Starting phenix.real_space_refine on Wed Mar 12 12:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7d_10394/03_2025/6t7d_10394.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7d_10394/03_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_10394/03_2025/6t7d_10394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7d_10394/03_2025/6t7d_10394.map" model { file = "/net/cci-nas-00/data/ceres_data/6t7d_10394/03_2025/6t7d_10394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7d_10394/03_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-5624/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: 7.25, per 1000 atoms: 0.88 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: 4.63 Conformation dependent library (CDL) restraints added in 902.7 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: 5.32 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: 4.63 Time building geometry restraints manager: 4.33 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: 30.940 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: 0.020 Extract box with map and model: 9.600 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 32.600 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.660 ------------------------------------------------------------------------------- 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 : 0.573 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0845 time to fit residues: 3.6172 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 : 0.602 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.055360 restraints weight = 59335.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.055929 restraints weight = 41276.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056393 restraints weight = 29107.552| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.642 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1080 time to fit residues: 4.4939 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 : 1.481 ------------------------------------------------------------------------------- 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: 20.0000 chunk 74 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 30.0000 chunk 62 optimal weight: 7.9990 overall best weight: 12.9996 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.074085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051311 restraints weight = 57134.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051519 restraints weight = 47287.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.051543 restraints weight = 38777.886| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 8782 Z= 0.369 Angle : 0.714 4.939 12534 Z= 0.456 Chirality : 0.040 0.146 936 Planarity : 0.004 0.017 1077 Dihedral : 32.025 150.944 3470 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.28 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: 1.79 (0.28), residues: 833 helix: 2.01 (0.20), residues: 589 sheet: None (None), residues: 0 loop : -0.89 (0.37), residues: 244 *********************** 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 : 0.622 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0865 time to fit residues: 3.4408 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 : 0.934 ------------------------------------------------------------------------------- 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: 20.0000 chunk 37 optimal weight: 40.0000 chunk 18 optimal weight: 50.0000 chunk 70 optimal weight: 40.0000 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 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 = 0.3514 r_free = 0.3514 target = 0.071365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.048806 restraints weight = 58088.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.049170 restraints weight = 44230.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.049105 restraints weight = 32135.481| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 8782 Z= 0.471 Angle : 0.805 7.260 12534 Z= 0.511 Chirality : 0.045 0.166 936 Planarity : 0.005 0.021 1077 Dihedral : 32.612 156.951 3470 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % 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: 0.67 (0.28), residues: 833 helix: 1.24 (0.20), residues: 585 sheet: None (None), residues: 0 loop : -1.45 (0.36), 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 : 0.582 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0741 time to fit residues: 3.0483 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 : 0.545 ------------------------------------------------------------------------------- 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: 30.0000 chunk 4 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 33 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 0 optimal weight: 80.0000 chunk 61 optimal weight: 40.0000 overall best weight: 11.5998 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.073396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.051467 restraints weight = 56670.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.050863 restraints weight = 66697.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.051502 restraints weight = 56492.409| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8782 Z= 0.335 Angle : 0.693 5.206 12534 Z= 0.441 Chirality : 0.039 0.147 936 Planarity : 0.003 0.019 1077 Dihedral : 32.330 154.892 3470 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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: 1.51 (0.29), residues: 833 helix: 1.94 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -1.44 (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 : 0.547 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0741 time to fit residues: 2.9911 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 : 0.523 ------------------------------------------------------------------------------- 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: 20.0000 chunk 97 optimal weight: 50.0000 chunk 94 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 96 optimal weight: 0.0570 chunk 66 optimal weight: 50.0000 chunk 9 optimal weight: 9.9990 overall best weight: 8.0112 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.075249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052942 restraints weight = 55602.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.052536 restraints weight = 61048.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.052787 restraints weight = 52274.179| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8782 Z= 0.251 Angle : 0.625 4.592 12534 Z= 0.399 Chirality : 0.036 0.148 936 Planarity : 0.003 0.019 1077 Dihedral : 32.051 149.536 3470 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.41 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: 2.58 (0.30), residues: 833 helix: 2.85 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.26 (0.37), residues: 248 *********************** 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 : 0.534 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0732 time to fit residues: 2.9054 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 : 0.559 ------------------------------------------------------------------------------- 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: 20.0000 chunk 19 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 overall best weight: 14.7998 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.072877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.050501 restraints weight = 57286.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.050565 restraints weight = 47701.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050401 restraints weight = 47284.482| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 8782 Z= 0.376 Angle : 0.705 5.910 12534 Z= 0.449 Chirality : 0.039 0.141 936 Planarity : 0.004 0.021 1077 Dihedral : 32.187 150.669 3470 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.29), residues: 833 helix: 2.33 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -1.45 (0.35), residues: 260 *********************** 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 : 0.552 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0732 time to fit residues: 2.9376 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 : 0.571 ------------------------------------------------------------------------------- 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: 60.0000 chunk 22 optimal weight: 50.0000 chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 overall best weight: 13.1998 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.072722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.050394 restraints weight = 57949.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050552 restraints weight = 47711.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.050327 restraints weight = 43740.639| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 8782 Z= 0.350 Angle : 0.700 6.501 12534 Z= 0.445 Chirality : 0.039 0.154 936 Planarity : 0.003 0.021 1077 Dihedral : 32.262 153.919 3470 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.59 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: 1.72 (0.29), residues: 833 helix: 2.38 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -1.75 (0.34), residues: 266 *********************** 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 : 0.549 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0759 time to fit residues: 3.1218 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 ------------------------------------------------------------------------------- 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: 0.9980 chunk 24 optimal weight: 20.0000 chunk 18 optimal weight: 50.0000 chunk 71 optimal weight: 30.0000 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: 16.1996 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.071693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.048615 restraints weight = 59003.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.048874 restraints weight = 45849.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.048899 restraints weight = 34879.068| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.6508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 8782 Z= 0.419 Angle : 0.737 7.063 12534 Z= 0.469 Chirality : 0.041 0.154 936 Planarity : 0.004 0.021 1077 Dihedral : 32.279 153.029 3470 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % 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: 1.17 (0.29), residues: 833 helix: 1.98 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -1.99 (0.34), residues: 268 *********************** 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 : 0.539 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0723 time to fit residues: 2.9145 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 : 0.517 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 40.0000 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: 8.9996 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.074051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.051909 restraints weight = 56364.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.051764 restraints weight = 50607.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.051835 restraints weight = 45657.394| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8782 Z= 0.269 Angle : 0.645 4.744 12534 Z= 0.410 Chirality : 0.037 0.158 936 Planarity : 0.003 0.020 1077 Dihedral : 32.186 152.103 3470 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % 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 (0.30), residues: 833 helix: 2.85 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -1.89 (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 : 0.620 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0787 time to fit residues: 3.2066 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 ------------------------------------------------------------------------------- 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: 50.0000 chunk 37 optimal weight: 40.0000 chunk 14 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 chunk 15 optimal weight: 40.0000 chunk 99 optimal weight: 120.0000 chunk 59 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 overall best weight: 17.3998 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.071183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.048030 restraints weight = 58810.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.048084 restraints weight = 43425.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.048299 restraints weight = 34659.336| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 8782 Z= 0.441 Angle : 0.756 7.204 12534 Z= 0.480 Chirality : 0.042 0.149 936 Planarity : 0.004 0.022 1077 Dihedral : 32.324 151.918 3470 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % 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: 0.93 (0.29), residues: 833 helix: 1.91 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -2.28 (0.34), residues: 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2005.63 seconds wall clock time: 37 minutes 31.70 seconds (2251.70 seconds total)