Starting phenix.real_space_refine on Wed Apr 30 11:27:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l6c_62852/04_2025/9l6c_62852.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l6c_62852/04_2025/9l6c_62852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l6c_62852/04_2025/9l6c_62852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l6c_62852/04_2025/9l6c_62852.map" model { file = "/net/cci-nas-00/data/ceres_data/9l6c_62852/04_2025/9l6c_62852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l6c_62852/04_2025/9l6c_62852.cif" } resolution = 3.33 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3402 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4279 2.51 5 N 1137 2.21 5 O 1322 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-5669/modules/chem_data/mon_lib" Total number of atoms: 6766 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 868 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "F" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.30, per 1000 atoms: 0.93 Number of scatterers: 6766 At special positions: 0 Unit cell: (68.64, 99.66, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1322 8.00 N 1137 7.00 C 4279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN E 343 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 907.0 milliseconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 22 sheets defined 5.0% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'E' and resid 364 through 368 removed outlier: 4.365A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.869A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 5.606A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.508A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN D 32 " --> pdb=" O VAL D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.713A pdb=" N LYS D 64 " --> pdb=" O ASP D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.840A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 33 removed outlier: 3.610A pdb=" N TYR F 33 " --> pdb=" O SER F 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 30 through 33' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 3.662A pdb=" N LEU A 81 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 5.961A pdb=" N GLY A 10 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET A 34 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 40 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 5.961A pdb=" N GLY A 10 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 97 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A 98 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.029A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.574A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.824A pdb=" N LEU B 10 " --> pdb=" O GLU B 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 21 removed outlier: 3.833A pdb=" N ILE B 75 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 73 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.782A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 98 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.529A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.834A pdb=" N THR H 114 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR H 93 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.834A pdb=" N THR H 114 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR H 93 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N CYS H 95 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TRP H 110 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ARG H 97 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.588A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.891A pdb=" N LEU L 11 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA L 13 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.552A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.819A pdb=" N TYR D 33 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET D 34 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.458A pdb=" N VAL D 106 " --> pdb=" O ARG D 97 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.552A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.552A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 21 through 22 removed outlier: 4.226A pdb=" N ASP F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER F 68 " --> pdb=" O ASP F 71 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 567 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: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2166 1.34 - 1.46: 1872 1.46 - 1.58: 2854 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 6928 Sorted by residual: bond pdb=" C LYS B 39 " pdb=" N PRO B 40 " ideal model delta sigma weight residual 1.331 1.360 -0.029 1.20e-02 6.94e+03 5.87e+00 bond pdb=" C LYS F 40 " pdb=" N PRO F 41 " ideal model delta sigma weight residual 1.331 1.360 -0.028 1.27e-02 6.20e+03 5.03e+00 bond pdb=" C ALA D 40 " pdb=" N PRO D 41 " ideal model delta sigma weight residual 1.332 1.359 -0.027 1.32e-02 5.74e+03 4.32e+00 bond pdb=" C TYR H 59 " pdb=" N PRO H 60 " ideal model delta sigma weight residual 1.330 1.355 -0.025 1.25e-02 6.40e+03 3.91e+00 bond pdb=" N PRO H 60 " pdb=" CD PRO H 60 " ideal model delta sigma weight residual 1.473 1.449 0.024 1.40e-02 5.10e+03 2.99e+00 ... (remaining 6923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 9184 1.63 - 3.27: 190 3.27 - 4.90: 23 4.90 - 6.53: 6 6.53 - 8.17: 1 Bond angle restraints: 9404 Sorted by residual: angle pdb=" CA GLU A 89 " pdb=" CB GLU A 89 " pdb=" CG GLU A 89 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 angle pdb=" O TYR H 59 " pdb=" C TYR H 59 " pdb=" N PRO H 60 " ideal model delta sigma weight residual 121.80 119.29 2.51 8.60e-01 1.35e+00 8.54e+00 angle pdb=" C SER A 56 " pdb=" N ASN A 57 " pdb=" CA ASN A 57 " ideal model delta sigma weight residual 121.54 126.68 -5.14 1.91e+00 2.74e-01 7.25e+00 angle pdb=" C GLY A 108 " pdb=" N LEU A 109 " pdb=" CA LEU A 109 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.44e+00 angle pdb=" N LEU A 109 " pdb=" CA LEU A 109 " pdb=" C LEU A 109 " ideal model delta sigma weight residual 110.80 116.08 -5.28 2.13e+00 2.20e-01 6.14e+00 ... (remaining 9399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3577 17.43 - 34.86: 387 34.86 - 52.28: 96 52.28 - 69.71: 15 69.71 - 87.14: 9 Dihedral angle restraints: 4084 sinusoidal: 1592 harmonic: 2492 Sorted by residual: dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual -86.00 -41.64 -44.36 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CA ASN E 440 " pdb=" C ASN E 440 " pdb=" N LEU E 441 " pdb=" CA LEU E 441 " ideal model delta harmonic sigma weight residual 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLY A 108 " pdb=" C GLY A 108 " pdb=" N LEU A 109 " pdb=" CA LEU A 109 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 4081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 664 0.033 - 0.066: 243 0.066 - 0.099: 64 0.099 - 0.131: 42 0.131 - 0.164: 3 Chirality restraints: 1016 Sorted by residual: chirality pdb=" CA PRO B 40 " pdb=" N PRO B 40 " pdb=" C PRO B 40 " pdb=" CB PRO B 40 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA ILE F 49 " pdb=" N ILE F 49 " pdb=" C ILE F 49 " pdb=" CB ILE F 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1013 not shown) Planarity restraints: 1210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 336 " -0.057 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO E 337 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 94 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO B 95 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 80 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO F 81 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 81 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 81 " -0.028 5.00e-02 4.00e+02 ... (remaining 1207 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1468 2.78 - 3.31: 5588 3.31 - 3.84: 10559 3.84 - 4.37: 11980 4.37 - 4.90: 21898 Nonbonded interactions: 51493 Sorted by model distance: nonbonded pdb=" O SER L 7 " pdb=" OG1 THR L 22 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR B 36 " pdb=" OE1 GLN B 89 " model vdw 2.259 3.040 nonbonded pdb=" O SER H 119 " pdb=" OG SER H 119 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN E 501 " pdb=" N GLY E 502 " model vdw 2.301 3.120 nonbonded pdb=" N GLY E 476 " pdb=" OD1 ASN E 487 " model vdw 2.305 3.120 ... (remaining 51488 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 'B' and (resid 1 through 95 or resid 98 through 100 or resid 102 through \ 104 or resid 106 through 108)) selection = (chain 'F' and (resid 2 through 99 or resid 101 through 103 or resid 105 through \ 107)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 45.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.560 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.002 0.029 6940 Z= 0.131 Angle : 0.575 8.165 9430 Z= 0.309 Chirality : 0.041 0.164 1016 Planarity : 0.005 0.087 1209 Dihedral : 15.305 87.139 2488 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.47 % Favored : 94.19 % Rotamer: Outliers : 0.27 % Allowed : 20.60 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.01 (0.29), residues: 860 helix: -5.52 (0.31), residues: 6 sheet: -0.49 (0.31), residues: 333 loop : -0.68 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS A 35 PHE 0.009 0.001 PHE A 107 TYR 0.013 0.001 TYR D 59 ARG 0.005 0.000 ARG A 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 1) link_NAG-ASN : angle 1.52723 ( 3) link_BETA1-4 : bond 0.00552 ( 1) link_BETA1-4 : angle 0.88947 ( 3) hydrogen bonds : bond 0.28428 ( 199) hydrogen bonds : angle 10.32523 ( 567) SS BOND : bond 0.00305 ( 10) SS BOND : angle 0.97029 ( 20) covalent geometry : bond 0.00240 ( 6928) covalent geometry : angle 0.57347 ( 9404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 97 TYR cc_start: 0.8271 (m-80) cc_final: 0.8047 (m-80) outliers start: 2 outliers final: 2 residues processed: 134 average time/residue: 0.1789 time to fit residues: 32.5858 Evaluate side-chains 134 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain F residue 90 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121008 restraints weight = 9698.862| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.58 r_work: 0.3510 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6940 Z= 0.170 Angle : 0.584 5.618 9430 Z= 0.312 Chirality : 0.042 0.144 1016 Planarity : 0.005 0.075 1209 Dihedral : 5.764 73.910 1017 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.63 % Favored : 93.02 % Rotamer: Outliers : 2.75 % Allowed : 18.13 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.99 (0.29), residues: 860 helix: -4.90 (0.34), residues: 13 sheet: -0.29 (0.31), residues: 308 loop : -0.74 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 107 HIS 0.005 0.001 HIS D 94 PHE 0.016 0.002 PHE E 400 TYR 0.015 0.002 TYR D 93 ARG 0.004 0.000 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 1) link_NAG-ASN : angle 0.87600 ( 3) link_BETA1-4 : bond 0.00662 ( 1) link_BETA1-4 : angle 0.59535 ( 3) hydrogen bonds : bond 0.04460 ( 199) hydrogen bonds : angle 6.70687 ( 567) SS BOND : bond 0.00504 ( 10) SS BOND : angle 1.26261 ( 20) covalent geometry : bond 0.00382 ( 6928) covalent geometry : angle 0.58119 ( 9404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 501 ASN cc_start: 0.8190 (t0) cc_final: 0.7952 (t0) REVERT: D 81 GLN cc_start: 0.7550 (tp40) cc_final: 0.7073 (tt0) outliers start: 20 outliers final: 16 residues processed: 141 average time/residue: 0.1899 time to fit residues: 36.2673 Evaluate side-chains 147 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 58 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 82 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 5 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.137346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121412 restraints weight = 9816.157| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.60 r_work: 0.3512 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6940 Z= 0.141 Angle : 0.539 5.319 9430 Z= 0.287 Chirality : 0.041 0.142 1016 Planarity : 0.005 0.069 1209 Dihedral : 4.765 27.492 1013 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.93 % Favored : 93.72 % Rotamer: Outliers : 3.02 % Allowed : 19.09 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.96 (0.29), residues: 860 helix: -5.50 (0.33), residues: 6 sheet: -0.33 (0.31), residues: 307 loop : -0.74 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 107 HIS 0.004 0.001 HIS D 94 PHE 0.014 0.001 PHE A 107 TYR 0.012 0.001 TYR D 93 ARG 0.002 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 1) link_NAG-ASN : angle 0.79860 ( 3) link_BETA1-4 : bond 0.00430 ( 1) link_BETA1-4 : angle 0.62786 ( 3) hydrogen bonds : bond 0.03789 ( 199) hydrogen bonds : angle 6.07401 ( 567) SS BOND : bond 0.00469 ( 10) SS BOND : angle 0.96575 ( 20) covalent geometry : bond 0.00319 ( 6928) covalent geometry : angle 0.53732 ( 9404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8425 (ttt90) cc_final: 0.8168 (ttt180) REVERT: E 501 ASN cc_start: 0.8129 (t0) cc_final: 0.7878 (t0) REVERT: H 82 MET cc_start: 0.7546 (mtm) cc_final: 0.7284 (mtp) REVERT: L 97 TYR cc_start: 0.8395 (m-80) cc_final: 0.8165 (m-80) REVERT: D 79 TYR cc_start: 0.7646 (m-10) cc_final: 0.7264 (m-10) REVERT: D 81 GLN cc_start: 0.7542 (tp40) cc_final: 0.7104 (tt0) outliers start: 22 outliers final: 21 residues processed: 143 average time/residue: 0.1694 time to fit residues: 32.8737 Evaluate side-chains 152 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 42 optimal weight: 0.0030 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.138096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122135 restraints weight = 9814.780| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.60 r_work: 0.3501 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6940 Z= 0.169 Angle : 0.545 5.256 9430 Z= 0.292 Chirality : 0.041 0.151 1016 Planarity : 0.005 0.065 1209 Dihedral : 4.739 28.785 1013 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.74 % Favored : 92.91 % Rotamer: Outliers : 3.57 % Allowed : 19.92 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.02 (0.28), residues: 860 helix: -5.49 (0.33), residues: 6 sheet: -0.38 (0.30), residues: 307 loop : -0.77 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 107 HIS 0.004 0.001 HIS D 94 PHE 0.016 0.002 PHE A 107 TYR 0.012 0.002 TYR D 93 ARG 0.006 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 1) link_NAG-ASN : angle 1.12381 ( 3) link_BETA1-4 : bond 0.00587 ( 1) link_BETA1-4 : angle 0.84146 ( 3) hydrogen bonds : bond 0.03575 ( 199) hydrogen bonds : angle 5.88711 ( 567) SS BOND : bond 0.00509 ( 10) SS BOND : angle 1.06174 ( 20) covalent geometry : bond 0.00386 ( 6928) covalent geometry : angle 0.54326 ( 9404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 501 ASN cc_start: 0.8111 (t0) cc_final: 0.7863 (t0) REVERT: L 4 MET cc_start: 0.6807 (tpp) cc_final: 0.6487 (mmm) REVERT: L 97 TYR cc_start: 0.8399 (m-80) cc_final: 0.8142 (m-80) REVERT: D 81 GLN cc_start: 0.7567 (tp40) cc_final: 0.7122 (tt0) outliers start: 26 outliers final: 24 residues processed: 147 average time/residue: 0.2018 time to fit residues: 40.2437 Evaluate side-chains 155 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 90 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 42 optimal weight: 0.0870 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.138328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122393 restraints weight = 9751.695| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.60 r_work: 0.3525 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6940 Z= 0.108 Angle : 0.508 5.172 9430 Z= 0.271 Chirality : 0.041 0.145 1016 Planarity : 0.005 0.059 1209 Dihedral : 4.515 27.179 1013 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.16 % Favored : 93.60 % Rotamer: Outliers : 3.71 % Allowed : 19.92 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.89 (0.29), residues: 860 helix: -5.46 (0.34), residues: 6 sheet: -0.29 (0.30), residues: 306 loop : -0.69 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 52 HIS 0.003 0.001 HIS D 94 PHE 0.011 0.001 PHE A 107 TYR 0.011 0.001 TYR H 105 ARG 0.006 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 1) link_NAG-ASN : angle 0.79447 ( 3) link_BETA1-4 : bond 0.00523 ( 1) link_BETA1-4 : angle 0.79762 ( 3) hydrogen bonds : bond 0.03066 ( 199) hydrogen bonds : angle 5.59752 ( 567) SS BOND : bond 0.00368 ( 10) SS BOND : angle 0.82617 ( 20) covalent geometry : bond 0.00243 ( 6928) covalent geometry : angle 0.50691 ( 9404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 501 ASN cc_start: 0.8057 (t0) cc_final: 0.7811 (t0) REVERT: H 82 MET cc_start: 0.7500 (mtm) cc_final: 0.7268 (mtp) REVERT: L 4 MET cc_start: 0.6714 (tpp) cc_final: 0.6371 (mmm) REVERT: D 79 TYR cc_start: 0.7588 (m-10) cc_final: 0.7177 (m-10) REVERT: D 81 GLN cc_start: 0.7540 (tp40) cc_final: 0.7097 (tt0) outliers start: 27 outliers final: 23 residues processed: 145 average time/residue: 0.1800 time to fit residues: 35.0780 Evaluate side-chains 151 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.0030 chunk 32 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.3528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.138651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.122707 restraints weight = 9721.436| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.62 r_work: 0.3534 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6940 Z= 0.107 Angle : 0.513 8.153 9430 Z= 0.269 Chirality : 0.040 0.141 1016 Planarity : 0.005 0.055 1209 Dihedral : 4.400 26.849 1013 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.40 % Favored : 93.37 % Rotamer: Outliers : 3.57 % Allowed : 19.78 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.81 (0.29), residues: 860 helix: -5.45 (0.34), residues: 6 sheet: -0.23 (0.30), residues: 306 loop : -0.63 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 52 HIS 0.003 0.001 HIS D 94 PHE 0.011 0.001 PHE A 107 TYR 0.013 0.001 TYR H 105 ARG 0.006 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 1) link_NAG-ASN : angle 0.84885 ( 3) link_BETA1-4 : bond 0.00445 ( 1) link_BETA1-4 : angle 0.81250 ( 3) hydrogen bonds : bond 0.02940 ( 199) hydrogen bonds : angle 5.45361 ( 567) SS BOND : bond 0.00359 ( 10) SS BOND : angle 0.86335 ( 20) covalent geometry : bond 0.00242 ( 6928) covalent geometry : angle 0.51181 ( 9404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7495 (p) REVERT: E 501 ASN cc_start: 0.8048 (t0) cc_final: 0.7822 (t0) REVERT: H 82 MET cc_start: 0.7526 (mtm) cc_final: 0.7285 (mtp) REVERT: L 4 MET cc_start: 0.6701 (tpp) cc_final: 0.6318 (mmm) REVERT: D 79 TYR cc_start: 0.7510 (m-10) cc_final: 0.7069 (m-10) REVERT: D 81 GLN cc_start: 0.7538 (tp40) cc_final: 0.7089 (tt0) outliers start: 26 outliers final: 24 residues processed: 143 average time/residue: 0.1716 time to fit residues: 33.0396 Evaluate side-chains 151 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 0.0270 chunk 8 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.123981 restraints weight = 9766.590| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.63 r_work: 0.3525 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6940 Z= 0.125 Angle : 0.518 7.315 9430 Z= 0.273 Chirality : 0.040 0.139 1016 Planarity : 0.005 0.055 1209 Dihedral : 4.421 26.998 1013 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.63 % Favored : 93.14 % Rotamer: Outliers : 3.57 % Allowed : 20.05 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.80 (0.29), residues: 860 helix: -5.45 (0.34), residues: 6 sheet: -0.22 (0.30), residues: 306 loop : -0.62 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 52 HIS 0.004 0.001 HIS D 94 PHE 0.013 0.001 PHE A 107 TYR 0.016 0.001 TYR H 105 ARG 0.007 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 1) link_NAG-ASN : angle 0.96753 ( 3) link_BETA1-4 : bond 0.00372 ( 1) link_BETA1-4 : angle 0.81862 ( 3) hydrogen bonds : bond 0.02997 ( 199) hydrogen bonds : angle 5.42365 ( 567) SS BOND : bond 0.00405 ( 10) SS BOND : angle 0.90573 ( 20) covalent geometry : bond 0.00286 ( 6928) covalent geometry : angle 0.51684 ( 9404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7510 (p) REVERT: E 501 ASN cc_start: 0.8048 (t0) cc_final: 0.7787 (t0) REVERT: H 82 MET cc_start: 0.7524 (mtm) cc_final: 0.7282 (mtp) REVERT: L 4 MET cc_start: 0.6728 (tpp) cc_final: 0.6316 (mmm) REVERT: D 79 TYR cc_start: 0.7537 (m-10) cc_final: 0.7122 (m-10) REVERT: D 81 GLN cc_start: 0.7536 (tp40) cc_final: 0.7091 (tt0) outliers start: 26 outliers final: 25 residues processed: 149 average time/residue: 0.1696 time to fit residues: 34.3164 Evaluate side-chains 161 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 10 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.136525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.120811 restraints weight = 9892.019| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.51 r_work: 0.3512 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6940 Z= 0.170 Angle : 0.550 6.902 9430 Z= 0.291 Chirality : 0.041 0.139 1016 Planarity : 0.005 0.055 1209 Dihedral : 4.668 28.824 1013 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.56 % Favored : 92.21 % Rotamer: Outliers : 4.26 % Allowed : 19.09 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.91 (0.29), residues: 860 helix: -5.47 (0.34), residues: 6 sheet: -0.29 (0.30), residues: 314 loop : -0.71 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 36 HIS 0.005 0.001 HIS D 94 PHE 0.016 0.002 PHE A 107 TYR 0.020 0.002 TYR H 105 ARG 0.008 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 1) link_NAG-ASN : angle 1.20401 ( 3) link_BETA1-4 : bond 0.00363 ( 1) link_BETA1-4 : angle 0.85965 ( 3) hydrogen bonds : bond 0.03310 ( 199) hydrogen bonds : angle 5.60605 ( 567) SS BOND : bond 0.00520 ( 10) SS BOND : angle 1.11482 ( 20) covalent geometry : bond 0.00387 ( 6928) covalent geometry : angle 0.54726 ( 9404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7620 (p) REVERT: E 423 TYR cc_start: 0.7491 (t80) cc_final: 0.7140 (t80) REVERT: E 501 ASN cc_start: 0.8206 (t0) cc_final: 0.7987 (t0) REVERT: D 32 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8345 (m110) REVERT: D 81 GLN cc_start: 0.7611 (tp40) cc_final: 0.7176 (tt0) outliers start: 31 outliers final: 26 residues processed: 151 average time/residue: 0.1689 time to fit residues: 35.2799 Evaluate side-chains 161 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 19 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 0.0370 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.137961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121971 restraints weight = 9808.934| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.62 r_work: 0.3532 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6940 Z= 0.117 Angle : 0.529 6.879 9430 Z= 0.278 Chirality : 0.041 0.144 1016 Planarity : 0.005 0.056 1209 Dihedral : 4.475 27.547 1013 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.51 % Favored : 93.26 % Rotamer: Outliers : 3.57 % Allowed : 20.05 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.87 (0.29), residues: 860 helix: -4.68 (0.73), residues: 8 sheet: -0.26 (0.30), residues: 313 loop : -0.67 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 HIS 0.004 0.001 HIS D 94 PHE 0.012 0.001 PHE A 107 TYR 0.013 0.001 TYR H 105 ARG 0.009 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 1) link_NAG-ASN : angle 0.90055 ( 3) link_BETA1-4 : bond 0.00466 ( 1) link_BETA1-4 : angle 0.86599 ( 3) hydrogen bonds : bond 0.02940 ( 199) hydrogen bonds : angle 5.45372 ( 567) SS BOND : bond 0.00407 ( 10) SS BOND : angle 1.04934 ( 20) covalent geometry : bond 0.00269 ( 6928) covalent geometry : angle 0.52753 ( 9404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7519 (p) REVERT: E 501 ASN cc_start: 0.8049 (t0) cc_final: 0.7815 (t0) REVERT: L 4 MET cc_start: 0.6896 (mmm) cc_final: 0.6622 (mmm) REVERT: D 79 TYR cc_start: 0.7547 (m-10) cc_final: 0.7165 (m-10) REVERT: D 81 GLN cc_start: 0.7535 (tp40) cc_final: 0.7104 (tt0) outliers start: 26 outliers final: 23 residues processed: 143 average time/residue: 0.1638 time to fit residues: 32.4378 Evaluate side-chains 153 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 62 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.136049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119884 restraints weight = 9944.542| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.65 r_work: 0.3493 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6940 Z= 0.187 Angle : 0.564 6.652 9430 Z= 0.299 Chirality : 0.041 0.145 1016 Planarity : 0.005 0.055 1209 Dihedral : 4.726 29.503 1013 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.67 % Favored : 92.09 % Rotamer: Outliers : 3.30 % Allowed : 20.74 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.99 (0.28), residues: 860 helix: -4.42 (0.97), residues: 8 sheet: -0.34 (0.30), residues: 314 loop : -0.76 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 36 HIS 0.005 0.002 HIS D 94 PHE 0.017 0.002 PHE A 107 TYR 0.019 0.002 TYR H 105 ARG 0.009 0.001 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 1) link_NAG-ASN : angle 1.22175 ( 3) link_BETA1-4 : bond 0.00302 ( 1) link_BETA1-4 : angle 0.87326 ( 3) hydrogen bonds : bond 0.03350 ( 199) hydrogen bonds : angle 5.67179 ( 567) SS BOND : bond 0.00539 ( 10) SS BOND : angle 1.33519 ( 20) covalent geometry : bond 0.00426 ( 6928) covalent geometry : angle 0.56070 ( 9404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7559 (p) REVERT: E 423 TYR cc_start: 0.7359 (t80) cc_final: 0.6985 (t80) REVERT: E 501 ASN cc_start: 0.8104 (t0) cc_final: 0.7863 (t0) REVERT: D 81 GLN cc_start: 0.7569 (tp40) cc_final: 0.7115 (tt0) outliers start: 24 outliers final: 22 residues processed: 140 average time/residue: 0.1621 time to fit residues: 31.2060 Evaluate side-chains 150 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120427 restraints weight = 9908.087| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.52 r_work: 0.3503 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6940 Z= 0.182 Angle : 0.561 6.613 9430 Z= 0.298 Chirality : 0.041 0.147 1016 Planarity : 0.005 0.055 1209 Dihedral : 4.756 29.166 1013 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.09 % Favored : 92.67 % Rotamer: Outliers : 3.57 % Allowed : 20.19 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 (0.28), residues: 860 helix: -4.47 (0.89), residues: 8 sheet: -0.33 (0.30), residues: 313 loop : -0.85 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 36 HIS 0.005 0.002 HIS D 94 PHE 0.017 0.002 PHE A 107 TYR 0.019 0.002 TYR H 105 ARG 0.009 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 1) link_NAG-ASN : angle 1.11547 ( 3) link_BETA1-4 : bond 0.00336 ( 1) link_BETA1-4 : angle 0.87117 ( 3) hydrogen bonds : bond 0.03308 ( 199) hydrogen bonds : angle 5.68472 ( 567) SS BOND : bond 0.00603 ( 10) SS BOND : angle 1.24146 ( 20) covalent geometry : bond 0.00415 ( 6928) covalent geometry : angle 0.55823 ( 9404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4721.34 seconds wall clock time: 84 minutes 31.08 seconds (5071.08 seconds total)