Starting phenix.real_space_refine on Wed Feb 12 11:45:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7d_10394/02_2025/6t7d_10394.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7d_10394/02_2025/6t7d_10394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t7d_10394/02_2025/6t7d_10394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7d_10394/02_2025/6t7d_10394.map" model { file = "/net/cci-nas-00/data/ceres_data/6t7d_10394/02_2025/6t7d_10394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7d_10394/02_2025/6t7d_10394.cif" } resolution = 4.4 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= 0.004 sd= 0.020 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 P 234 5.49 5 C 4002 2.51 5 N 1716 2.21 5 O 2257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8209 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 392 Classifications: {'peptide': 98} Incomplete info: {'backbone_only': 95} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 610 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 123 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 206 Chain: "B" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 336 Classifications: {'peptide': 84} Incomplete info: {'backbone_only': 76} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 162 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 440 Classifications: {'peptide': 110} Incomplete info: {'backbone_only': 101} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 175 Chain: "D" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 380 Classifications: {'peptide': 95} Incomplete info: {'backbone_only': 90} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 388 Classifications: {'peptide': 97} Incomplete info: {'backbone_only': 94} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 425 Unresolved non-hydrogen angles: 604 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 206 Chain: "F" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 349 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 78} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 363 Unresolved non-hydrogen angles: 515 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 167 Chain: "G" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 440 Classifications: {'peptide': 110} Incomplete info: {'backbone_only': 101} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 175 Chain: "H" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 380 Classifications: {'peptide': 95} Incomplete info: {'backbone_only': 90} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 159 Chain: "I" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2376 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "J" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2421 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "K" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 307 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 74, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 178 Time building chain proxies: 5.34, per 1000 atoms: 0.65 Number of scatterers: 8209 At special positions: 0 Unit cell: (74.55, 124.95, 115.5, 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) P 234 15.00 O 2257 8.00 N 1716 7.00 C 4002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 702.0 milliseconds 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 67.6% alpha, 1.9% beta 117 base pairs and 202 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.829A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.901A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.925A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.811A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.677A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.670A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.603A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.745A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.769A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.677A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 removed outlier: 3.668A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 90 through 95' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.604A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 removed outlier: 4.078A pdb=" N ILE K 62 " --> pdb=" O VAL K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 90 Processing helix chain 'K' and resid 92 through 94 No H-bonds generated for 'chain 'K' and resid 92 through 94' Processing helix chain 'K' and resid 95 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.154A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.888A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.124A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.562A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.195A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 419 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 278 hydrogen bonds 552 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 202 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.29: 1087 1.29 - 1.37: 2209 1.37 - 1.46: 2150 1.46 - 1.54: 2868 1.54 - 1.62: 468 Bond restraints: 8782 Sorted by residual: bond pdb=" C ILE K 96 " pdb=" N PRO K 97 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.22e+00 bond pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.48e+00 bond pdb=" C3' DG I 110 " pdb=" O3' DG I 110 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.42e+00 bond pdb=" C3' DT I 38 " pdb=" O3' DT I 38 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.38e+00 bond pdb=" C LEU E 65 " pdb=" N PRO E 66 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.30e+00 ... (remaining 8777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 11129 1.31 - 2.62: 1212 2.62 - 3.93: 162 3.93 - 5.24: 27 5.24 - 6.55: 4 Bond angle restraints: 12534 Sorted by residual: angle pdb=" CA LYS F 20 " pdb=" C LYS F 20 " pdb=" N VAL F 21 " ideal model delta sigma weight residual 119.63 115.92 3.71 8.10e-01 1.52e+00 2.10e+01 angle pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " ideal model delta sigma weight residual 119.63 115.95 3.68 8.10e-01 1.52e+00 2.06e+01 angle pdb=" C2' DA J 53 " pdb=" C1' DA J 53 " pdb=" N9 DA J 53 " ideal model delta sigma weight residual 113.50 119.97 -6.47 1.50e+00 4.44e-01 1.86e+01 angle pdb=" C PRO K 72 " pdb=" N ASP K 73 " pdb=" CA ASP K 73 " ideal model delta sigma weight residual 122.07 127.37 -5.30 1.43e+00 4.89e-01 1.38e+01 angle pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " pdb=" P DT I 14 " ideal model delta sigma weight residual 120.20 125.32 -5.12 1.50e+00 4.44e-01 1.17e+01 ... (remaining 12529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.40: 2011 30.40 - 60.80: 1387 60.80 - 91.20: 69 91.20 - 121.60: 0 121.60 - 152.00: 3 Dihedral angle restraints: 3470 sinusoidal: 2627 harmonic: 843 Sorted by residual: dihedral pdb=" CA TYR H 34 " pdb=" C TYR H 34 " pdb=" N SER H 35 " pdb=" CA SER H 35 " ideal model delta harmonic sigma weight residual 180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA TYR D 34 " pdb=" C TYR D 34 " pdb=" N SER D 35 " pdb=" CA SER D 35 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LYS D 43 " pdb=" C LYS D 43 " pdb=" N GLN D 44 " pdb=" CA GLN D 44 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 3467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 863 0.080 - 0.159: 68 0.159 - 0.239: 4 0.239 - 0.318: 0 0.318 - 0.398: 1 Chirality restraints: 936 Sorted by residual: chirality pdb=" C1' DA J 53 " pdb=" O4' DA J 53 " pdb=" C2' DA J 53 " pdb=" N9 DA J 53 " both_signs ideal model delta sigma weight residual False 2.42 2.02 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" P DC I 111 " pdb=" OP1 DC I 111 " pdb=" OP2 DC I 111 " pdb=" O5' DC I 111 " both_signs ideal model delta sigma weight residual True 2.35 -2.55 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" P DT I 14 " pdb=" OP1 DT I 14 " pdb=" OP2 DT I 14 " pdb=" O5' DT I 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 933 not shown) Planarity restraints: 1077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 53 " -0.013 2.00e-02 2.50e+03 3.54e-02 3.44e+01 pdb=" N9 DA J 53 " 0.086 2.00e-02 2.50e+03 pdb=" C8 DA J 53 " -0.072 2.00e-02 2.50e+03 pdb=" N7 DA J 53 " 0.016 2.00e-02 2.50e+03 pdb=" C5 DA J 53 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DA J 53 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA J 53 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA J 53 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DA J 53 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA J 53 " -0.019 2.00e-02 2.50e+03 pdb=" C4 DA J 53 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 95 " -0.029 2.00e-02 2.50e+03 1.61e-02 6.45e+00 pdb=" N1 DT I 95 " 0.041 2.00e-02 2.50e+03 pdb=" C2 DT I 95 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 95 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT I 95 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 95 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 95 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DT I 95 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 95 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT I 95 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 60 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C VAL F 60 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL F 60 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE F 61 " 0.014 2.00e-02 2.50e+03 ... (remaining 1074 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 344 2.67 - 3.22: 6460 3.22 - 3.78: 15338 3.78 - 4.34: 17796 4.34 - 4.90: 23191 Nonbonded interactions: 63129 Sorted by model distance: nonbonded pdb=" N3 DC I 2 " pdb=" N1 DG J 145 " model vdw 2.107 3.200 nonbonded pdb=" O2 DC I 2 " pdb=" C2 DG J 145 " model vdw 2.130 3.260 nonbonded pdb=" C2 DC I 2 " pdb=" N1 DG J 145 " model vdw 2.198 3.340 nonbonded pdb=" O2 DC I 2 " pdb=" N2 DG J 145 " model vdw 2.292 3.120 nonbonded pdb=" N4 DC I 2 " pdb=" O6 DG J 145 " model vdw 2.340 3.120 ... (remaining 63124 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.620 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.005 0.070 8782 Z= 0.291 Angle : 0.858 6.553 12534 Z= 0.554 Chirality : 0.047 0.398 936 Planarity : 0.005 0.035 1077 Dihedral : 32.584 152.004 3470 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.24), residues: 833 helix: -1.43 (0.18), residues: 571 sheet: None (None), residues: 0 loop : -1.42 (0.35), residues: 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.560 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0782 time to fit residues: 3.0509 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 52 optimal weight: 0.0770 chunk 41 optimal weight: 50.0000 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 overall best weight: 7.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.077519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.055289 restraints weight = 59335.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.055834 restraints weight = 41982.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056390 restraints weight = 29347.895| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8782 Z= 0.250 Angle : 0.624 4.432 12534 Z= 0.401 Chirality : 0.035 0.138 936 Planarity : 0.003 0.018 1077 Dihedral : 31.703 145.562 3470 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.28), residues: 833 helix: 1.55 (0.20), residues: 586 sheet: None (None), residues: 0 loop : -0.58 (0.38), residues: 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.431 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0735 time to fit residues: 2.8796 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 40.0000 chunk 26 optimal weight: 40.0000 chunk 89 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 62 optimal weight: 0.0670 overall best weight: 9.6132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.075758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053295 restraints weight = 56615.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053462 restraints weight = 48874.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.053584 restraints weight = 40371.686| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8782 Z= 0.289 Angle : 0.654 4.744 12534 Z= 0.419 Chirality : 0.037 0.145 936 Planarity : 0.003 0.017 1077 Dihedral : 31.857 149.960 3470 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.29), residues: 833 helix: 2.29 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.549 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0723 time to fit residues: 2.9774 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 67 optimal weight: 30.0000 chunk 50 optimal weight: 40.0000 chunk 36 optimal weight: 9.9990 chunk 37 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 70 optimal weight: 40.0000 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 50.0000 chunk 87 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 38 optimal weight: 40.0000 overall best weight: 17.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.071924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.049876 restraints weight = 57826.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049934 restraints weight = 47691.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.049834 restraints weight = 41508.337| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 8782 Z= 0.467 Angle : 0.786 6.207 12534 Z= 0.500 Chirality : 0.044 0.163 936 Planarity : 0.005 0.020 1077 Dihedral : 32.399 154.438 3470 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.28), residues: 833 helix: 1.45 (0.20), residues: 585 sheet: None (None), residues: 0 loop : -1.24 (0.37), residues: 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.569 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0741 time to fit residues: 2.9971 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 0 optimal weight: 80.0000 chunk 61 optimal weight: 40.0000 overall best weight: 9.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.074640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052169 restraints weight = 56137.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.051890 restraints weight = 62146.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.052050 restraints weight = 48863.351| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8782 Z= 0.285 Angle : 0.652 5.142 12534 Z= 0.416 Chirality : 0.037 0.143 936 Planarity : 0.003 0.018 1077 Dihedral : 32.162 154.482 3470 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.29), residues: 833 helix: 2.40 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -1.22 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.567 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0735 time to fit residues: 2.9676 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 97 optimal weight: 40.0000 chunk 94 optimal weight: 20.0000 chunk 2 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 96 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 chunk 9 optimal weight: 0.0980 overall best weight: 5.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.077283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054508 restraints weight = 54890.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054592 restraints weight = 47734.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.054543 restraints weight = 38608.923| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8782 Z= 0.198 Angle : 0.577 4.517 12534 Z= 0.369 Chirality : 0.033 0.147 936 Planarity : 0.002 0.017 1077 Dihedral : 31.759 147.656 3470 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.30), residues: 833 helix: 3.49 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -0.92 (0.39), residues: 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.581 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0724 time to fit residues: 2.9540 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 78 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 65 optimal weight: 50.0000 chunk 32 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 55 optimal weight: 50.0000 chunk 94 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 12 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.071955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.049355 restraints weight = 57731.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.049295 restraints weight = 51882.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.049427 restraints weight = 45890.112| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 8782 Z= 0.460 Angle : 0.755 6.891 12534 Z= 0.481 Chirality : 0.042 0.154 936 Planarity : 0.004 0.020 1077 Dihedral : 32.099 149.011 3470 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.28), residues: 833 helix: 1.86 (0.20), residues: 589 sheet: None (None), residues: 0 loop : -1.51 (0.37), residues: 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.591 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0742 time to fit residues: 3.0685 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 47 optimal weight: 30.0000 chunk 96 optimal weight: 0.0020 chunk 22 optimal weight: 50.0000 chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 overall best weight: 9.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.074276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.051954 restraints weight = 56702.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051430 restraints weight = 65092.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.051781 restraints weight = 55176.890| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8782 Z= 0.280 Angle : 0.638 4.924 12534 Z= 0.407 Chirality : 0.036 0.151 936 Planarity : 0.003 0.019 1077 Dihedral : 32.031 152.142 3470 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.30), residues: 833 helix: 2.65 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.522 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0730 time to fit residues: 2.9842 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 35 optimal weight: 50.0000 chunk 65 optimal weight: 50.0000 chunk 43 optimal weight: 30.0000 chunk 39 optimal weight: 0.0070 chunk 24 optimal weight: 20.0000 chunk 18 optimal weight: 50.0000 chunk 71 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 overall best weight: 16.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.071937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.049138 restraints weight = 58823.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.049085 restraints weight = 52863.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.049264 restraints weight = 44242.099| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 8782 Z= 0.412 Angle : 0.730 6.963 12534 Z= 0.464 Chirality : 0.041 0.149 936 Planarity : 0.004 0.020 1077 Dihedral : 32.246 152.387 3470 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 833 helix: 2.09 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -1.71 (0.35), residues: 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.544 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0723 time to fit residues: 2.9670 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 95 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 50.0000 chunk 53 optimal weight: 30.0000 chunk 70 optimal weight: 50.0000 chunk 51 optimal weight: 40.0000 chunk 89 optimal weight: 10.0000 chunk 0 optimal weight: 70.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.073841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.051251 restraints weight = 56404.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.051332 restraints weight = 49870.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.051203 restraints weight = 43663.389| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 8782 Z= 0.291 Angle : 0.649 5.033 12534 Z= 0.414 Chirality : 0.036 0.155 936 Planarity : 0.003 0.019 1077 Dihedral : 32.076 152.912 3470 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.30), residues: 833 helix: 2.73 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.601 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0758 time to fit residues: 3.0876 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 43 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 47 optimal weight: 40.0000 chunk 15 optimal weight: 40.0000 chunk 99 optimal weight: 50.0000 chunk 59 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 overall best weight: 12.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.073130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.050094 restraints weight = 57461.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050674 restraints weight = 48459.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050484 restraints weight = 37335.347| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8782 Z= 0.333 Angle : 0.672 5.602 12534 Z= 0.428 Chirality : 0.037 0.155 936 Planarity : 0.003 0.019 1077 Dihedral : 32.061 151.697 3470 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.29), residues: 833 helix: 2.60 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -1.77 (0.35), residues: 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1737.84 seconds wall clock time: 31 minutes 51.31 seconds (1911.31 seconds total)