Starting phenix.real_space_refine on Tue Feb 11 13:31:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srm_40735/02_2025/8srm_40735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srm_40735/02_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_40735/02_2025/8srm_40735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srm_40735/02_2025/8srm_40735.map" model { file = "/net/cci-nas-00/data/ceres_data/8srm_40735/02_2025/8srm_40735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srm_40735/02_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-5592/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: 5.02, per 1000 atoms: 0.87 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: 1.85 Conformation dependent library (CDL) restraints added in 1.2 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: 0.58 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: 1.89 Time building geometry restraints manager: 2.02 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: 3.400 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.290 Find NCS groups from input model: 0.160 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.980 ------------------------------------------------------------------------------- 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 : 0.641 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0557 time to fit residues: 3.3415 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 : 0.722 ------------------------------------------------------------------------------- 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 = 0.3041 r_free = 0.3041 target = 0.042411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.025593 restraints weight = 70877.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.025593 restraints weight = 65624.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.025593 restraints weight = 65601.774| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 : 0.732 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0556 time to fit residues: 3.5454 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 : 0.699 ------------------------------------------------------------------------------- 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: 10.0000 chunk 48 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.043483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.030665 restraints weight = 75863.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.029972 restraints weight = 57444.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.029819 restraints weight = 62957.229| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 5760 Z= 0.270 Angle : 0.442 4.850 8018 Z= 0.322 Chirality : 0.034 0.123 1121 Planarity : 0.003 0.014 1150 Dihedral : 4.612 22.215 1150 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: 1.83 (0.25), residues: 1137 helix: 1.81 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -0.78 (0.43), 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 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 : 0.641 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0533 time to fit residues: 3.2944 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 : 0.658 ------------------------------------------------------------------------------- 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: 7.9990 chunk 110 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 40 optimal weight: 0.0770 overall best weight: 4.5944 ------------------------------------------------------------------------------- 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 = 0.042439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.025460 restraints weight = 71844.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.025460 restraints weight = 67167.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.025460 restraints weight = 67167.589| |-----------------------------------------------------------------------------| r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5760 Z= 0.303 Angle : 0.471 5.357 8018 Z= 0.346 Chirality : 0.034 0.123 1121 Planarity : 0.003 0.014 1150 Dihedral : 4.778 23.324 1150 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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: 1.49 (0.25), residues: 1137 helix: 1.58 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -0.92 (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 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 : 0.748 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0543 time to fit residues: 3.4419 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 : 0.750 ------------------------------------------------------------------------------- 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: 8.9990 chunk 18 optimal weight: 0.0870 chunk 55 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 = 0.3131 r_free = 0.3131 target = 0.044813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.031098 restraints weight = 72776.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030723 restraints weight = 56777.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.030650 restraints weight = 54967.230| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 5760 Z= 0.101 Angle : 0.328 3.217 8018 Z= 0.219 Chirality : 0.033 0.131 1121 Planarity : 0.002 0.011 1150 Dihedral : 4.154 19.237 1150 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: 3.20 (0.25), residues: 1137 helix: 2.98 (0.16), residues: 874 sheet: -3.82 (1.18), residues: 11 loop : -0.88 (0.43), residues: 252 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 : 0.658 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0462 time to fit residues: 2.9204 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 : 0.610 ------------------------------------------------------------------------------- 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: 9.9990 chunk 100 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 59 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3006 r_free = 0.3006 target = 0.041448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.025249 restraints weight = 68811.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.025338 restraints weight = 63406.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.025424 restraints weight = 59916.950| |-----------------------------------------------------------------------------| r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 5760 Z= 0.518 Angle : 0.659 7.664 8018 Z= 0.504 Chirality : 0.037 0.145 1121 Planarity : 0.004 0.017 1150 Dihedral : 5.195 26.209 1150 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.54 % Favored : 94.37 % 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: 0.39 (0.24), residues: 1137 helix: 0.73 (0.16), residues: 870 sheet: None (None), residues: 0 loop : -1.08 (0.42), residues: 267 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 : 0.690 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0640 time to fit residues: 3.8571 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 : 0.650 ------------------------------------------------------------------------------- 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: 7.9990 chunk 20 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3038 r_free = 0.3038 target = 0.042362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.025435 restraints weight = 71349.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.025518 restraints weight = 66597.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.025518 restraints weight = 62959.013| |-----------------------------------------------------------------------------| r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1880 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= 0.305 Angle : 0.469 5.013 8018 Z= 0.345 Chirality : 0.034 0.123 1121 Planarity : 0.003 0.013 1150 Dihedral : 4.881 23.254 1150 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: 1.05 (0.25), residues: 1137 helix: 1.28 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -1.20 (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 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 : 0.674 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0565 time to fit residues: 3.4897 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 : 0.765 ------------------------------------------------------------------------------- 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: 9.9990 chunk 92 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 88 optimal weight: 0.0060 chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 25 optimal weight: 30.0000 overall best weight: 3.8004 ------------------------------------------------------------------------------- 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 = 0.3049 r_free = 0.3049 target = 0.042762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.025752 restraints weight = 68116.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.025825 restraints weight = 63919.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 13)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.025826 restraints weight = 60490.386| |-----------------------------------------------------------------------------| r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1917 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= 0.254 Angle : 0.427 4.656 8018 Z= 0.310 Chirality : 0.034 0.125 1121 Planarity : 0.003 0.012 1150 Dihedral : 4.622 22.684 1150 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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: 1.71 (0.25), residues: 1137 helix: 1.79 (0.17), residues: 872 sheet: None (None), residues: 0 loop : -1.07 (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 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 : 0.651 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0541 time to fit residues: 3.3832 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 : 0.717 ------------------------------------------------------------------------------- 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: 8.9990 chunk 64 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3028 r_free = 0.3028 target = 0.042078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.025398 restraints weight = 68511.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.025494 restraints weight = 63952.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.025556 restraints weight = 60341.464| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2107 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= 0.360 Angle : 0.520 6.285 8018 Z= 0.387 Chirality : 0.035 0.121 1121 Planarity : 0.003 0.013 1150 Dihedral : 5.025 24.085 1150 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % 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: 0.79 (0.25), residues: 1137 helix: 1.11 (0.17), residues: 872 sheet: None (None), residues: 0 loop : -1.33 (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 : 0.672 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0536 time to fit residues: 3.3850 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3064 r_free = 0.3064 target = 0.043240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.026043 restraints weight = 75300.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.026154 restraints weight = 69584.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.026218 restraints weight = 65477.074| |-----------------------------------------------------------------------------| r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 5760 Z= 0.185 Angle : 0.383 4.263 8018 Z= 0.270 Chirality : 0.033 0.127 1121 Planarity : 0.002 0.011 1150 Dihedral : 4.467 21.493 1150 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: 2.14 (0.25), residues: 1137 helix: 2.13 (0.17), residues: 877 sheet: None (None), residues: 0 loop : -1.13 (0.43), residues: 260 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 : 0.577 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0573 time to fit residues: 3.5811 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 : 0.759 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 39 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- 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 = 0.3025 r_free = 0.3025 target = 0.042038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.025329 restraints weight = 68734.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.025416 restraints weight = 64392.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.025492 restraints weight = 61115.081| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 5760 Z= 0.372 Angle : 0.530 6.840 8018 Z= 0.396 Chirality : 0.035 0.122 1121 Planarity : 0.003 0.013 1150 Dihedral : 4.914 23.634 1150 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % 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: 1.00 (0.25), residues: 1137 helix: 1.27 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -1.26 (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: 1902.19 seconds wall clock time: 34 minutes 40.32 seconds (2080.32 seconds total)