Starting phenix.real_space_refine on Fri Dec 8 07:08:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/12_2023/6vcc_21148.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/12_2023/6vcc_21148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/12_2023/6vcc_21148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/12_2023/6vcc_21148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/12_2023/6vcc_21148.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/12_2023/6vcc_21148.pdb" } resolution = 3.6 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4896 2.51 5 N 1236 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L GLU 23": "OE1" <-> "OE2" Residue "L GLU 24": "OE1" <-> "OE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7572 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "B" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "C" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "D" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "E" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "F" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "H" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "I" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "J" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "K" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "L" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Time building chain proxies: 4.53, per 1000 atoms: 0.60 Number of scatterers: 7572 At special positions: 0 Unit cell: (90, 92, 132, 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 24 16.00 O 1416 8.00 N 1236 7.00 C 4896 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.4 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 15.7% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.620A pdb=" N PHE A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.655A pdb=" N GLY A 83 " --> pdb=" O CYS A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 46 removed outlier: 3.636A pdb=" N PHE B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 46 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.765A pdb=" N GLY B 83 " --> pdb=" O CYS B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 46 removed outlier: 3.750A pdb=" N PHE C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 46 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.609A pdb=" N GLY C 83 " --> pdb=" O CYS C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 46 removed outlier: 3.663A pdb=" N PHE D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.757A pdb=" N PHE E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 46 removed outlier: 3.587A pdb=" N PHE F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.598A pdb=" N GLY F 83 " --> pdb=" O CYS F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 48 removed outlier: 3.867A pdb=" N VAL G 46 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 47 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.800A pdb=" N GLY G 83 " --> pdb=" O CYS G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 48 removed outlier: 3.946A pdb=" N VAL H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU H 47 " --> pdb=" O PHE H 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.529A pdb=" N GLY H 83 " --> pdb=" O CYS H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.575A pdb=" N GLY I 83 " --> pdb=" O CYS I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 48 removed outlier: 3.921A pdb=" N VAL J 46 " --> pdb=" O ASP J 42 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU J 47 " --> pdb=" O PHE J 43 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN J 48 " --> pdb=" O LYS J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.527A pdb=" N GLY J 83 " --> pdb=" O CYS J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 45 Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.559A pdb=" N GLY K 83 " --> pdb=" O CYS K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 48 removed outlier: 3.895A pdb=" N VAL L 46 " --> pdb=" O ASP L 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU L 47 " --> pdb=" O PHE L 43 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70 removed outlier: 5.164A pdb=" N VAL A 86 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N SER A 87 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 17 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 89 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 28 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 18 removed outlier: 6.963A pdb=" N LEU B 28 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.940A pdb=" N LEU C 28 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL D 86 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N SER D 87 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE D 17 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 18 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU D 28 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL E 86 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER E 87 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 17 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 18 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU E 28 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL F 86 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N SER F 87 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE F 17 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 14 through 18 removed outlier: 3.543A pdb=" N THR G 14 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL G 29 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 87 through 89 removed outlier: 4.586A pdb=" N LYS H 30 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 17 through 18 removed outlier: 6.794A pdb=" N ILE H 17 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU H 89 " --> pdb=" O ILE H 17 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL H 86 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS I 30 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR I 18 " --> pdb=" O TYR I 27 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR I 14 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER I 87 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE I 17 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU I 89 " --> pdb=" O ILE I 17 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL I 86 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS J 30 " --> pdb=" O GLU I 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 17 through 18 removed outlier: 6.863A pdb=" N ILE J 17 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU J 89 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL J 86 " --> pdb=" O LYS J 58 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS K 30 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR K 18 " --> pdb=" O TYR K 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR K 14 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER K 87 " --> pdb=" O LYS K 15 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE K 17 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU K 89 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL K 86 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS L 30 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR L 14 " --> pdb=" O ILE L 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 17 through 18 removed outlier: 6.658A pdb=" N ILE L 17 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU L 89 " --> pdb=" O ILE L 17 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL L 86 " --> pdb=" O LYS L 58 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 489 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: 1.81 Time building geometry restraints manager: 2.89 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: 2431 1.34 - 1.46: 1687 1.46 - 1.58: 3598 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 7752 Sorted by residual: bond pdb=" N LYS L 54 " pdb=" CA LYS L 54 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.23e-02 6.61e+03 3.96e+00 bond pdb=" N GLN F 48 " pdb=" CA GLN F 48 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.54e-02 4.22e+03 2.06e+00 bond pdb=" C VAL A 33 " pdb=" N PRO A 34 " ideal model delta sigma weight residual 1.326 1.345 -0.019 1.44e-02 4.82e+03 1.73e+00 bond pdb=" C VAL B 33 " pdb=" N PRO B 34 " ideal model delta sigma weight residual 1.326 1.344 -0.018 1.44e-02 4.82e+03 1.51e+00 bond pdb=" CA GLN F 48 " pdb=" CB GLN F 48 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.70e-02 3.46e+03 1.24e+00 ... (remaining 7747 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.28: 320 107.28 - 113.95: 4183 113.95 - 120.63: 3075 120.63 - 127.30: 2853 127.30 - 133.98: 69 Bond angle restraints: 10500 Sorted by residual: angle pdb=" C LEU F 47 " pdb=" N GLN F 48 " pdb=" CA GLN F 48 " ideal model delta sigma weight residual 122.46 127.44 -4.98 1.41e+00 5.03e-01 1.25e+01 angle pdb=" CA GLN F 48 " pdb=" CB GLN F 48 " pdb=" CG GLN F 48 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.50e+00 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 106.55 110.06 -3.51 1.45e+00 4.76e-01 5.86e+00 angle pdb=" C LEU H 89 " pdb=" N VAL H 90 " pdb=" CA VAL H 90 " ideal model delta sigma weight residual 121.70 125.73 -4.03 1.80e+00 3.09e-01 5.01e+00 angle pdb=" C LEU J 89 " pdb=" N VAL J 90 " pdb=" CA VAL J 90 " ideal model delta sigma weight residual 121.70 125.70 -4.00 1.80e+00 3.09e-01 4.94e+00 ... (remaining 10495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4277 17.65 - 35.30: 347 35.30 - 52.95: 47 52.95 - 70.60: 4 70.60 - 88.24: 5 Dihedral angle restraints: 4680 sinusoidal: 1944 harmonic: 2736 Sorted by residual: dihedral pdb=" CB GLU H 24 " pdb=" CG GLU H 24 " pdb=" CD GLU H 24 " pdb=" OE1 GLU H 24 " ideal model delta sinusoidal sigma weight residual 0.00 88.24 -88.24 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU I 24 " pdb=" CG GLU I 24 " pdb=" CD GLU I 24 " pdb=" OE1 GLU I 24 " ideal model delta sinusoidal sigma weight residual 0.00 88.11 -88.11 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA ASP D 61 " pdb=" CB ASP D 61 " pdb=" CG ASP D 61 " pdb=" OD1 ASP D 61 " ideal model delta sinusoidal sigma weight residual -30.00 -80.47 50.47 1 2.00e+01 2.50e-03 8.72e+00 ... (remaining 4677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 684 0.039 - 0.078: 292 0.078 - 0.118: 135 0.118 - 0.157: 31 0.157 - 0.196: 10 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CB ILE F 38 " pdb=" CA ILE F 38 " pdb=" CG1 ILE F 38 " pdb=" CG2 ILE F 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CB ILE A 38 " pdb=" CA ILE A 38 " pdb=" CG1 ILE A 38 " pdb=" CG2 ILE A 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CB ILE E 38 " pdb=" CA ILE E 38 " pdb=" CG1 ILE E 38 " pdb=" CG2 ILE E 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.23e-01 ... (remaining 1149 not shown) Planarity restraints: 1356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 33 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO C 34 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 33 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO H 34 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 34 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 34 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 77 " 0.108 9.50e-02 1.11e+02 5.00e-02 3.19e+00 pdb=" NE ARG H 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG H 77 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG H 77 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 77 " 0.012 2.00e-02 2.50e+03 ... (remaining 1353 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1573 2.78 - 3.31: 6085 3.31 - 3.84: 12354 3.84 - 4.37: 13207 4.37 - 4.90: 24311 Nonbonded interactions: 57530 Sorted by model distance: nonbonded pdb=" ND2 ASN D 82 " pdb=" OD1 ASP I 63 " model vdw 2.253 2.520 nonbonded pdb=" OD1 ASP E 63 " pdb=" ND2 ASN J 82 " model vdw 2.273 2.520 nonbonded pdb=" OD1 ASP D 63 " pdb=" ND2 ASN I 82 " model vdw 2.425 2.520 nonbonded pdb=" ND2 ASN E 82 " pdb=" OD1 ASP J 63 " model vdw 2.433 2.520 nonbonded pdb=" OD1 ASP B 63 " pdb=" ND2 ASN G 82 " model vdw 2.442 2.520 ... (remaining 57525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.170 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: 1.190 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.660 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 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 : 0.004 0.036 7752 Z= 0.236 Angle : 0.664 6.330 10500 Z= 0.376 Chirality : 0.054 0.196 1152 Planarity : 0.006 0.050 1356 Dihedral : 12.504 88.244 2904 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.24), residues: 912 helix: -3.99 (0.12), residues: 72 sheet: -3.22 (0.23), residues: 360 loop : -2.61 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 88 HIS 0.004 0.002 HIS J 19 PHE 0.008 0.001 PHE E 64 TYR 0.015 0.002 TYR D 18 ARG 0.023 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2520 time to fit residues: 72.1923 Evaluate side-chains 182 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.0060 chunk 65 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN G 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7752 Z= 0.303 Angle : 0.635 8.814 10500 Z= 0.311 Chirality : 0.050 0.189 1152 Planarity : 0.005 0.055 1356 Dihedral : 4.232 12.547 1008 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.81 % Allowed : 15.36 % Favored : 80.83 % 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: -3.93 (0.25), residues: 912 helix: -1.34 (0.42), residues: 72 sheet: -3.11 (0.23), residues: 360 loop : -2.33 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 88 HIS 0.005 0.002 HIS F 19 PHE 0.017 0.002 PHE E 43 TYR 0.016 0.002 TYR A 27 ARG 0.004 0.000 ARG L 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 217 average time/residue: 0.2517 time to fit residues: 68.8980 Evaluate side-chains 195 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0703 time to fit residues: 3.7631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7752 Z= 0.287 Angle : 0.601 8.716 10500 Z= 0.295 Chirality : 0.051 0.167 1152 Planarity : 0.005 0.048 1356 Dihedral : 4.379 14.306 1008 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.62 % Allowed : 19.40 % Favored : 77.98 % 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: -3.46 (0.26), residues: 912 helix: 0.09 (0.57), residues: 84 sheet: -2.91 (0.24), residues: 360 loop : -2.15 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 88 HIS 0.005 0.002 HIS D 19 PHE 0.013 0.002 PHE G 57 TYR 0.013 0.002 TYR A 27 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 206 average time/residue: 0.2516 time to fit residues: 65.5089 Evaluate side-chains 199 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0698 time to fit residues: 3.0079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 0.0980 chunk 21 optimal weight: 10.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7752 Z= 0.352 Angle : 0.634 9.605 10500 Z= 0.309 Chirality : 0.051 0.186 1152 Planarity : 0.005 0.051 1356 Dihedral : 4.599 14.244 1008 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.50 % Allowed : 20.71 % Favored : 76.79 % 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: -3.26 (0.27), residues: 912 helix: 0.78 (0.65), residues: 84 sheet: -2.90 (0.24), residues: 360 loop : -2.02 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 88 HIS 0.005 0.002 HIS D 19 PHE 0.019 0.002 PHE L 43 TYR 0.013 0.002 TYR B 27 ARG 0.005 0.000 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 0.923 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 211 average time/residue: 0.2516 time to fit residues: 66.9170 Evaluate side-chains 205 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0678 time to fit residues: 2.9987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7752 Z= 0.293 Angle : 0.618 9.483 10500 Z= 0.301 Chirality : 0.051 0.145 1152 Planarity : 0.005 0.050 1356 Dihedral : 4.479 14.144 1008 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.86 % Allowed : 21.07 % Favored : 76.07 % 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: -2.96 (0.27), residues: 912 helix: 1.17 (0.66), residues: 84 sheet: -2.62 (0.25), residues: 348 loop : -1.98 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 88 HIS 0.004 0.002 HIS I 19 PHE 0.022 0.002 PHE L 64 TYR 0.012 0.001 TYR A 27 ARG 0.003 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 0.874 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 206 average time/residue: 0.2416 time to fit residues: 63.8599 Evaluate side-chains 205 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0791 time to fit residues: 3.7155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 10.0000 chunk 73 optimal weight: 0.3980 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7752 Z= 0.371 Angle : 0.665 10.347 10500 Z= 0.325 Chirality : 0.052 0.168 1152 Planarity : 0.005 0.053 1356 Dihedral : 4.662 16.432 1008 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.50 % Allowed : 22.26 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.27), residues: 912 helix: 1.04 (0.64), residues: 84 sheet: -2.60 (0.25), residues: 348 loop : -1.98 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 88 HIS 0.005 0.002 HIS F 19 PHE 0.018 0.002 PHE I 64 TYR 0.013 0.002 TYR A 27 ARG 0.003 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 0.920 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 206 average time/residue: 0.2519 time to fit residues: 65.3658 Evaluate side-chains 193 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0664 time to fit residues: 2.2363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7752 Z= 0.209 Angle : 0.597 9.525 10500 Z= 0.287 Chirality : 0.050 0.135 1152 Planarity : 0.005 0.051 1356 Dihedral : 4.327 14.788 1008 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.19 % Allowed : 24.17 % Favored : 74.64 % 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: -2.67 (0.28), residues: 912 helix: 1.47 (0.65), residues: 84 sheet: -2.40 (0.26), residues: 348 loop : -1.82 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 88 HIS 0.003 0.001 HIS F 19 PHE 0.021 0.002 PHE I 64 TYR 0.011 0.001 TYR B 27 ARG 0.003 0.000 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 0.979 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 198 average time/residue: 0.2362 time to fit residues: 59.6301 Evaluate side-chains 193 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0735 time to fit residues: 2.1785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7752 Z= 0.332 Angle : 0.663 10.442 10500 Z= 0.317 Chirality : 0.052 0.161 1152 Planarity : 0.005 0.055 1356 Dihedral : 4.625 16.186 1008 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.02 % Allowed : 23.21 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.28), residues: 912 helix: 1.33 (0.63), residues: 84 sheet: -2.23 (0.25), residues: 384 loop : -1.88 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 88 HIS 0.004 0.002 HIS F 19 PHE 0.019 0.002 PHE I 64 TYR 0.014 0.002 TYR A 27 ARG 0.008 0.000 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 0.810 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 201 average time/residue: 0.2476 time to fit residues: 62.7372 Evaluate side-chains 199 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0652 time to fit residues: 2.5415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN E 19 HIS ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7752 Z= 0.164 Angle : 0.594 9.698 10500 Z= 0.282 Chirality : 0.050 0.136 1152 Planarity : 0.004 0.050 1356 Dihedral : 4.211 15.575 1008 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.07 % Allowed : 23.81 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.29), residues: 912 helix: 1.79 (0.65), residues: 84 sheet: -2.06 (0.25), residues: 384 loop : -1.68 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 88 HIS 0.002 0.001 HIS J 19 PHE 0.022 0.001 PHE I 64 TYR 0.009 0.001 TYR A 27 ARG 0.007 0.000 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 0.898 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 194 average time/residue: 0.2498 time to fit residues: 61.4758 Evaluate side-chains 192 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1224 time to fit residues: 2.3634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 0.0050 chunk 77 optimal weight: 7.9990 chunk 66 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 52 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7752 Z= 0.137 Angle : 0.568 9.486 10500 Z= 0.270 Chirality : 0.049 0.136 1152 Planarity : 0.004 0.053 1356 Dihedral : 3.889 15.748 1008 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.12 % Allowed : 25.71 % Favored : 74.17 % 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: -2.10 (0.29), residues: 912 helix: 1.91 (0.64), residues: 84 sheet: -1.89 (0.25), residues: 384 loop : -1.48 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 88 HIS 0.002 0.001 HIS F 19 PHE 0.019 0.001 PHE I 64 TYR 0.008 0.001 TYR A 27 ARG 0.007 0.000 ARG D 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 0.969 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 196 average time/residue: 0.2459 time to fit residues: 61.3960 Evaluate side-chains 182 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0657 time to fit residues: 1.2340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.0030 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 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 = 0.4187 r_free = 0.4187 target = 0.197300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.165544 restraints weight = 7407.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168564 restraints weight = 5723.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.171243 restraints weight = 4781.544| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7752 Z= 0.148 Angle : 0.578 10.668 10500 Z= 0.273 Chirality : 0.049 0.131 1152 Planarity : 0.004 0.052 1356 Dihedral : 3.812 14.592 1008 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 27.74 % Favored : 72.26 % 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: -1.97 (0.29), residues: 912 helix: 1.96 (0.64), residues: 84 sheet: -1.80 (0.25), residues: 384 loop : -1.38 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 88 HIS 0.003 0.001 HIS F 19 PHE 0.021 0.001 PHE I 64 TYR 0.009 0.001 TYR A 27 ARG 0.004 0.000 ARG L 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1887.00 seconds wall clock time: 34 minutes 40.65 seconds (2080.65 seconds total)