Starting phenix.real_space_refine on Thu Mar 6 10:16:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srm_40735/03_2025/8srm_40735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srm_40735/03_2025/8srm_40735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8srm_40735/03_2025/8srm_40735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srm_40735/03_2025/8srm_40735.map" model { file = "/net/cci-nas-00/data/ceres_data/8srm_40735/03_2025/8srm_40735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srm_40735/03_2025/8srm_40735.cif" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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: 3 Type Number sf(0) Gaussians C 3447 2.51 5 N 1163 2.21 5 O 1163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5773 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 2126 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 388} Link IDs: {'PTRANS': 12, 'TRANS': 415} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1407 Unresolved non-hydrogen angles: 1781 Unresolved non-hydrogen dihedrals: 1177 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLN:plan1': 23, 'ARG:plan': 25, 'TYR:plan': 11, 'ASN:plan1': 17, 'TRP:plan': 5, 'ASP:plan': 23, 'PHE:plan': 21, 'GLU:plan': 27, 'HIS:plan': 11} Unresolved non-hydrogen planarities: 748 Chain: "B" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1169 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 218} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 2 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 798 Unresolved non-hydrogen angles: 1006 Unresolved non-hydrogen dihedrals: 674 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 18, 'TYR:plan': 6, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 13, 'PHE:plan': 14, 'GLU:plan': 16, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 423 Chain: "C" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1015 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 2, 'TRANS': 202} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 627 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 508 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 15, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 340 Chain: "D" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1015 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 2, 'TRANS': 202} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 627 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 508 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 15, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 340 Chain: "E" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 224 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 96 Chain: "F" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 224 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 96 Time building chain proxies: 7.43, per 1000 atoms: 1.29 Number of scatterers: 5773 At special positions: 0 Unit cell: (178.4, 101.465, 160.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1163 8.00 N 1163 7.00 C 3447 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.3 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 83.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.842A pdb=" N LEU A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 127 through 202 removed outlier: 4.109A pdb=" N CYS A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 212 removed outlier: 3.647A pdb=" N SER A 212 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.719A pdb=" N GLN A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 320 through 335 Processing helix chain 'A' and resid 336 through 364 Proline residue: A 342 - end of helix removed outlier: 3.564A pdb=" N ILE A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 387 removed outlier: 3.878A pdb=" N ALA A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 490 removed outlier: 4.045A pdb=" N LYS A 429 " --> pdb=" O GLN A 425 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 543 removed outlier: 3.618A pdb=" N VAL A 501 " --> pdb=" O CYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.953A pdb=" N LEU A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 Processing helix chain 'A' and resid 590 through 597 Proline residue: A 595 - end of helix Processing helix chain 'B' and resid 161 through 202 removed outlier: 4.473A pdb=" N LEU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.956A pdb=" N ASP B 316 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 335 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 462 through 541 Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 578 through 589 Processing helix chain 'C' and resid 841 through 866 Processing helix chain 'C' and resid 869 through 873 Processing helix chain 'C' and resid 877 through 891 Processing helix chain 'C' and resid 891 through 923 Processing helix chain 'C' and resid 929 through 964 removed outlier: 4.819A pdb=" N ARG C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE C 960 " --> pdb=" O ARG C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 971 Processing helix chain 'C' and resid 975 through 996 Processing helix chain 'C' and resid 1002 through 1020 Processing helix chain 'C' and resid 1023 through 1041 removed outlier: 4.298A pdb=" N ASN C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1044 No H-bonds generated for 'chain 'C' and resid 1042 through 1044' Processing helix chain 'D' and resid 841 through 866 removed outlier: 4.428A pdb=" N LEU D 847 " --> pdb=" O ILE D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 891 Processing helix chain 'D' and resid 891 through 915 removed outlier: 3.815A pdb=" N GLY D 895 " --> pdb=" O SER D 891 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 909 " --> pdb=" O LYS D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 923 Processing helix chain 'D' and resid 929 through 963 Processing helix chain 'D' and resid 964 through 970 Processing helix chain 'D' and resid 975 through 997 Processing helix chain 'D' and resid 999 through 1020 removed outlier: 3.956A pdb=" N CYS D1003 " --> pdb=" O HIS D 999 " (cutoff:3.500A) Proline residue: D1005 - end of helix Processing helix chain 'D' and resid 1023 through 1044 Processing helix chain 'E' and resid 463 through 471 removed outlier: 3.848A pdb=" N TYR E 467 " --> pdb=" O LEU E 463 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU E 469 " --> pdb=" O THR E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 515 Proline residue: E 496 - end of helix removed outlier: 3.534A pdb=" N THR E 515 " --> pdb=" O ALA E 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 488 through 494 removed outlier: 4.183A pdb=" N SER F 494 " --> pdb=" O GLU F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 513 Processing helix chain 'F' and resid 514 through 516 No H-bonds generated for 'chain 'F' and resid 514 through 516' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 733 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1163 1.29 - 1.35: 1150 1.35 - 1.42: 0 1.42 - 1.49: 1163 1.49 - 1.56: 2284 Bond restraints: 5760 Sorted by residual: bond pdb=" CA PRO C 874 " pdb=" CB PRO C 874 " ideal model delta sigma weight residual 1.533 1.559 -0.025 1.42e-02 4.96e+03 3.22e+00 bond pdb=" CA PRO B 318 " pdb=" CB PRO B 318 " ideal model delta sigma weight residual 1.534 1.559 -0.025 1.40e-02 5.10e+03 3.17e+00 bond pdb=" C VAL B 492 " pdb=" O VAL B 492 " ideal model delta sigma weight residual 1.240 1.218 0.021 1.26e-02 6.30e+03 2.85e+00 bond pdb=" CA PRO B 590 " pdb=" CB PRO B 590 " ideal model delta sigma weight residual 1.534 1.557 -0.023 1.40e-02 5.10e+03 2.67e+00 bond pdb=" CA PRO A 493 " pdb=" CB PRO A 493 " ideal model delta sigma weight residual 1.533 1.554 -0.021 1.42e-02 4.96e+03 2.23e+00 ... (remaining 5755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 7726 1.13 - 2.27: 228 2.27 - 3.40: 47 3.40 - 4.53: 13 4.53 - 5.67: 4 Bond angle restraints: 8018 Sorted by residual: angle pdb=" N PRO B 559 " pdb=" CA PRO B 559 " pdb=" CB PRO B 559 " ideal model delta sigma weight residual 103.19 105.27 -2.08 5.60e-01 3.19e+00 1.39e+01 angle pdb=" N PRO E 474 " pdb=" CA PRO E 474 " pdb=" CB PRO E 474 " ideal model delta sigma weight residual 102.35 104.97 -2.62 7.10e-01 1.98e+00 1.36e+01 angle pdb=" C MET B 495 " pdb=" N TYR B 496 " pdb=" CA TYR B 496 " ideal model delta sigma weight residual 120.44 125.40 -4.96 1.36e+00 5.41e-01 1.33e+01 angle pdb=" CA VAL D1004 " pdb=" C VAL D1004 " pdb=" N PRO D1005 " ideal model delta sigma weight residual 120.83 118.65 2.18 6.10e-01 2.69e+00 1.27e+01 angle pdb=" C GLN B 494 " pdb=" N MET B 495 " pdb=" CA MET B 495 " ideal model delta sigma weight residual 120.28 125.05 -4.77 1.44e+00 4.82e-01 1.10e+01 ... (remaining 8013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.23: 3033 4.23 - 8.46: 307 8.46 - 12.69: 41 12.69 - 16.91: 9 16.91 - 21.14: 2 Dihedral angle restraints: 3392 sinusoidal: 0 harmonic: 3392 Sorted by residual: dihedral pdb=" CA GLN C 998 " pdb=" C GLN C 998 " pdb=" N HIS C 999 " pdb=" CA HIS C 999 " ideal model delta harmonic sigma weight residual 180.00 158.86 21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA SER B 490 " pdb=" C SER B 490 " pdb=" N THR B 491 " pdb=" CA THR B 491 " ideal model delta harmonic sigma weight residual 180.00 162.51 17.49 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ILE B 339 " pdb=" C ILE B 339 " pdb=" N ILE B 340 " pdb=" CA ILE B 340 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 3389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 917 0.045 - 0.090: 185 0.090 - 0.134: 17 0.134 - 0.179: 1 0.179 - 0.224: 1 Chirality restraints: 1121 Sorted by residual: chirality pdb=" CA PRO B 595 " pdb=" N PRO B 595 " pdb=" C PRO B 595 " pdb=" CB PRO B 595 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA PRO B 493 " pdb=" N PRO B 493 " pdb=" C PRO B 493 " pdb=" CB PRO B 493 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ILE A 577 " pdb=" N ILE A 577 " pdb=" C ILE A 577 " pdb=" CB ILE A 577 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1118 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 497 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C CYS B 497 " 0.030 2.00e-02 2.50e+03 pdb=" O CYS B 497 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 498 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 487 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C GLU B 487 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU B 487 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B 488 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 545 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.51e+00 pdb=" C SER A 545 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A 545 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 546 " 0.009 2.00e-02 2.50e+03 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1360 2.77 - 3.30: 6953 3.30 - 3.84: 10053 3.84 - 4.37: 9492 4.37 - 4.90: 14322 Nonbonded interactions: 42180 Sorted by model distance: nonbonded pdb=" O ASP C 969 " pdb=" N SER E 487 " model vdw 2.238 3.120 nonbonded pdb=" O PHE B 304 " pdb=" N LYS D 964 " model vdw 2.266 3.120 nonbonded pdb=" O ILE C 971 " pdb=" N SER E 487 " model vdw 2.322 3.120 nonbonded pdb=" O LEU B 547 " pdb=" N LEU B 551 " model vdw 2.325 3.120 nonbonded pdb=" O ASP B 336 " pdb=" N ARG B 341 " model vdw 2.341 3.120 ... (remaining 42175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 23.290 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:3.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5760 Z= 0.210 Angle : 0.512 5.667 8018 Z= 0.376 Chirality : 0.034 0.224 1121 Planarity : 0.003 0.017 1150 Dihedral : 4.378 21.143 1150 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: 2.57 (0.25), residues: 1137 helix: 2.49 (0.17), residues: 838 sheet: None (None), residues: 0 loop : -0.65 (0.40), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.656 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0604 time to fit residues: 3.6632 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.042414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.025595 restraints weight = 70436.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.025661 restraints weight = 65426.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.025661 restraints weight = 62088.290| |-----------------------------------------------------------------------------| r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5760 Z= 0.380 Angle : 0.535 4.298 8018 Z= 0.401 Chirality : 0.035 0.119 1121 Planarity : 0.004 0.017 1150 Dihedral : 4.708 21.471 1150 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: 1.55 (0.24), residues: 1137 helix: 1.61 (0.16), residues: 872 sheet: None (None), residues: 0 loop : -0.83 (0.42), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 1.651 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0853 time to fit residues: 5.7683 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 30.0000 chunk 80 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.042510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.025536 restraints weight = 70676.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.025556 restraints weight = 66085.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.025572 restraints weight = 65203.906| |-----------------------------------------------------------------------------| r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 5760 Z= 0.300 Angle : 0.467 5.065 8018 Z= 0.343 Chirality : 0.034 0.123 1121 Planarity : 0.003 0.014 1150 Dihedral : 4.751 22.857 1150 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: 1.47 (0.25), residues: 1137 helix: 1.56 (0.17), residues: 868 sheet: None (None), residues: 0 loop : -0.86 (0.42), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.714 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0557 time to fit residues: 3.4135 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 110 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 83 optimal weight: 0.0000 chunk 40 optimal weight: 20.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.043909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030824 restraints weight = 76037.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.030144 restraints weight = 54038.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.030046 restraints weight = 58862.343| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 5760 Z= 0.187 Angle : 0.380 3.512 8018 Z= 0.270 Chirality : 0.033 0.126 1121 Planarity : 0.002 0.012 1150 Dihedral : 4.423 21.525 1150 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: 2.42 (0.25), residues: 1137 helix: 2.31 (0.17), residues: 874 sheet: None (None), residues: 0 loop : -0.87 (0.43), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.760 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0784 time to fit residues: 4.5640 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 77 optimal weight: 10.0000 chunk 18 optimal weight: 0.0170 chunk 55 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 41 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 1.6824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.044485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.030852 restraints weight = 73389.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.030409 restraints weight = 53128.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.030208 restraints weight = 58448.627| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 5760 Z= 0.133 Angle : 0.344 3.212 8018 Z= 0.239 Chirality : 0.033 0.129 1121 Planarity : 0.002 0.010 1150 Dihedral : 4.019 19.094 1150 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: 3.21 (0.25), residues: 1137 helix: 2.93 (0.17), residues: 880 sheet: None (None), residues: 0 loop : -0.96 (0.43), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.647 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0641 time to fit residues: 3.8946 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 59 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.041244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.024996 restraints weight = 70814.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 13)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.025059 restraints weight = 65993.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.025133 restraints weight = 62683.363| |-----------------------------------------------------------------------------| r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 5760 Z= 0.540 Angle : 0.685 8.310 8018 Z= 0.521 Chirality : 0.037 0.143 1121 Planarity : 0.005 0.020 1150 Dihedral : 5.463 28.315 1150 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: -0.07 (0.24), residues: 1137 helix: 0.41 (0.16), residues: 874 sheet: None (None), residues: 0 loop : -1.30 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.653 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0559 time to fit residues: 3.4483 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 6 optimal weight: 0.0050 chunk 72 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.042867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.025777 restraints weight = 71739.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.025873 restraints weight = 66123.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.025978 restraints weight = 62293.860| |-----------------------------------------------------------------------------| r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 5760 Z= 0.223 Angle : 0.412 4.337 8018 Z= 0.295 Chirality : 0.033 0.125 1121 Planarity : 0.002 0.012 1150 Dihedral : 4.722 22.315 1150 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: 1.54 (0.25), residues: 1137 helix: 1.66 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -1.09 (0.42), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 1.815 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0884 time to fit residues: 5.2143 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.042519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.025557 restraints weight = 69446.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.025629 restraints weight = 65279.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.025629 restraints weight = 61959.013| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 5760 Z= 0.293 Angle : 0.459 5.362 8018 Z= 0.337 Chirality : 0.034 0.126 1121 Planarity : 0.003 0.012 1150 Dihedral : 4.726 23.153 1150 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: 1.46 (0.25), residues: 1137 helix: 1.62 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -1.19 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.831 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1025 time to fit residues: 5.9326 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.041899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.025294 restraints weight = 70256.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.025363 restraints weight = 65186.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.025363 restraints weight = 61940.210| |-----------------------------------------------------------------------------| r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 5760 Z= 0.384 Angle : 0.541 6.404 8018 Z= 0.406 Chirality : 0.035 0.121 1121 Planarity : 0.003 0.014 1150 Dihedral : 5.049 24.105 1150 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: 0.62 (0.25), residues: 1137 helix: 0.98 (0.17), residues: 872 sheet: None (None), residues: 0 loop : -1.34 (0.42), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.713 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0542 time to fit residues: 3.4013 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 0.0770 chunk 72 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030692 restraints weight = 74120.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.030150 restraints weight = 63740.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.029953 restraints weight = 65241.270| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 5760 Z= 0.136 Angle : 0.351 3.736 8018 Z= 0.241 Chirality : 0.033 0.127 1121 Planarity : 0.002 0.011 1150 Dihedral : 4.370 20.575 1150 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: 2.43 (0.25), residues: 1137 helix: 2.37 (0.17), residues: 882 sheet: None (None), residues: 0 loop : -1.23 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.621 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0519 time to fit residues: 3.2252 Evaluate side-chains 24 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 69 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.025512 restraints weight = 68564.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.025612 restraints weight = 63934.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.025675 restraints weight = 60336.961| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 5760 Z= 0.356 Angle : 0.510 6.507 8018 Z= 0.381 Chirality : 0.035 0.121 1121 Planarity : 0.003 0.012 1150 Dihedral : 4.753 23.092 1150 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 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: 1.45 (0.25), residues: 1137 helix: 1.61 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -1.17 (0.42), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 150 PHE 0.000 0.000 PHE A 6 TYR 0.000 0.000 TYR A 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2240.94 seconds wall clock time: 40 minutes 47.85 seconds (2447.85 seconds total)