 2.253 2.520 nonbonded pdb=" ND2 ASN B 233 " pdb=" OE2 GLU B 236 " model vdw 2.288 2.520 nonbonded pdb=" ND2 ASN A 233 " pdb=" OE2 GLU A 236 " model vdw 2.289 2.520 ... (remaining 78732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.910 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.000 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 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 : 0.001 0.018 10605 Z= 0.079 Angle : 0.368 5.198 14418 Z= 0.189 Chirality : 0.039 0.125 1755 Planarity : 0.002 0.020 1854 Dihedral : 13.974 82.248 3915 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.86 % Favored : 96.92 % Rotamer: Outliers : 4.30 % Allowed : 14.94 % Favored : 80.76 % 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: 0.48 (0.24), residues: 1362 helix: 2.10 (0.26), residues: 444 sheet: 0.30 (0.38), residues: 165 loop : -0.81 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 303 HIS 0.000 0.000 HIS A 130 PHE 0.002 0.000 PHE C 371 TYR 0.008 0.000 TYR C 270 ARG 0.001 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 0.409 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 58 average time/residue: 0.1629 time to fit residues: 11.5660 Evaluate side-chains 21 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0342 time to fit residues: 0.6673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.7980 chunk 102 optimal weight: 0.0670 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 69 optimal weight: 0.4980 chunk 54 optimal weight: 20.0000 chunk 105 optimal weight: 0.0870 chunk 40 optimal weight: 0.0370 chunk 64 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.1774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10605 Z= 0.172 Angle : 0.541 7.664 14418 Z= 0.275 Chirality : 0.044 0.245 1755 Planarity : 0.003 0.046 1854 Dihedral : 3.023 17.017 1461 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.51 % Allowed : 2.03 % Favored : 97.47 % 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: 0.62 (0.24), residues: 1362 helix: 2.29 (0.25), residues: 444 sheet: 0.28 (0.39), residues: 165 loop : -0.74 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.000 HIS B 24 PHE 0.012 0.002 PHE B 105 TYR 0.016 0.002 TYR B 74 ARG 0.033 0.001 ARG A 232 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.406 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.1612 time to fit residues: 5.8926 Evaluate side-chains 18 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0349 time to fit residues: 0.6033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.0030 chunk 38 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 0.0070 chunk 132 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 10605 Z= 0.144 Angle : 0.480 6.733 14418 Z= 0.242 Chirality : 0.042 0.170 1755 Planarity : 0.003 0.039 1854 Dihedral : 2.954 11.257 1461 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 0.34 (0.23), residues: 1362 helix: 2.13 (0.25), residues: 441 sheet: 0.06 (0.39), residues: 165 loop : -0.93 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.000 HIS C 24 PHE 0.010 0.001 PHE B 105 TYR 0.011 0.001 TYR B 74 ARG 0.022 0.001 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.411 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1327 time to fit residues: 4.1845 Evaluate side-chains 16 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 0.0000 chunk 123 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 224 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10605 Z= 0.120 Angle : 0.456 7.567 14418 Z= 0.228 Chirality : 0.041 0.128 1755 Planarity : 0.005 0.118 1854 Dihedral : 2.933 13.684 1461 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.63 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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: -0.19 (0.22), residues: 1362 helix: 1.52 (0.24), residues: 432 sheet: -0.24 (0.37), residues: 165 loop : -1.11 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 303 HIS 0.001 0.000 HIS B 253 PHE 0.008 0.001 PHE B 230 TYR 0.007 0.001 TYR B 74 ARG 0.002 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.414 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1359 time to fit residues: 4.1293 Evaluate side-chains 16 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 117 optimal weight: 0.0020 chunk 32 optimal weight: 2.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN B 289 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10605 Z= 0.113 Angle : 0.474 6.382 14418 Z= 0.237 Chirality : 0.041 0.141 1755 Planarity : 0.004 0.063 1854 Dihedral : 3.053 17.517 1461 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.07 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -0.33 (0.22), residues: 1362 helix: 1.41 (0.24), residues: 438 sheet: -0.23 (0.38), residues: 165 loop : -1.25 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.000 HIS B 253 PHE 0.011 0.001 PHE B 230 TYR 0.005 0.001 TYR B 74 ARG 0.001 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.418 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1366 time to fit residues: 4.1140 Evaluate side-chains 16 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 0.0270 chunk 68 optimal weight: 0.2980 chunk 125 optimal weight: 3.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 224 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 10605 Z= 0.105 Angle : 0.444 6.813 14418 Z= 0.220 Chirality : 0.041 0.126 1755 Planarity : 0.003 0.040 1854 Dihedral : 2.976 12.801 1461 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.95 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.42 (0.22), residues: 1362 helix: 1.41 (0.24), residues: 438 sheet: -0.25 (0.38), residues: 165 loop : -1.36 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.001 0.000 HIS B 253 PHE 0.013 0.001 PHE A 230 TYR 0.005 0.001 TYR B 74 ARG 0.001 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1360 time to fit residues: 3.9869 Evaluate side-chains 17 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 0.0000 chunk 95 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 72 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 79 optimal weight: 8.9990 chunk 60 optimal weight: 0.0010 chunk 80 optimal weight: 7.9990 overall best weight: 0.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10605 Z= 0.100 Angle : 0.455 7.624 14418 Z= 0.218 Chirality : 0.041 0.167 1755 Planarity : 0.003 0.030 1854 Dihedral : 2.879 12.029 1461 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.51 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.54 (0.22), residues: 1362 helix: 1.25 (0.23), residues: 441 sheet: -0.22 (0.38), residues: 165 loop : -1.42 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 303 HIS 0.000 0.000 HIS C 130 PHE 0.014 0.001 PHE B 230 TYR 0.006 0.001 TYR A 202 ARG 0.001 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2053 time to fit residues: 5.1659 Evaluate side-chains 15 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 39 optimal weight: 0.0770 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 88 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 0.0670 chunk 102 optimal weight: 0.0670 chunk 118 optimal weight: 0.0980 chunk 124 optimal weight: 0.0770 overall best weight: 0.0772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10605 Z= 0.110 Angle : 0.464 6.975 14418 Z= 0.226 Chirality : 0.041 0.161 1755 Planarity : 0.004 0.059 1854 Dihedral : 2.886 11.578 1461 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.39 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1362 helix: 1.30 (0.24), residues: 438 sheet: -0.25 (0.37), residues: 165 loop : -1.39 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.000 0.000 HIS C 130 PHE 0.016 0.001 PHE B 230 TYR 0.007 0.001 TYR B 202 ARG 0.010 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.460 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1597 time to fit residues: 4.9939 Evaluate side-chains 15 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0970 chunk 121 optimal weight: 0.5980 chunk 124 optimal weight: 0.0470 chunk 72 optimal weight: 0.0570 chunk 52 optimal weight: 0.3980 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 0.0020 chunk 114 optimal weight: 0.0870 chunk 120 optimal weight: 3.9990 chunk 79 optimal weight: 0.0470 overall best weight: 0.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10605 Z= 0.112 Angle : 0.472 7.074 14418 Z= 0.230 Chirality : 0.041 0.157 1755 Planarity : 0.003 0.047 1854 Dihedral : 2.917 11.206 1461 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1362 helix: 1.12 (0.23), residues: 438 sheet: -0.23 (0.37), residues: 165 loop : -1.41 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 303 HIS 0.000 0.000 HIS C 130 PHE 0.012 0.001 PHE B 230 TYR 0.006 0.001 TYR C 202 ARG 0.008 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1445 time to fit residues: 3.7660 Evaluate side-chains 15 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.4980 chunk 78 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 0.0000 chunk 85 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10605 Z= 0.124 Angle : 0.480 6.654 14418 Z= 0.238 Chirality : 0.041 0.158 1755 Planarity : 0.003 0.047 1854 Dihedral : 2.988 10.462 1461 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.39 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1362 helix: 1.40 (0.24), residues: 426 sheet: -0.27 (0.37), residues: 165 loop : -1.33 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 303 HIS 0.001 0.000 HIS B 253 PHE 0.011 0.001 PHE A 230 TYR 0.007 0.001 TYR A 433 ARG 0.008 0.001 ARG B 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1371 time to fit residues: 4.2124 Evaluate side-chains 17 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.0670 chunk 107 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 0.0870 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.052675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.042945 restraints weight = 60278.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.043546 restraints weight = 49889.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.043966 restraints weight = 43220.777| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10605 Z= 0.121 Angle : 0.492 6.858 14418 Z= 0.245 Chirality : 0.041 0.161 1755 Planarity : 0.003 0.045 1854 Dihedral : 3.010 10.173 1461 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.95 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.44 (0.22), residues: 1362 helix: 1.38 (0.25), residues: 426 sheet: -0.33 (0.36), residues: 165 loop : -1.30 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 303 HIS 0.000 0.000 HIS B 253 PHE 0.012 0.001 PHE C 230 TYR 0.005 0.001 TYR A 433 ARG 0.006 0.000 ARG B 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1664.07 seconds wall clock time: 31 minutes 23.64 seconds (1883.64 seconds total)