Starting phenix.real_space_refine on Sat Aug 23 07:24:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cqd_16796/08_2025/8cqd_16796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cqd_16796/08_2025/8cqd_16796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cqd_16796/08_2025/8cqd_16796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cqd_16796/08_2025/8cqd_16796.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cqd_16796/08_2025/8cqd_16796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cqd_16796/08_2025/8cqd_16796.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.030 sd= 0.168 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 7306 2.51 5 N 1612 2.21 5 O 1842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10828 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1884 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 1 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1735 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 1 Chain: "C" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1735 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 1 Chain: "E" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1735 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 1 Chain: "F" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1735 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 1 Chain: "D" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1884 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.03, per 1000 atoms: 0.28 Number of scatterers: 10828 At special positions: 0 Unit cell: (111.769, 104.234, 67.815, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1842 8.00 N 1612 7.00 C 7306 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 419.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 88.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 28 through 51 removed outlier: 4.398A pdb=" N VAL A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 60 through 87 removed outlier: 3.945A pdb=" N THR A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 118 Proline residue: A 104 - end of helix removed outlier: 4.094A pdb=" N PHE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 144 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.752A pdb=" N SER A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 199 through 209 removed outlier: 3.619A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 248 removed outlier: 4.910A pdb=" N PHE A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 61 through 87 removed outlier: 3.905A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 118 removed outlier: 3.611A pdb=" N ARG B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Proline residue: B 104 - end of helix removed outlier: 4.155A pdb=" N PHE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 144 removed outlier: 3.643A pdb=" N LYS B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 169 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.758A pdb=" N THR B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 197 Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 220 through 248 removed outlier: 4.804A pdb=" N PHE B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 51 removed outlier: 4.378A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 61 through 87 Processing helix chain 'C' and resid 91 through 118 removed outlier: 3.527A pdb=" N ARG C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Proline residue: C 104 - end of helix removed outlier: 4.253A pdb=" N PHE C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 145 Processing helix chain 'C' and resid 148 through 169 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.839A pdb=" N THR C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 197 Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 220 through 250 removed outlier: 4.498A pdb=" N PHE C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 51 removed outlier: 3.574A pdb=" N SER E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 61 through 87 removed outlier: 3.905A pdb=" N SER E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 118 removed outlier: 3.595A pdb=" N ARG E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) Proline residue: E 104 - end of helix removed outlier: 4.152A pdb=" N PHE E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 144 removed outlier: 3.626A pdb=" N LYS E 126 " --> pdb=" O GLY E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 169 Processing helix chain 'E' and resid 170 through 178 removed outlier: 3.752A pdb=" N THR E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 197 Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 220 through 248 removed outlier: 4.806A pdb=" N PHE E 235 " --> pdb=" O ASN E 231 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 51 removed outlier: 4.361A pdb=" N VAL F 32 " --> pdb=" O ASP F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 87 removed outlier: 3.701A pdb=" N LEU F 63 " --> pdb=" O TRP F 59 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER F 66 " --> pdb=" O SER F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 118 removed outlier: 3.531A pdb=" N ARG F 95 " --> pdb=" O PRO F 91 " (cutoff:3.500A) Proline residue: F 104 - end of helix removed outlier: 4.267A pdb=" N PHE F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR F 111 " --> pdb=" O ILE F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 145 Processing helix chain 'F' and resid 148 through 169 Processing helix chain 'F' and resid 170 through 178 removed outlier: 3.839A pdb=" N THR F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 197 Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 220 through 249 removed outlier: 4.484A pdb=" N PHE F 235 " --> pdb=" O ASN F 231 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY F 236 " --> pdb=" O LYS F 232 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN F 249 " --> pdb=" O LYS F 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 18 Proline residue: D 15 - end of helix removed outlier: 3.977A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 51 removed outlier: 4.376A pdb=" N VAL D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 60 through 87 removed outlier: 3.981A pdb=" N THR D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 118 Proline residue: D 104 - end of helix removed outlier: 4.092A pdb=" N PHE D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 144 Processing helix chain 'D' and resid 148 through 170 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.728A pdb=" N SER D 174 " --> pdb=" O GLY D 170 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 197 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.643A pdb=" N VAL D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 248 removed outlier: 4.912A pdb=" N PHE D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY D 236 " --> pdb=" O LYS D 232 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2649 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1629 1.32 - 1.44: 3379 1.44 - 1.56: 6018 1.56 - 1.69: 0 1.69 - 1.81: 118 Bond restraints: 11144 Sorted by residual: bond pdb=" C MET C 135 " pdb=" N LEU C 136 " ideal model delta sigma weight residual 1.334 1.235 0.100 1.27e-02 6.20e+03 6.16e+01 bond pdb=" C GLY A 139 " pdb=" N TYR A 140 " ideal model delta sigma weight residual 1.335 1.248 0.087 1.36e-02 5.41e+03 4.12e+01 bond pdb=" C GLY D 67 " pdb=" N LEU D 68 " ideal model delta sigma weight residual 1.335 1.248 0.086 1.36e-02 5.41e+03 4.04e+01 bond pdb=" C LEU D 68 " pdb=" N VAL D 69 " ideal model delta sigma weight residual 1.335 1.403 -0.068 1.19e-02 7.06e+03 3.22e+01 bond pdb=" C VAL E 46 " pdb=" N PHE E 47 " ideal model delta sigma weight residual 1.334 1.406 -0.072 1.27e-02 6.20e+03 3.20e+01 ... (remaining 11139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 14747 1.36 - 2.73: 290 2.73 - 4.09: 104 4.09 - 5.45: 54 5.45 - 6.82: 21 Bond angle restraints: 15216 Sorted by residual: angle pdb=" O VAL E 46 " pdb=" C VAL E 46 " pdb=" N PHE E 47 " ideal model delta sigma weight residual 121.87 126.86 -4.99 9.70e-01 1.06e+00 2.64e+01 angle pdb=" O VAL B 46 " pdb=" C VAL B 46 " pdb=" N PHE B 47 " ideal model delta sigma weight residual 121.87 126.83 -4.96 9.70e-01 1.06e+00 2.61e+01 angle pdb=" O MET C 135 " pdb=" C MET C 135 " pdb=" N LEU C 136 " ideal model delta sigma weight residual 122.07 116.87 5.20 1.03e+00 9.43e-01 2.55e+01 angle pdb=" N PHE A 17 " pdb=" CA PHE A 17 " pdb=" C PHE A 17 " ideal model delta sigma weight residual 111.28 105.79 5.49 1.09e+00 8.42e-01 2.54e+01 angle pdb=" O GLY A 139 " pdb=" C GLY A 139 " pdb=" N TYR A 140 " ideal model delta sigma weight residual 122.19 117.37 4.82 9.60e-01 1.09e+00 2.52e+01 ... (remaining 15211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 5923 17.01 - 34.02: 240 34.02 - 51.03: 27 51.03 - 68.04: 0 68.04 - 85.05: 2 Dihedral angle restraints: 6192 sinusoidal: 2252 harmonic: 3940 Sorted by residual: dihedral pdb=" CB GLU D 51 " pdb=" CG GLU D 51 " pdb=" CD GLU D 51 " pdb=" OE1 GLU D 51 " ideal model delta sinusoidal sigma weight residual 0.00 85.05 -85.05 1 3.00e+01 1.11e-03 9.75e+00 dihedral pdb=" CB GLU A 51 " pdb=" CG GLU A 51 " pdb=" CD GLU A 51 " pdb=" OE1 GLU A 51 " ideal model delta sinusoidal sigma weight residual 0.00 84.84 -84.84 1 3.00e+01 1.11e-03 9.71e+00 dihedral pdb=" CA ASP A 98 " pdb=" CB ASP A 98 " pdb=" CG ASP A 98 " pdb=" OD1 ASP A 98 " ideal model delta sinusoidal sigma weight residual -30.00 -80.16 50.16 1 2.00e+01 2.50e-03 8.62e+00 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1326 0.042 - 0.083: 317 0.083 - 0.125: 68 0.125 - 0.166: 8 0.166 - 0.208: 3 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA TYR A 77 " pdb=" N TYR A 77 " pdb=" C TYR A 77 " pdb=" CB TYR A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ASN D 231 " pdb=" N ASN D 231 " pdb=" C ASN D 231 " pdb=" CB ASN D 231 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA ASN A 231 " pdb=" N ASN A 231 " pdb=" C ASN A 231 " pdb=" CB ASN A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 1719 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 246 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C GLU A 246 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU A 246 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 247 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 246 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C GLU D 246 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU D 246 " 0.012 2.00e-02 2.50e+03 pdb=" N SER D 247 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 76 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C HIS A 76 " -0.029 2.00e-02 2.50e+03 pdb=" O HIS A 76 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 77 " 0.010 2.00e-02 2.50e+03 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1925 2.76 - 3.29: 11079 3.29 - 3.83: 19080 3.83 - 4.36: 20582 4.36 - 4.90: 37276 Nonbonded interactions: 89942 Sorted by model distance: nonbonded pdb=" OG1 THR E 61 " pdb=" OE2 GLU D 51 " model vdw 2.223 3.040 nonbonded pdb=" OE2 GLU A 51 " pdb=" OG1 THR B 61 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR D 201 " pdb=" OD1 ASP D 228 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A 201 " pdb=" OD1 ASP A 228 " model vdw 2.231 3.040 nonbonded pdb=" O ALA D 13 " pdb=" OG1 THR D 16 " model vdw 2.299 3.040 ... (remaining 89937 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 23 through 301) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 23 through 301) selection = chain 'E' selection = chain 'F' } 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: 0.200 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.300 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 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 : 0.006 0.124 11150 Z= 0.404 Angle : 0.607 6.815 15216 Z= 0.364 Chirality : 0.038 0.208 1722 Planarity : 0.004 0.040 1812 Dihedral : 9.169 85.053 3688 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.23), residues: 1340 helix: 2.30 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -2.00 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 54 TYR 0.009 0.001 TYR A 96 PHE 0.010 0.001 PHE A 229 TRP 0.019 0.001 TRP C 75 HIS 0.001 0.000 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00517 (11144) covalent geometry : angle 0.60680 (15216) hydrogen bonds : bond 0.10097 ( 884) hydrogen bonds : angle 4.79136 ( 2649) Misc. bond : bond 0.10149 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.7180 (m-80) cc_final: 0.6969 (m-10) REVERT: A 191 MET cc_start: 0.8540 (tmm) cc_final: 0.8117 (tmm) REVERT: A 195 ILE cc_start: 0.8861 (mt) cc_final: 0.8654 (mt) REVERT: B 77 TYR cc_start: 0.8567 (m-80) cc_final: 0.8315 (m-80) REVERT: B 80 MET cc_start: 0.7067 (mtm) cc_final: 0.6763 (mtt) REVERT: B 107 ILE cc_start: 0.8431 (tp) cc_final: 0.7969 (tp) REVERT: B 125 PHE cc_start: 0.7691 (t80) cc_final: 0.7471 (t80) REVERT: B 184 GLN cc_start: 0.8412 (mt0) cc_final: 0.8069 (mt0) REVERT: B 185 SER cc_start: 0.8879 (m) cc_final: 0.8487 (p) REVERT: C 100 LEU cc_start: 0.8887 (tp) cc_final: 0.8580 (mt) REVERT: E 77 TYR cc_start: 0.8563 (m-80) cc_final: 0.8314 (m-80) REVERT: E 80 MET cc_start: 0.7158 (mtm) cc_final: 0.6842 (mtt) REVERT: E 125 PHE cc_start: 0.7702 (t80) cc_final: 0.7476 (t80) REVERT: E 161 VAL cc_start: 0.8702 (t) cc_final: 0.8496 (m) REVERT: E 184 GLN cc_start: 0.8420 (mt0) cc_final: 0.8083 (mt0) REVERT: E 185 SER cc_start: 0.8877 (m) cc_final: 0.8490 (p) REVERT: F 100 LEU cc_start: 0.8888 (tp) cc_final: 0.8565 (mt) REVERT: F 133 LEU cc_start: 0.7580 (mt) cc_final: 0.7284 (mt) REVERT: D 29 TYR cc_start: 0.7136 (m-80) cc_final: 0.6905 (m-10) REVERT: D 98 ASP cc_start: 0.7799 (t70) cc_final: 0.7534 (t0) REVERT: D 191 MET cc_start: 0.8483 (tmm) cc_final: 0.8075 (tmm) REVERT: D 195 ILE cc_start: 0.8809 (mt) cc_final: 0.8599 (mt) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.0989 time to fit residues: 54.1189 Evaluate side-chains 283 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN B 177 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.207392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.150603 restraints weight = 12166.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151438 restraints weight = 10547.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.153024 restraints weight = 10425.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.153511 restraints weight = 7541.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154136 restraints weight = 7250.179| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11150 Z= 0.136 Angle : 0.523 6.241 15216 Z= 0.270 Chirality : 0.039 0.263 1722 Planarity : 0.004 0.052 1812 Dihedral : 3.598 26.120 1520 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.18 % Allowed : 13.86 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.23), residues: 1340 helix: 2.21 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.12 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 81 TYR 0.012 0.001 TYR E 205 PHE 0.012 0.002 PHE F 229 TRP 0.019 0.001 TRP C 75 HIS 0.001 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00305 (11144) covalent geometry : angle 0.52329 (15216) hydrogen bonds : bond 0.03861 ( 884) hydrogen bonds : angle 3.74784 ( 2649) Misc. bond : bond 0.00083 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 300 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8517 (tmm) cc_final: 0.8186 (tmm) REVERT: A 246 GLU cc_start: 0.7990 (tp30) cc_final: 0.7369 (mm-30) REVERT: B 80 MET cc_start: 0.7117 (mtm) cc_final: 0.6580 (mtt) REVERT: B 127 LYS cc_start: 0.6416 (ptpt) cc_final: 0.6041 (ptpt) REVERT: B 162 TYR cc_start: 0.8182 (t80) cc_final: 0.7958 (t80) REVERT: B 184 GLN cc_start: 0.8381 (mt0) cc_final: 0.8113 (mt0) REVERT: C 100 LEU cc_start: 0.8759 (tp) cc_final: 0.8474 (mt) REVERT: C 141 MET cc_start: 0.7843 (mmt) cc_final: 0.7425 (mmt) REVERT: C 167 LEU cc_start: 0.7644 (mt) cc_final: 0.7256 (mt) REVERT: C 184 GLN cc_start: 0.8168 (mt0) cc_final: 0.7819 (mm-40) REVERT: C 187 TYR cc_start: 0.8374 (t80) cc_final: 0.8046 (t80) REVERT: E 80 MET cc_start: 0.7055 (mtm) cc_final: 0.6492 (mtt) REVERT: E 127 LYS cc_start: 0.6427 (ptpt) cc_final: 0.6050 (ptpt) REVERT: E 162 TYR cc_start: 0.8130 (t80) cc_final: 0.7817 (t80) REVERT: E 184 GLN cc_start: 0.8339 (mt0) cc_final: 0.8093 (mt0) REVERT: F 100 LEU cc_start: 0.8757 (tp) cc_final: 0.8477 (mt) REVERT: F 141 MET cc_start: 0.7808 (mmt) cc_final: 0.7367 (mmt) REVERT: F 184 GLN cc_start: 0.8177 (mt0) cc_final: 0.7835 (mm-40) REVERT: D 98 ASP cc_start: 0.7933 (t70) cc_final: 0.7725 (t0) REVERT: D 191 MET cc_start: 0.8457 (tmm) cc_final: 0.8122 (tmm) REVERT: D 246 GLU cc_start: 0.7959 (tp30) cc_final: 0.7320 (mm-30) outliers start: 13 outliers final: 11 residues processed: 308 average time/residue: 0.1021 time to fit residues: 45.4198 Evaluate side-chains 276 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 265 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 chunk 104 optimal weight: 9.9990 chunk 96 optimal weight: 0.3980 chunk 135 optimal weight: 0.0980 chunk 16 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.210241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.154586 restraints weight = 12214.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.153596 restraints weight = 10480.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155235 restraints weight = 10478.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.159566 restraints weight = 7933.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159784 restraints weight = 6406.276| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11150 Z= 0.114 Angle : 0.501 6.502 15216 Z= 0.257 Chirality : 0.037 0.217 1722 Planarity : 0.004 0.040 1812 Dihedral : 3.712 25.552 1520 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.81 % Allowed : 15.67 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.23), residues: 1340 helix: 2.32 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -2.01 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 81 TYR 0.019 0.001 TYR E 140 PHE 0.026 0.001 PHE C 153 TRP 0.019 0.001 TRP C 35 HIS 0.001 0.000 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00245 (11144) covalent geometry : angle 0.50126 (15216) hydrogen bonds : bond 0.03504 ( 884) hydrogen bonds : angle 3.61218 ( 2649) Misc. bond : bond 0.00044 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 291 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLU cc_start: 0.8662 (tp30) cc_final: 0.8435 (tp30) REVERT: A 191 MET cc_start: 0.8367 (tmm) cc_final: 0.8024 (tmm) REVERT: A 246 GLU cc_start: 0.7947 (tp30) cc_final: 0.7336 (mm-30) REVERT: B 80 MET cc_start: 0.7037 (mtm) cc_final: 0.6779 (mtt) REVERT: B 162 TYR cc_start: 0.8184 (t80) cc_final: 0.7728 (t80) REVERT: B 184 GLN cc_start: 0.8382 (mt0) cc_final: 0.7971 (mt0) REVERT: C 78 MET cc_start: 0.8222 (mmt) cc_final: 0.7850 (mmm) REVERT: C 100 LEU cc_start: 0.8807 (tp) cc_final: 0.8428 (mt) REVERT: C 135 MET cc_start: 0.7499 (ptp) cc_final: 0.6911 (ptp) REVERT: C 184 GLN cc_start: 0.8159 (mt0) cc_final: 0.7836 (mm-40) REVERT: C 185 SER cc_start: 0.8251 (m) cc_final: 0.7813 (t) REVERT: E 80 MET cc_start: 0.6984 (mtm) cc_final: 0.6629 (mtt) REVERT: E 166 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6642 (mt-10) REVERT: E 184 GLN cc_start: 0.8419 (mt0) cc_final: 0.8026 (mt0) REVERT: F 78 MET cc_start: 0.8238 (mmt) cc_final: 0.7858 (mmm) REVERT: F 100 LEU cc_start: 0.8807 (tp) cc_final: 0.8491 (mt) REVERT: F 135 MET cc_start: 0.7514 (ptp) cc_final: 0.6925 (ptp) REVERT: F 184 GLN cc_start: 0.8213 (mt0) cc_final: 0.7878 (mm-40) REVERT: D 98 ASP cc_start: 0.7915 (t70) cc_final: 0.7693 (t0) REVERT: D 143 GLU cc_start: 0.8711 (tp30) cc_final: 0.8473 (tp30) REVERT: D 191 MET cc_start: 0.8299 (tmm) cc_final: 0.7984 (tmm) REVERT: D 246 GLU cc_start: 0.7929 (tp30) cc_final: 0.7684 (mm-30) outliers start: 20 outliers final: 10 residues processed: 300 average time/residue: 0.0990 time to fit residues: 42.9931 Evaluate side-chains 274 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 264 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 103 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.207910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.151179 restraints weight = 12271.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.152998 restraints weight = 10789.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.154488 restraints weight = 10066.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154847 restraints weight = 7404.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.155437 restraints weight = 7128.581| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11150 Z= 0.123 Angle : 0.500 6.809 15216 Z= 0.257 Chirality : 0.037 0.195 1722 Planarity : 0.004 0.055 1812 Dihedral : 3.657 25.925 1520 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.45 % Allowed : 16.21 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.23), residues: 1340 helix: 2.23 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.07 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 81 TYR 0.016 0.001 TYR A 165 PHE 0.012 0.001 PHE F 34 TRP 0.027 0.001 TRP E 160 HIS 0.001 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00281 (11144) covalent geometry : angle 0.49951 (15216) hydrogen bonds : bond 0.03569 ( 884) hydrogen bonds : angle 3.60474 ( 2649) Misc. bond : bond 0.00060 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 293 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8410 (ttmt) REVERT: A 138 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: A 191 MET cc_start: 0.8300 (tmm) cc_final: 0.7938 (tmm) REVERT: A 246 GLU cc_start: 0.7962 (tp30) cc_final: 0.7762 (tp30) REVERT: B 80 MET cc_start: 0.6981 (mtm) cc_final: 0.6666 (mtt) REVERT: B 184 GLN cc_start: 0.8415 (mt0) cc_final: 0.8110 (mt0) REVERT: C 100 LEU cc_start: 0.8693 (tp) cc_final: 0.8479 (mt) REVERT: C 140 TYR cc_start: 0.7649 (t80) cc_final: 0.7378 (t80) REVERT: C 141 MET cc_start: 0.7768 (mmt) cc_final: 0.7529 (mmt) REVERT: C 184 GLN cc_start: 0.8165 (mt0) cc_final: 0.7841 (mm-40) REVERT: C 185 SER cc_start: 0.8303 (m) cc_final: 0.7831 (t) REVERT: C 190 MET cc_start: 0.8377 (mtm) cc_final: 0.8161 (mtt) REVERT: C 246 GLU cc_start: 0.7755 (tp30) cc_final: 0.7207 (tm-30) REVERT: E 80 MET cc_start: 0.7013 (mtm) cc_final: 0.6663 (mtt) REVERT: E 166 GLU cc_start: 0.6529 (mt-10) cc_final: 0.6264 (mt-10) REVERT: E 184 GLN cc_start: 0.8420 (mt0) cc_final: 0.8068 (mt0) REVERT: E 188 ASN cc_start: 0.8338 (m-40) cc_final: 0.7930 (t0) REVERT: F 100 LEU cc_start: 0.8695 (tp) cc_final: 0.8467 (mt) REVERT: F 135 MET cc_start: 0.7433 (ptp) cc_final: 0.7233 (ptp) REVERT: F 184 GLN cc_start: 0.8176 (mt0) cc_final: 0.7854 (mm-40) REVERT: F 185 SER cc_start: 0.8317 (m) cc_final: 0.7835 (t) REVERT: F 246 GLU cc_start: 0.7840 (tp30) cc_final: 0.7232 (tm-30) REVERT: D 98 ASP cc_start: 0.7974 (t70) cc_final: 0.7743 (t0) REVERT: D 138 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: D 191 MET cc_start: 0.8214 (tmm) cc_final: 0.7885 (tmm) outliers start: 27 outliers final: 15 residues processed: 305 average time/residue: 0.0999 time to fit residues: 44.6828 Evaluate side-chains 290 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 273 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 138 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 32 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 0.0060 chunk 16 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.207794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152766 restraints weight = 12181.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.152526 restraints weight = 10250.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.153934 restraints weight = 10246.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157749 restraints weight = 7682.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157728 restraints weight = 6432.408| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11150 Z= 0.110 Angle : 0.500 7.510 15216 Z= 0.253 Chirality : 0.037 0.248 1722 Planarity : 0.004 0.041 1812 Dihedral : 3.681 27.240 1520 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.81 % Allowed : 17.39 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.23), residues: 1340 helix: 2.24 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.06 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 81 TYR 0.019 0.001 TYR B 205 PHE 0.028 0.001 PHE C 153 TRP 0.016 0.001 TRP E 160 HIS 0.001 0.000 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00242 (11144) covalent geometry : angle 0.49997 (15216) hydrogen bonds : bond 0.03350 ( 884) hydrogen bonds : angle 3.55443 ( 2649) Misc. bond : bond 0.00037 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8852 (mtmm) cc_final: 0.8444 (ttmt) REVERT: A 138 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: A 143 GLU cc_start: 0.8398 (tp30) cc_final: 0.8190 (tp30) REVERT: A 191 MET cc_start: 0.8231 (tmm) cc_final: 0.7864 (tmm) REVERT: A 205 TYR cc_start: 0.5772 (t80) cc_final: 0.5519 (t80) REVERT: B 80 MET cc_start: 0.6951 (mtm) cc_final: 0.6599 (mtt) REVERT: B 184 GLN cc_start: 0.8440 (mt0) cc_final: 0.8135 (mt0) REVERT: C 100 LEU cc_start: 0.8802 (tp) cc_final: 0.8425 (mt) REVERT: C 140 TYR cc_start: 0.7674 (t80) cc_final: 0.7452 (t80) REVERT: C 141 MET cc_start: 0.7758 (mmt) cc_final: 0.7512 (mmt) REVERT: C 184 GLN cc_start: 0.8154 (mt0) cc_final: 0.7913 (mm-40) REVERT: C 185 SER cc_start: 0.8337 (m) cc_final: 0.7828 (t) REVERT: C 246 GLU cc_start: 0.7777 (tp30) cc_final: 0.7269 (tm-30) REVERT: E 80 MET cc_start: 0.6938 (mtm) cc_final: 0.6569 (mtt) REVERT: E 141 MET cc_start: 0.7830 (mtm) cc_final: 0.7535 (mtt) REVERT: E 184 GLN cc_start: 0.8435 (mt0) cc_final: 0.8113 (mt0) REVERT: E 188 ASN cc_start: 0.8248 (m-40) cc_final: 0.7718 (t0) REVERT: E 191 MET cc_start: 0.7540 (ttp) cc_final: 0.7237 (tmm) REVERT: F 100 LEU cc_start: 0.8709 (tp) cc_final: 0.8418 (mt) REVERT: F 184 GLN cc_start: 0.8212 (mt0) cc_final: 0.7911 (mm-40) REVERT: F 185 SER cc_start: 0.8344 (m) cc_final: 0.7835 (t) REVERT: F 246 GLU cc_start: 0.7836 (tp30) cc_final: 0.7585 (tm-30) REVERT: D 98 ASP cc_start: 0.7893 (t70) cc_final: 0.7683 (t0) REVERT: D 138 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: D 143 GLU cc_start: 0.8537 (tp30) cc_final: 0.8259 (tp30) REVERT: D 191 MET cc_start: 0.8146 (tmm) cc_final: 0.7831 (tmm) outliers start: 20 outliers final: 16 residues processed: 309 average time/residue: 0.0961 time to fit residues: 43.5299 Evaluate side-chains 288 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 270 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 138 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 14 optimal weight: 0.0040 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.209375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.153881 restraints weight = 12194.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153398 restraints weight = 10619.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155073 restraints weight = 10211.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.158911 restraints weight = 7684.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159159 restraints weight = 6424.828| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11150 Z= 0.114 Angle : 0.502 7.994 15216 Z= 0.258 Chirality : 0.037 0.244 1722 Planarity : 0.004 0.036 1812 Dihedral : 3.727 28.595 1520 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.90 % Allowed : 17.39 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.23), residues: 1340 helix: 2.16 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.11 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 54 TYR 0.020 0.001 TYR D 205 PHE 0.025 0.001 PHE C 153 TRP 0.011 0.001 TRP C 35 HIS 0.001 0.000 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00254 (11144) covalent geometry : angle 0.50196 (15216) hydrogen bonds : bond 0.03396 ( 884) hydrogen bonds : angle 3.58689 ( 2649) Misc. bond : bond 0.00040 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 285 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8442 (ttmt) REVERT: A 138 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: A 191 MET cc_start: 0.8238 (tmm) cc_final: 0.7939 (tmm) REVERT: B 80 MET cc_start: 0.6959 (mtm) cc_final: 0.6600 (mtt) REVERT: B 184 GLN cc_start: 0.8445 (mt0) cc_final: 0.8111 (mt0) REVERT: B 188 ASN cc_start: 0.8184 (m110) cc_final: 0.7807 (t0) REVERT: B 194 ILE cc_start: 0.8532 (tp) cc_final: 0.8313 (tp) REVERT: C 100 LEU cc_start: 0.8801 (tp) cc_final: 0.8424 (mt) REVERT: C 141 MET cc_start: 0.7746 (mmt) cc_final: 0.7485 (mmt) REVERT: C 184 GLN cc_start: 0.8179 (mt0) cc_final: 0.7934 (mm-40) REVERT: C 185 SER cc_start: 0.8398 (m) cc_final: 0.7837 (t) REVERT: C 246 GLU cc_start: 0.7730 (tp30) cc_final: 0.7146 (tm-30) REVERT: E 80 MET cc_start: 0.6943 (mtm) cc_final: 0.6564 (mtt) REVERT: E 184 GLN cc_start: 0.8445 (mt0) cc_final: 0.8127 (mt0) REVERT: E 188 ASN cc_start: 0.8221 (m-40) cc_final: 0.7645 (t0) REVERT: E 191 MET cc_start: 0.7525 (ttp) cc_final: 0.7207 (tmm) REVERT: E 246 GLU cc_start: 0.8485 (tp30) cc_final: 0.8118 (tp30) REVERT: F 100 LEU cc_start: 0.8771 (tp) cc_final: 0.8455 (mt) REVERT: F 143 GLU cc_start: 0.7258 (tp30) cc_final: 0.6971 (tp30) REVERT: F 184 GLN cc_start: 0.8218 (mt0) cc_final: 0.7893 (mm-40) REVERT: F 185 SER cc_start: 0.8316 (m) cc_final: 0.7832 (t) REVERT: F 246 GLU cc_start: 0.7863 (tp30) cc_final: 0.7535 (tm-30) REVERT: D 75 TRP cc_start: 0.8028 (t60) cc_final: 0.6742 (t-100) REVERT: D 98 ASP cc_start: 0.7933 (t70) cc_final: 0.7710 (t0) REVERT: D 138 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: D 191 MET cc_start: 0.8139 (tmm) cc_final: 0.7776 (tmm) REVERT: D 246 GLU cc_start: 0.7987 (tp30) cc_final: 0.7587 (mm-30) outliers start: 21 outliers final: 16 residues processed: 296 average time/residue: 0.0914 time to fit residues: 39.7001 Evaluate side-chains 291 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 138 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 17 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 0.0060 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.209798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.154453 restraints weight = 12176.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153126 restraints weight = 10433.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.154648 restraints weight = 10517.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.158470 restraints weight = 8001.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.158495 restraints weight = 6863.848| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11150 Z= 0.112 Angle : 0.513 8.417 15216 Z= 0.262 Chirality : 0.037 0.225 1722 Planarity : 0.004 0.036 1812 Dihedral : 3.703 28.821 1520 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.99 % Allowed : 17.93 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.23), residues: 1340 helix: 2.18 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -2.10 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 81 TYR 0.020 0.001 TYR A 165 PHE 0.027 0.001 PHE C 153 TRP 0.026 0.001 TRP E 160 HIS 0.001 0.000 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00250 (11144) covalent geometry : angle 0.51314 (15216) hydrogen bonds : bond 0.03387 ( 884) hydrogen bonds : angle 3.55653 ( 2649) Misc. bond : bond 0.00040 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 289 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8646 (tppt) REVERT: A 138 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: A 150 TRP cc_start: 0.7519 (m100) cc_final: 0.7184 (m100) REVERT: A 176 CYS cc_start: 0.7607 (p) cc_final: 0.7389 (p) REVERT: A 191 MET cc_start: 0.8147 (tmm) cc_final: 0.7818 (tmm) REVERT: A 205 TYR cc_start: 0.5732 (t80) cc_final: 0.5235 (t80) REVERT: A 246 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 80 MET cc_start: 0.6875 (mtm) cc_final: 0.6598 (mtt) REVERT: B 184 GLN cc_start: 0.8447 (mt0) cc_final: 0.8178 (mt0) REVERT: B 188 ASN cc_start: 0.8202 (m110) cc_final: 0.7996 (t0) REVERT: C 78 MET cc_start: 0.8130 (mmt) cc_final: 0.7867 (mmm) REVERT: C 100 LEU cc_start: 0.8869 (tp) cc_final: 0.8471 (mt) REVERT: C 135 MET cc_start: 0.7212 (ptp) cc_final: 0.6465 (ptp) REVERT: C 184 GLN cc_start: 0.8177 (mt0) cc_final: 0.7956 (mm-40) REVERT: C 185 SER cc_start: 0.8407 (m) cc_final: 0.7838 (t) REVERT: C 246 GLU cc_start: 0.7718 (tp30) cc_final: 0.7144 (tm-30) REVERT: E 80 MET cc_start: 0.6963 (mtm) cc_final: 0.6608 (mtt) REVERT: E 140 TYR cc_start: 0.7376 (t80) cc_final: 0.7117 (t80) REVERT: E 184 GLN cc_start: 0.8462 (mt0) cc_final: 0.8199 (mt0) REVERT: E 188 ASN cc_start: 0.8357 (m-40) cc_final: 0.7927 (t0) REVERT: E 191 MET cc_start: 0.7460 (ttp) cc_final: 0.7206 (tmm) REVERT: F 100 LEU cc_start: 0.8805 (tp) cc_final: 0.8418 (mt) REVERT: F 143 GLU cc_start: 0.7308 (tp30) cc_final: 0.7008 (tp30) REVERT: F 184 GLN cc_start: 0.8198 (mt0) cc_final: 0.7874 (mm-40) REVERT: F 185 SER cc_start: 0.8336 (m) cc_final: 0.7855 (t) REVERT: F 246 GLU cc_start: 0.7866 (tp30) cc_final: 0.7512 (tm-30) REVERT: D 75 TRP cc_start: 0.7978 (t60) cc_final: 0.6642 (t-100) REVERT: D 98 ASP cc_start: 0.7942 (t70) cc_final: 0.7680 (t0) REVERT: D 150 TRP cc_start: 0.7600 (m100) cc_final: 0.7199 (m100) REVERT: D 191 MET cc_start: 0.8097 (tmm) cc_final: 0.7728 (tmm) REVERT: D 231 ASN cc_start: 0.7786 (m-40) cc_final: 0.7545 (m-40) outliers start: 22 outliers final: 15 residues processed: 300 average time/residue: 0.0916 time to fit residues: 40.0570 Evaluate side-chains 285 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 269 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 67 optimal weight: 0.2980 chunk 102 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.209726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154282 restraints weight = 12117.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.154013 restraints weight = 10200.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155600 restraints weight = 10046.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.159322 restraints weight = 7616.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.159422 restraints weight = 6495.816| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11150 Z= 0.116 Angle : 0.538 9.469 15216 Z= 0.273 Chirality : 0.037 0.217 1722 Planarity : 0.004 0.038 1812 Dihedral : 3.729 29.083 1520 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.54 % Allowed : 18.84 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.23), residues: 1340 helix: 2.11 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.03 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 81 TYR 0.023 0.001 TYR A 165 PHE 0.027 0.001 PHE C 153 TRP 0.031 0.001 TRP E 160 HIS 0.001 0.000 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00263 (11144) covalent geometry : angle 0.53784 (15216) hydrogen bonds : bond 0.03428 ( 884) hydrogen bonds : angle 3.59993 ( 2649) Misc. bond : bond 0.00039 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 286 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8644 (tppt) REVERT: A 138 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: A 150 TRP cc_start: 0.7523 (m100) cc_final: 0.7205 (m100) REVERT: A 191 MET cc_start: 0.8113 (tmm) cc_final: 0.7757 (tmm) REVERT: A 209 TYR cc_start: 0.6549 (m-80) cc_final: 0.6217 (m-80) REVERT: A 246 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7838 (mm-30) REVERT: B 80 MET cc_start: 0.6885 (mtm) cc_final: 0.6593 (mtt) REVERT: B 184 GLN cc_start: 0.8456 (mt0) cc_final: 0.8175 (mt0) REVERT: B 188 ASN cc_start: 0.8196 (m110) cc_final: 0.7968 (t0) REVERT: C 78 MET cc_start: 0.8201 (mmt) cc_final: 0.7888 (mmm) REVERT: C 100 LEU cc_start: 0.8872 (tp) cc_final: 0.8473 (mt) REVERT: C 135 MET cc_start: 0.7169 (ptp) cc_final: 0.6454 (ptp) REVERT: C 184 GLN cc_start: 0.8230 (mt0) cc_final: 0.8023 (mm-40) REVERT: C 185 SER cc_start: 0.8414 (m) cc_final: 0.7876 (t) REVERT: C 246 GLU cc_start: 0.7705 (tp30) cc_final: 0.7136 (tm-30) REVERT: E 80 MET cc_start: 0.6974 (mtm) cc_final: 0.6613 (mtt) REVERT: E 140 TYR cc_start: 0.7357 (t80) cc_final: 0.7119 (t80) REVERT: E 163 MET cc_start: 0.8370 (tpp) cc_final: 0.7940 (mtm) REVERT: E 184 GLN cc_start: 0.8462 (mt0) cc_final: 0.8215 (mt0) REVERT: E 188 ASN cc_start: 0.8352 (m-40) cc_final: 0.7894 (t0) REVERT: E 191 MET cc_start: 0.7472 (ttp) cc_final: 0.7230 (tmm) REVERT: F 100 LEU cc_start: 0.8796 (tp) cc_final: 0.8398 (mt) REVERT: F 143 GLU cc_start: 0.7310 (tp30) cc_final: 0.7012 (tp30) REVERT: F 184 GLN cc_start: 0.8180 (mt0) cc_final: 0.7923 (mm-40) REVERT: F 185 SER cc_start: 0.8433 (m) cc_final: 0.7878 (t) REVERT: F 246 GLU cc_start: 0.7897 (tp30) cc_final: 0.7529 (tm-30) REVERT: D 75 TRP cc_start: 0.8020 (t60) cc_final: 0.6615 (t-100) REVERT: D 98 ASP cc_start: 0.7935 (t70) cc_final: 0.7710 (t0) REVERT: D 150 TRP cc_start: 0.7685 (m100) cc_final: 0.7227 (m100) REVERT: D 191 MET cc_start: 0.8061 (tmm) cc_final: 0.7543 (tmm) REVERT: D 231 ASN cc_start: 0.7754 (m-40) cc_final: 0.7498 (m-40) REVERT: D 246 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7741 (mm-30) outliers start: 17 outliers final: 14 residues processed: 295 average time/residue: 0.0938 time to fit residues: 40.4324 Evaluate side-chains 287 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 272 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 113 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.0010 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.208627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.152548 restraints weight = 12028.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152070 restraints weight = 10576.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.154056 restraints weight = 10289.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.155126 restraints weight = 7679.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.155792 restraints weight = 7394.679| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11150 Z= 0.130 Angle : 0.555 9.180 15216 Z= 0.281 Chirality : 0.038 0.215 1722 Planarity : 0.004 0.038 1812 Dihedral : 3.750 30.090 1520 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.54 % Allowed : 19.20 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.23), residues: 1340 helix: 2.06 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.04 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 81 TYR 0.022 0.001 TYR A 165 PHE 0.027 0.001 PHE C 153 TRP 0.038 0.001 TRP B 160 HIS 0.001 0.001 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00304 (11144) covalent geometry : angle 0.55496 (15216) hydrogen bonds : bond 0.03636 ( 884) hydrogen bonds : angle 3.63221 ( 2649) Misc. bond : bond 0.00054 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 272 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8855 (mtmm) cc_final: 0.8630 (tppt) REVERT: A 191 MET cc_start: 0.7985 (tmm) cc_final: 0.7711 (tmm) REVERT: A 231 ASN cc_start: 0.7908 (m-40) cc_final: 0.7668 (m-40) REVERT: A 246 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7883 (mm-30) REVERT: B 80 MET cc_start: 0.6837 (mtm) cc_final: 0.6577 (mtt) REVERT: B 184 GLN cc_start: 0.8438 (mt0) cc_final: 0.8187 (mt0) REVERT: B 188 ASN cc_start: 0.8193 (m110) cc_final: 0.7898 (t0) REVERT: C 100 LEU cc_start: 0.8786 (tp) cc_final: 0.8475 (mt) REVERT: C 184 GLN cc_start: 0.8229 (mt0) cc_final: 0.7982 (mm-40) REVERT: C 185 SER cc_start: 0.8404 (m) cc_final: 0.7866 (t) REVERT: C 246 GLU cc_start: 0.7730 (tp30) cc_final: 0.7170 (tm-30) REVERT: E 80 MET cc_start: 0.6876 (mtm) cc_final: 0.6360 (mtt) REVERT: E 140 TYR cc_start: 0.7452 (t80) cc_final: 0.7205 (t80) REVERT: E 163 MET cc_start: 0.8426 (tpp) cc_final: 0.7949 (mtm) REVERT: E 184 GLN cc_start: 0.8450 (mt0) cc_final: 0.8204 (mt0) REVERT: E 188 ASN cc_start: 0.8357 (m-40) cc_final: 0.7896 (t0) REVERT: E 191 MET cc_start: 0.7495 (ttp) cc_final: 0.7240 (tmm) REVERT: E 246 GLU cc_start: 0.8479 (tp30) cc_final: 0.8182 (tp30) REVERT: F 100 LEU cc_start: 0.8781 (tp) cc_final: 0.8453 (mt) REVERT: F 143 GLU cc_start: 0.7433 (tp30) cc_final: 0.7107 (tp30) REVERT: F 184 GLN cc_start: 0.8173 (mt0) cc_final: 0.7846 (mm-40) REVERT: F 185 SER cc_start: 0.8394 (m) cc_final: 0.7837 (t) REVERT: F 246 GLU cc_start: 0.7909 (tp30) cc_final: 0.7523 (tm-30) REVERT: D 75 TRP cc_start: 0.8000 (t60) cc_final: 0.6634 (t-100) REVERT: D 98 ASP cc_start: 0.7972 (t70) cc_final: 0.7715 (t0) REVERT: D 138 PHE cc_start: 0.8441 (t80) cc_final: 0.8080 (t80) REVERT: D 150 TRP cc_start: 0.7640 (m100) cc_final: 0.7259 (m100) REVERT: D 163 MET cc_start: 0.5998 (ptt) cc_final: 0.5335 (mtm) REVERT: D 191 MET cc_start: 0.8088 (tmm) cc_final: 0.7762 (tmm) REVERT: D 231 ASN cc_start: 0.7845 (m-40) cc_final: 0.7596 (m-40) REVERT: D 246 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7776 (mm-30) outliers start: 17 outliers final: 16 residues processed: 281 average time/residue: 0.0940 time to fit residues: 38.4793 Evaluate side-chains 281 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 265 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.207772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.152055 restraints weight = 12078.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151672 restraints weight = 10136.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153666 restraints weight = 9801.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.156471 restraints weight = 7325.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156863 restraints weight = 6635.231| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11150 Z= 0.125 Angle : 0.556 9.730 15216 Z= 0.282 Chirality : 0.038 0.218 1722 Planarity : 0.004 0.040 1812 Dihedral : 3.745 29.909 1520 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.45 % Allowed : 19.20 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.23), residues: 1340 helix: 2.09 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -2.10 (0.38), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.023 0.001 TYR A 165 PHE 0.028 0.001 PHE C 153 TRP 0.033 0.001 TRP B 160 HIS 0.001 0.000 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.00290 (11144) covalent geometry : angle 0.55599 (15216) hydrogen bonds : bond 0.03574 ( 884) hydrogen bonds : angle 3.64888 ( 2649) Misc. bond : bond 0.00047 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8836 (mtmm) cc_final: 0.8619 (tppt) REVERT: A 163 MET cc_start: 0.6777 (ptp) cc_final: 0.6494 (mtm) REVERT: A 191 MET cc_start: 0.7938 (tmm) cc_final: 0.7699 (tmm) REVERT: A 231 ASN cc_start: 0.7897 (m-40) cc_final: 0.7646 (m-40) REVERT: A 246 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7870 (mm-30) REVERT: B 80 MET cc_start: 0.6864 (mtm) cc_final: 0.6564 (mtt) REVERT: B 184 GLN cc_start: 0.8435 (mt0) cc_final: 0.8183 (mt0) REVERT: B 188 ASN cc_start: 0.8187 (m110) cc_final: 0.7926 (t0) REVERT: C 100 LEU cc_start: 0.8784 (tp) cc_final: 0.8477 (mt) REVERT: C 135 MET cc_start: 0.7227 (ptp) cc_final: 0.6608 (ptp) REVERT: C 184 GLN cc_start: 0.8203 (mt0) cc_final: 0.7895 (mm-40) REVERT: C 185 SER cc_start: 0.8378 (m) cc_final: 0.7812 (t) REVERT: C 246 GLU cc_start: 0.7780 (tp30) cc_final: 0.7138 (tm-30) REVERT: E 80 MET cc_start: 0.6910 (mtm) cc_final: 0.6355 (mtt) REVERT: E 140 TYR cc_start: 0.7431 (t80) cc_final: 0.7190 (t80) REVERT: E 163 MET cc_start: 0.8425 (tpp) cc_final: 0.7974 (mtm) REVERT: E 184 GLN cc_start: 0.8423 (mt0) cc_final: 0.8205 (mt0) REVERT: E 188 ASN cc_start: 0.8329 (m-40) cc_final: 0.7872 (t0) REVERT: E 191 MET cc_start: 0.7482 (ttp) cc_final: 0.7234 (tmm) REVERT: E 246 GLU cc_start: 0.8481 (tp30) cc_final: 0.8200 (tp30) REVERT: F 100 LEU cc_start: 0.8777 (tp) cc_final: 0.8459 (mt) REVERT: F 143 GLU cc_start: 0.7463 (tp30) cc_final: 0.7024 (tp30) REVERT: F 184 GLN cc_start: 0.8189 (mt0) cc_final: 0.7886 (mm-40) REVERT: F 185 SER cc_start: 0.8394 (m) cc_final: 0.7823 (t) REVERT: F 246 GLU cc_start: 0.7912 (tp30) cc_final: 0.7540 (tm-30) REVERT: D 75 TRP cc_start: 0.8028 (t60) cc_final: 0.6684 (t-100) REVERT: D 98 ASP cc_start: 0.7957 (t70) cc_final: 0.7704 (t0) REVERT: D 138 PHE cc_start: 0.8418 (t80) cc_final: 0.8088 (t80) REVERT: D 143 GLU cc_start: 0.8228 (tp30) cc_final: 0.7991 (tp30) REVERT: D 150 TRP cc_start: 0.7640 (m100) cc_final: 0.7260 (m100) REVERT: D 163 MET cc_start: 0.5994 (ptt) cc_final: 0.5349 (mtm) REVERT: D 191 MET cc_start: 0.8063 (tmm) cc_final: 0.7748 (tmm) REVERT: D 231 ASN cc_start: 0.7825 (m-40) cc_final: 0.7573 (m-40) REVERT: D 246 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7763 (mm-30) outliers start: 16 outliers final: 15 residues processed: 281 average time/residue: 0.0915 time to fit residues: 37.7178 Evaluate side-chains 283 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 268 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 93 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.208158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.152676 restraints weight = 12215.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151552 restraints weight = 10402.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153726 restraints weight = 9917.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.154621 restraints weight = 7517.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155355 restraints weight = 7218.028| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11150 Z= 0.126 Angle : 0.565 9.581 15216 Z= 0.286 Chirality : 0.038 0.209 1722 Planarity : 0.004 0.039 1812 Dihedral : 3.761 31.025 1520 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.72 % Allowed : 19.20 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.23), residues: 1340 helix: 2.12 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -2.11 (0.38), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.023 0.001 TYR A 165 PHE 0.027 0.001 PHE C 153 TRP 0.027 0.001 TRP B 160 HIS 0.001 0.000 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00292 (11144) covalent geometry : angle 0.56522 (15216) hydrogen bonds : bond 0.03575 ( 884) hydrogen bonds : angle 3.65284 ( 2649) Misc. bond : bond 0.00048 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.52 seconds wall clock time: 31 minutes 35.24 seconds (1895.24 seconds total)