Starting phenix.real_space_refine on Fri Feb 16 19:50:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njx_12426/02_2024/7njx_12426.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njx_12426/02_2024/7njx_12426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njx_12426/02_2024/7njx_12426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njx_12426/02_2024/7njx_12426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njx_12426/02_2024/7njx_12426.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njx_12426/02_2024/7njx_12426.pdb" } resolution = 4.32 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= 0.001 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: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 5346 2.51 5 N 1316 2.21 5 O 1399 1.98 5 H 8337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 65": "OE1" <-> "OE2" Residue "Q TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 48": "OE1" <-> "OE2" Residue "T GLU 65": "OE1" <-> "OE2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16426 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 979 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "d" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 952 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Time building chain proxies: 6.97, per 1000 atoms: 0.42 Number of scatterers: 16426 At special positions: 0 Unit cell: (93.79, 81.34, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 O 1399 8.00 N 1316 7.00 C 5346 6.00 H 8337 1.00 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: 13.17 Conformation dependent library (CDL) restraints added in 1.9 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 87.9% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.657A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 50 Processing helix chain 'L' and resid 51 through 52 No H-bonds generated for 'chain 'L' and resid 51 through 52' Processing helix chain 'L' and resid 53 through 81 removed outlier: 3.986A pdb=" N PHE L 57 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE L 58 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE L 59 " --> pdb=" O THR L 55 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 Processing helix chain 'M' and resid 49 through 81 removed outlier: 3.603A pdb=" N PHE M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.655A pdb=" N ILE M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.828A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 81 removed outlier: 3.991A pdb=" N PHE N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.629A pdb=" N TYR N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.624A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 78 removed outlier: 4.788A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.714A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.833A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 80 removed outlier: 4.537A pdb=" N ARG P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.775A pdb=" N ILE P 59 " --> pdb=" O THR P 55 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.503A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 80 removed outlier: 4.999A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 3.606A pdb=" N LEU Q 63 " --> pdb=" O ILE Q 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 46 removed outlier: 4.043A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 78 removed outlier: 3.800A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.994A pdb=" N GLY R 62 " --> pdb=" O PHE R 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 46 removed outlier: 3.563A pdb=" N ILE S 8 " --> pdb=" O ASP S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 81 removed outlier: 4.519A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.507A pdb=" N ASN S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.730A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 82 removed outlier: 3.888A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 4.946A pdb=" N ALA T 66 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR T 68 " --> pdb=" O VAL T 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 53 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.845A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 165 removed outlier: 3.972A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE a 155 " --> pdb=" O TRP a 151 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N VAL a 156 " --> pdb=" O ARG a 152 " (cutoff:3.500A) Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 204 removed outlier: 3.552A pdb=" N ILE a 175 " --> pdb=" O ALA a 171 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 4.174A pdb=" N ARG a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 244 removed outlier: 6.100A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix Processing helix chain 'b' and resid 29 through 49 removed outlier: 4.490A pdb=" N LEU b 35 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 84 Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 61 removed outlier: 3.900A pdb=" N VAL d 26 " --> pdb=" O VAL d 22 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 19 through 22 Processing sheet with id=AA2, first strand: chain 'a' and resid 113 through 114 removed outlier: 3.505A pdb=" N TYR a 113 " --> pdb=" O ALA a 121 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA a 121 " --> pdb=" O TYR a 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 780 hydrogen bonds defined for protein. 2331 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: 5.67 Time building geometry restraints manager: 13.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8336 1.03 - 1.23: 2 1.23 - 1.42: 3358 1.42 - 1.62: 4843 1.62 - 1.81: 55 Bond restraints: 16594 Sorted by residual: bond pdb=" CG1 ILE L 30 " pdb=" CD1 ILE L 30 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CG1 ILE P 26 " pdb=" CD1 ILE P 26 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.29e-01 bond pdb=" CG1 ILE S 15 " pdb=" CD1 ILE S 15 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.76e-01 bond pdb=" CG1 ILE T 15 " pdb=" CD1 ILE T 15 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.60e-01 bond pdb=" CG1 ILE Q 26 " pdb=" CD1 ILE Q 26 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.52e-01 ... (remaining 16589 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.84: 191 105.84 - 112.87: 19580 112.87 - 119.91: 4377 119.91 - 126.94: 5891 126.94 - 133.98: 77 Bond angle restraints: 30116 Sorted by residual: angle pdb=" N VAL R 79 " pdb=" CA VAL R 79 " pdb=" C VAL R 79 " ideal model delta sigma weight residual 113.71 110.83 2.88 9.50e-01 1.11e+00 9.18e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 118.86 -4.96 1.80e+00 3.09e-01 7.59e+00 angle pdb=" CB MET N 21 " pdb=" CG MET N 21 " pdb=" SD MET N 21 " ideal model delta sigma weight residual 112.70 119.76 -7.06 3.00e+00 1.11e-01 5.53e+00 angle pdb=" CA PHE a 213 " pdb=" C PHE a 213 " pdb=" N PRO a 214 " ideal model delta sigma weight residual 120.58 118.92 1.66 7.40e-01 1.83e+00 5.01e+00 angle pdb=" C PHE L 69 " pdb=" N ILE L 70 " pdb=" CA ILE L 70 " ideal model delta sigma weight residual 120.46 117.49 2.97 1.37e+00 5.33e-01 4.71e+00 ... (remaining 30111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 6667 16.75 - 33.50: 626 33.50 - 50.25: 226 50.25 - 67.01: 226 67.01 - 83.76: 14 Dihedral angle restraints: 7759 sinusoidal: 4150 harmonic: 3609 Sorted by residual: dihedral pdb=" CA ASN a 192 " pdb=" CB ASN a 192 " pdb=" CG ASN a 192 " pdb=" OD1 ASN a 192 " ideal model delta sinusoidal sigma weight residual 120.00 -170.68 -69.32 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" N ALA T 25 " pdb=" CA ALA T 25 " pdb=" CB ALA T 25 " pdb=" HB3 ALA T 25 " ideal model delta sinusoidal sigma weight residual 180.00 127.39 52.61 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CA ALA a 186 " pdb=" C ALA a 186 " pdb=" N LEU a 187 " pdb=" CA LEU a 187 " ideal model delta harmonic sigma weight residual 180.00 -164.90 -15.10 0 5.00e+00 4.00e-02 9.12e+00 ... (remaining 7756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 798 0.026 - 0.051: 275 0.051 - 0.077: 145 0.077 - 0.102: 85 0.102 - 0.128: 19 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA ILE b 26 " pdb=" N ILE b 26 " pdb=" C ILE b 26 " pdb=" CB ILE b 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE M 20 " pdb=" N ILE M 20 " pdb=" C ILE M 20 " pdb=" CB ILE M 20 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE Q 26 " pdb=" N ILE Q 26 " pdb=" C ILE Q 26 " pdb=" CB ILE Q 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 1319 not shown) Planarity restraints: 2495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR L 68 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C TYR L 68 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR L 68 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE L 69 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 70 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ILE L 70 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE L 70 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN L 71 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 40 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ILE b 40 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE b 40 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL b 41 " 0.008 2.00e-02 2.50e+03 ... (remaining 2492 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1559 2.22 - 2.81: 36132 2.81 - 3.41: 48699 3.41 - 4.00: 60488 4.00 - 4.60: 94682 Nonbonded interactions: 241560 Sorted by model distance: nonbonded pdb=" O PHE T 78 " pdb=" HG1 THR T 82 " model vdw 1.622 1.850 nonbonded pdb=" O PHE S 78 " pdb=" HG1 THR S 82 " model vdw 1.627 1.850 nonbonded pdb=" O PHE P 78 " pdb=" HG1 THR P 82 " model vdw 1.637 1.850 nonbonded pdb=" O MET d 1 " pdb=" H ILE d 5 " model vdw 1.639 1.850 nonbonded pdb=" O PHE R 54 " pdb=" H PHE R 58 " model vdw 1.647 1.850 ... (remaining 241555 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 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 6.690 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: 0.290 Extract box with map and model: 25.510 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 53.170 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8257 Z= 0.198 Angle : 0.519 7.056 11218 Z= 0.289 Chirality : 0.039 0.128 1322 Planarity : 0.004 0.033 1440 Dihedral : 14.389 83.757 2789 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 1.56 (0.26), residues: 1094 helix: 1.31 (0.18), residues: 851 sheet: None (None), residues: 0 loop : 0.32 (0.46), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.015 0.001 PHE a 47 TYR 0.018 0.001 TYR a 145 ARG 0.003 0.000 ARG S 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 21 MET cc_start: 0.7487 (tmm) cc_final: 0.7243 (tmm) REVERT: O 75 MET cc_start: 0.7986 (tmm) cc_final: 0.7752 (tmm) REVERT: P 63 LEU cc_start: 0.9201 (tp) cc_final: 0.8884 (tp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3054 time to fit residues: 51.0235 Evaluate side-chains 89 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8257 Z= 0.228 Angle : 0.533 5.738 11218 Z= 0.296 Chirality : 0.040 0.124 1322 Planarity : 0.004 0.026 1440 Dihedral : 3.539 15.672 1149 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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 (0.25), residues: 1094 helix: 2.18 (0.17), residues: 852 sheet: None (None), residues: 0 loop : 0.40 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.014 0.001 PHE a 140 TYR 0.024 0.002 TYR a 145 ARG 0.003 0.000 ARG S 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 21 MET cc_start: 0.7613 (tmm) cc_final: 0.7383 (tmm) REVERT: O 75 MET cc_start: 0.8308 (tmm) cc_final: 0.7921 (tmm) REVERT: P 63 LEU cc_start: 0.9070 (tp) cc_final: 0.8778 (tp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3078 time to fit residues: 52.1266 Evaluate side-chains 87 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8257 Z= 0.226 Angle : 0.535 5.257 11218 Z= 0.292 Chirality : 0.040 0.123 1322 Planarity : 0.004 0.026 1440 Dihedral : 3.613 15.098 1149 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: 3.13 (0.25), residues: 1094 helix: 2.54 (0.16), residues: 852 sheet: None (None), residues: 0 loop : 0.41 (0.46), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.020 0.001 PHE a 241 TYR 0.020 0.001 TYR a 145 ARG 0.002 0.000 ARG M 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 75 MET cc_start: 0.8373 (tmm) cc_final: 0.8021 (tmm) REVERT: P 63 LEU cc_start: 0.9054 (tp) cc_final: 0.8776 (tp) REVERT: Q 21 MET cc_start: 0.8418 (ppp) cc_final: 0.8056 (ppp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3014 time to fit residues: 52.3717 Evaluate side-chains 88 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 211 GLN d 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8257 Z= 0.256 Angle : 0.549 6.727 11218 Z= 0.306 Chirality : 0.040 0.135 1322 Planarity : 0.004 0.027 1440 Dihedral : 3.706 15.013 1149 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 3.06 (0.25), residues: 1094 helix: 2.52 (0.16), residues: 851 sheet: None (None), residues: 0 loop : 0.25 (0.45), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.023 0.001 PHE N 58 TYR 0.013 0.001 TYR S 68 ARG 0.002 0.000 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8362 (tmm) cc_final: 0.8085 (tmm) REVERT: O 21 MET cc_start: 0.7822 (tmm) cc_final: 0.7576 (tmm) REVERT: O 75 MET cc_start: 0.8411 (tmm) cc_final: 0.8105 (tmm) REVERT: P 63 LEU cc_start: 0.9091 (tp) cc_final: 0.8816 (tp) REVERT: Q 21 MET cc_start: 0.8434 (ppp) cc_final: 0.8216 (ppp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3459 time to fit residues: 59.3098 Evaluate side-chains 86 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 71 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 92 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8257 Z= 0.210 Angle : 0.521 5.516 11218 Z= 0.282 Chirality : 0.039 0.135 1322 Planarity : 0.003 0.030 1440 Dihedral : 3.632 14.749 1149 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: 3.42 (0.25), residues: 1094 helix: 2.78 (0.16), residues: 851 sheet: None (None), residues: 0 loop : 0.36 (0.45), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.004 0.001 HIS a 146 PHE 0.016 0.001 PHE a 241 TYR 0.014 0.001 TYR a 145 ARG 0.002 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 75 MET cc_start: 0.8394 (tmm) cc_final: 0.8101 (tmm) REVERT: P 63 LEU cc_start: 0.9013 (tp) cc_final: 0.8775 (tp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3331 time to fit residues: 55.7709 Evaluate side-chains 89 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8257 Z= 0.285 Angle : 0.555 6.864 11218 Z= 0.311 Chirality : 0.040 0.136 1322 Planarity : 0.004 0.029 1440 Dihedral : 3.749 14.732 1149 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 3.10 (0.25), residues: 1094 helix: 2.53 (0.16), residues: 869 sheet: None (None), residues: 0 loop : 0.16 (0.47), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.042 0.002 PHE S 58 TYR 0.018 0.001 TYR a 145 ARG 0.003 0.000 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 21 MET cc_start: 0.7849 (tmm) cc_final: 0.7506 (tmm) REVERT: O 75 MET cc_start: 0.8465 (tmm) cc_final: 0.8219 (tmm) REVERT: P 63 LEU cc_start: 0.9026 (tp) cc_final: 0.8710 (tp) REVERT: Q 21 MET cc_start: 0.8296 (ppp) cc_final: 0.7912 (ppp) REVERT: b 31 PHE cc_start: 0.7813 (t80) cc_final: 0.7447 (t80) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3195 time to fit residues: 55.0652 Evaluate side-chains 90 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8257 Z= 0.213 Angle : 0.522 6.697 11218 Z= 0.283 Chirality : 0.040 0.128 1322 Planarity : 0.003 0.031 1440 Dihedral : 3.683 14.685 1149 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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 (0.25), residues: 1094 helix: 2.76 (0.16), residues: 869 sheet: None (None), residues: 0 loop : 0.36 (0.48), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS a 146 PHE 0.039 0.001 PHE O 69 TYR 0.017 0.001 TYR a 145 ARG 0.002 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 21 MET cc_start: 0.7813 (tmm) cc_final: 0.7457 (tmm) REVERT: O 75 MET cc_start: 0.8440 (tmm) cc_final: 0.8187 (tmm) REVERT: P 63 LEU cc_start: 0.8913 (tp) cc_final: 0.8684 (tp) REVERT: Q 21 MET cc_start: 0.8318 (ppp) cc_final: 0.8010 (ppp) REVERT: S 46 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7190 (pt0) REVERT: b 31 PHE cc_start: 0.7829 (t80) cc_final: 0.7400 (t80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3183 time to fit residues: 57.5215 Evaluate side-chains 92 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8257 Z= 0.206 Angle : 0.512 5.599 11218 Z= 0.275 Chirality : 0.039 0.122 1322 Planarity : 0.003 0.030 1440 Dihedral : 3.629 14.301 1149 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 3.64 (0.25), residues: 1094 helix: 2.90 (0.16), residues: 869 sheet: None (None), residues: 0 loop : 0.39 (0.48), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.023 0.001 PHE O 69 TYR 0.018 0.001 TYR a 145 ARG 0.002 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 75 MET cc_start: 0.8300 (tmm) cc_final: 0.8079 (tmm) REVERT: O 21 MET cc_start: 0.7785 (tmm) cc_final: 0.7448 (tmm) REVERT: O 75 MET cc_start: 0.8426 (tmm) cc_final: 0.8188 (tmm) REVERT: a 205 MET cc_start: 0.5539 (ptt) cc_final: 0.5219 (ptt) REVERT: b 31 PHE cc_start: 0.7856 (t80) cc_final: 0.7401 (t80) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3166 time to fit residues: 55.0077 Evaluate side-chains 93 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 98 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8257 Z= 0.209 Angle : 0.525 6.064 11218 Z= 0.283 Chirality : 0.039 0.125 1322 Planarity : 0.003 0.031 1440 Dihedral : 3.622 14.532 1149 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 3.66 (0.25), residues: 1094 helix: 2.91 (0.16), residues: 869 sheet: None (None), residues: 0 loop : 0.42 (0.49), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS a 146 PHE 0.048 0.001 PHE O 54 TYR 0.019 0.001 TYR a 145 ARG 0.002 0.000 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 21 MET cc_start: 0.7738 (tmm) cc_final: 0.7383 (tmm) REVERT: O 75 MET cc_start: 0.8442 (tmm) cc_final: 0.8223 (tmm) REVERT: T 63 LEU cc_start: 0.9012 (pp) cc_final: 0.8548 (tt) REVERT: a 205 MET cc_start: 0.5474 (ptt) cc_final: 0.5125 (ptt) REVERT: b 31 PHE cc_start: 0.7872 (t80) cc_final: 0.7404 (t80) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3044 time to fit residues: 50.7457 Evaluate side-chains 90 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8257 Z= 0.279 Angle : 0.556 6.008 11218 Z= 0.309 Chirality : 0.040 0.125 1322 Planarity : 0.004 0.030 1440 Dihedral : 3.742 15.330 1149 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.25), residues: 1094 helix: 2.60 (0.16), residues: 869 sheet: None (None), residues: 0 loop : 0.16 (0.47), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 218 HIS 0.003 0.001 HIS a 158 PHE 0.032 0.002 PHE O 54 TYR 0.023 0.002 TYR a 145 ARG 0.002 0.000 ARG a 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 21 MET cc_start: 0.7707 (tmm) cc_final: 0.7249 (tmm) REVERT: O 75 MET cc_start: 0.8496 (tmm) cc_final: 0.8271 (tmm) REVERT: S 46 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7372 (tt0) REVERT: T 63 LEU cc_start: 0.8962 (pp) cc_final: 0.8514 (tt) REVERT: a 205 MET cc_start: 0.5639 (ptt) cc_final: 0.5228 (ptt) REVERT: b 31 PHE cc_start: 0.7993 (t80) cc_final: 0.7388 (t80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3310 time to fit residues: 53.7430 Evaluate side-chains 89 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 23 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 46 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 = 0.3640 r_free = 0.3640 target = 0.081739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.076037 restraints weight = 120867.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.078008 restraints weight = 56352.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.079141 restraints weight = 29750.117| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8257 Z= 0.192 Angle : 0.519 5.935 11218 Z= 0.275 Chirality : 0.039 0.122 1322 Planarity : 0.003 0.032 1440 Dihedral : 3.631 15.148 1149 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 3.70 (0.25), residues: 1094 helix: 2.93 (0.16), residues: 869 sheet: None (None), residues: 0 loop : 0.42 (0.48), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.005 0.001 HIS a 146 PHE 0.030 0.001 PHE O 54 TYR 0.020 0.001 TYR a 145 ARG 0.002 0.000 ARG O 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3435.81 seconds wall clock time: 62 minutes 11.36 seconds (3731.36 seconds total)