Starting phenix.real_space_refine on Thu Feb 13 04:39:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyw_60581/02_2025/8zyw_60581.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyw_60581/02_2025/8zyw_60581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zyw_60581/02_2025/8zyw_60581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyw_60581/02_2025/8zyw_60581.map" model { file = "/net/cci-nas-00/data/ceres_data/8zyw_60581/02_2025/8zyw_60581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyw_60581/02_2025/8zyw_60581.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 77 5.16 5 C 5741 2.51 5 N 1469 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8910 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 361 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 368 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "C" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 Chain: "D" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1621 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain breaks: 1 Chain: "F" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1729 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Chain: "G" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O HOH A 601 " occ=0.76 Time building chain proxies: 5.34, per 1000 atoms: 0.60 Number of scatterers: 8910 At special positions: 0 Unit cell: (102.6, 98.55, 103.95, 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 77 16.00 O 1623 8.00 N 1469 7.00 C 5741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 1 sheets defined 92.2% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.833A pdb=" N GLY A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 58 Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.084A pdb=" N PHE B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 Processing helix chain 'C' and resid 31 through 50 Processing helix chain 'C' and resid 51 through 68 removed outlier: 3.544A pdb=" N PHE C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 87 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.615A pdb=" N ASP C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 168 removed outlier: 3.560A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Proline residue: C 151 - end of helix Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 174 through 195 removed outlier: 3.543A pdb=" N ALA C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET C 179 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 228 Processing helix chain 'C' and resid 230 through 240 Processing helix chain 'C' and resid 241 through 244 removed outlier: 3.539A pdb=" N GLU C 244 " --> pdb=" O TYR C 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing helix chain 'D' and resid 26 through 30 removed outlier: 3.733A pdb=" N VAL D 30 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 50 removed outlier: 4.007A pdb=" N LYS D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 68 Processing helix chain 'D' and resid 72 through 87 removed outlier: 4.095A pdb=" N ASP D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 87 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 115 Processing helix chain 'D' and resid 117 through 167 Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 175 through 196 removed outlier: 4.059A pdb=" N ALA D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 228 removed outlier: 3.500A pdb=" N ILE D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 239 removed outlier: 4.121A pdb=" N ILE D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 removed outlier: 3.561A pdb=" N LEU D 249 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 50 removed outlier: 3.850A pdb=" N ASP E 31 " --> pdb=" O GLY E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 68 Processing helix chain 'E' and resid 72 through 87 Processing helix chain 'E' and resid 102 through 114 Processing helix chain 'E' and resid 117 through 168 Proline residue: E 151 - end of helix Processing helix chain 'E' and resid 171 through 196 removed outlier: 3.523A pdb=" N ILE E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY E 176 " --> pdb=" O PRO E 172 " (cutoff:3.500A) Proline residue: E 177 - end of helix Processing helix chain 'E' and resid 197 through 228 Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.792A pdb=" N TYR E 241 " --> pdb=" O TYR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 248 removed outlier: 6.561A pdb=" N GLY E 245 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS E 246 " --> pdb=" O ASN E 243 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG E 247 " --> pdb=" O GLU E 244 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA E 248 " --> pdb=" O GLY E 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 242 through 248' Processing helix chain 'F' and resid 4 through 23 Processing helix chain 'F' and resid 32 through 47 removed outlier: 3.650A pdb=" N VAL F 38 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 68 Processing helix chain 'F' and resid 72 through 87 Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.748A pdb=" N GLY F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 168 removed outlier: 3.522A pdb=" N VAL F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Proline residue: F 151 - end of helix Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 174 through 195 removed outlier: 3.768A pdb=" N ALA F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR F 186 " --> pdb=" O ALA F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 228 Processing helix chain 'F' and resid 230 through 243 Processing helix chain 'F' and resid 244 through 250 removed outlier: 4.196A pdb=" N ARG F 247 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 249 " --> pdb=" O LYS F 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 50 Processing helix chain 'G' and resid 51 through 68 removed outlier: 3.728A pdb=" N PHE G 68 " --> pdb=" O LYS G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 87 removed outlier: 3.545A pdb=" N LEU G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 115 Processing helix chain 'G' and resid 117 through 169 removed outlier: 3.978A pdb=" N VAL G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 171 through 196 removed outlier: 3.743A pdb=" N GLY G 176 " --> pdb=" O PRO G 172 " (cutoff:3.500A) Proline residue: G 177 - end of helix removed outlier: 3.631A pdb=" N VAL G 196 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 228 Processing helix chain 'G' and resid 230 through 243 removed outlier: 3.610A pdb=" N LYS G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR G 241 " --> pdb=" O TYR G 237 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 250 removed outlier: 3.743A pdb=" N ARG G 247 " --> pdb=" O GLU G 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 810 hydrogen bonds defined for protein. 2403 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: 2.70 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2896 1.34 - 1.46: 1813 1.46 - 1.58: 4168 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 9029 Sorted by residual: bond pdb=" CB ASN C 102 " pdb=" CG ASN C 102 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" CB MET G 219 " pdb=" CG MET G 219 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CG GLN B 49 " pdb=" CD GLN B 49 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" CB VAL C 142 " pdb=" CG1 VAL C 142 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.54e-01 bond pdb=" CA ASN C 102 " pdb=" CB ASN C 102 " ideal model delta sigma weight residual 1.528 1.542 -0.013 1.66e-02 3.63e+03 6.49e-01 ... (remaining 9024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 12053 2.22 - 4.45: 83 4.45 - 6.67: 16 6.67 - 8.89: 7 8.89 - 11.11: 1 Bond angle restraints: 12160 Sorted by residual: angle pdb=" CA GLN B 49 " pdb=" CB GLN B 49 " pdb=" CG GLN B 49 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 angle pdb=" CA LEU F 112 " pdb=" CB LEU F 112 " pdb=" CG LEU F 112 " ideal model delta sigma weight residual 116.30 127.41 -11.11 3.50e+00 8.16e-02 1.01e+01 angle pdb=" CB MET G 153 " pdb=" CG MET G 153 " pdb=" SD MET G 153 " ideal model delta sigma weight residual 112.70 121.30 -8.60 3.00e+00 1.11e-01 8.23e+00 angle pdb=" N GLN B 49 " pdb=" CA GLN B 49 " pdb=" CB GLN B 49 " ideal model delta sigma weight residual 110.39 114.98 -4.59 1.66e+00 3.63e-01 7.65e+00 angle pdb=" CB MET E 52 " pdb=" CG MET E 52 " pdb=" SD MET E 52 " ideal model delta sigma weight residual 112.70 104.84 7.86 3.00e+00 1.11e-01 6.87e+00 ... (remaining 12155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4600 17.60 - 35.20: 598 35.20 - 52.80: 194 52.80 - 70.40: 43 70.40 - 88.00: 8 Dihedral angle restraints: 5443 sinusoidal: 2129 harmonic: 3314 Sorted by residual: dihedral pdb=" CA ASP E 71 " pdb=" CB ASP E 71 " pdb=" CG ASP E 71 " pdb=" OD1 ASP E 71 " ideal model delta sinusoidal sigma weight residual -30.00 -89.12 59.12 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 119 " pdb=" CB ASP C 119 " pdb=" CG ASP C 119 " pdb=" OD1 ASP C 119 " ideal model delta sinusoidal sigma weight residual -30.00 -87.51 57.51 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP E 85 " pdb=" CB ASP E 85 " pdb=" CG ASP E 85 " pdb=" OD1 ASP E 85 " ideal model delta sinusoidal sigma weight residual -30.00 -85.29 55.29 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 5440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1095 0.038 - 0.077: 282 0.077 - 0.115: 63 0.115 - 0.153: 3 0.153 - 0.192: 3 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA GLN B 49 " pdb=" N GLN B 49 " pdb=" C GLN B 49 " pdb=" CB GLN B 49 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CB ILE C 100 " pdb=" CA ILE C 100 " pdb=" CG1 ILE C 100 " pdb=" CG2 ILE C 100 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CG LEU F 112 " pdb=" CB LEU F 112 " pdb=" CD1 LEU F 112 " pdb=" CD2 LEU F 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1443 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 28 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C LEU B 28 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 28 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 29 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 25 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C LEU B 25 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU B 25 " -0.011 2.00e-02 2.50e+03 pdb=" N MET B 26 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 26 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C MET B 26 " 0.029 2.00e-02 2.50e+03 pdb=" O MET B 26 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 27 " -0.010 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 66 2.67 - 3.23: 8730 3.23 - 3.78: 14305 3.78 - 4.34: 17710 4.34 - 4.90: 30708 Nonbonded interactions: 71519 Sorted by model distance: nonbonded pdb=" OG1 THR E 158 " pdb=" OG1 THR E 186 " model vdw 2.109 3.040 nonbonded pdb=" OG1 THR G 158 " pdb=" OG1 THR G 186 " model vdw 2.201 3.040 nonbonded pdb=" O LEU B 45 " pdb=" NE2 GLN B 49 " model vdw 2.204 3.120 nonbonded pdb=" O PHE D 29 " pdb=" OH TYR D 188 " model vdw 2.218 3.040 nonbonded pdb=" O LEU A 35 " pdb=" OG SER A 38 " model vdw 2.303 3.040 ... (remaining 71514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 59) } ncs_group { reference = (chain 'C' and resid 29 through 250) selection = (chain 'D' and resid 29 through 250) selection = (chain 'E' and resid 29 through 250) selection = (chain 'F' and (resid 15 through 16 or resid 31 through 250)) selection = (chain 'G' and resid 29 through 250) } 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=0.76 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.890 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9029 Z= 0.189 Angle : 0.546 11.114 12160 Z= 0.286 Chirality : 0.037 0.192 1446 Planarity : 0.004 0.040 1543 Dihedral : 17.928 88.000 3305 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.32 % Allowed : 26.81 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.25), residues: 1148 helix: 2.40 (0.16), residues: 992 sheet: None (None), residues: 0 loop : -0.55 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 18 HIS 0.002 0.000 HIS E 136 PHE 0.019 0.001 PHE E 56 TYR 0.005 0.001 TYR D 237 ARG 0.004 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.900 Fit side-chains REVERT: D 36 LEU cc_start: 0.8892 (tp) cc_final: 0.8607 (tt) REVERT: D 83 MET cc_start: 0.5710 (mmp) cc_final: 0.4761 (tpp) REVERT: E 195 MET cc_start: 0.8676 (mmm) cc_final: 0.8386 (mtm) REVERT: F 169 MET cc_start: 0.8613 (tpp) cc_final: 0.8226 (tpp) REVERT: G 219 MET cc_start: 0.6050 (mmm) cc_final: 0.5741 (mmp) outliers start: 3 outliers final: 1 residues processed: 132 average time/residue: 0.2422 time to fit residues: 43.2114 Evaluate side-chains 130 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 105 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 40.0000 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.209571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.148829 restraints weight = 8865.327| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.15 r_work: 0.3106 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9029 Z= 0.182 Angle : 0.473 8.208 12160 Z= 0.250 Chirality : 0.036 0.163 1446 Planarity : 0.003 0.033 1543 Dihedral : 3.537 34.114 1224 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.49 % Allowed : 26.49 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.25), residues: 1148 helix: 2.73 (0.16), residues: 1001 sheet: None (None), residues: 0 loop : -0.61 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.003 0.000 HIS E 136 PHE 0.015 0.001 PHE E 56 TYR 0.004 0.001 TYR D 237 ARG 0.003 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.843 Fit side-chains REVERT: B 49 GLN cc_start: 0.6792 (mp10) cc_final: 0.6530 (mp10) REVERT: C 36 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8091 (mp) REVERT: C 83 MET cc_start: 0.5607 (mmt) cc_final: 0.5207 (tpt) REVERT: D 36 LEU cc_start: 0.8935 (tp) cc_final: 0.8663 (tt) REVERT: D 68 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6953 (m-10) REVERT: D 219 MET cc_start: 0.6033 (tmm) cc_final: 0.5531 (tmm) REVERT: E 179 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8442 (tpt) REVERT: E 202 ASP cc_start: 0.7526 (m-30) cc_final: 0.7194 (m-30) REVERT: F 153 MET cc_start: 0.9021 (mmm) cc_final: 0.8801 (mmm) REVERT: G 105 MET cc_start: 0.5965 (ttp) cc_final: 0.5686 (ttp) REVERT: G 148 ASP cc_start: 0.7682 (m-30) cc_final: 0.7439 (m-30) outliers start: 14 outliers final: 8 residues processed: 143 average time/residue: 0.2194 time to fit residues: 42.6643 Evaluate side-chains 140 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 0.0170 chunk 55 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN E 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.211481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149186 restraints weight = 9004.612| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.52 r_work: 0.3127 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9029 Z= 0.145 Angle : 0.434 8.688 12160 Z= 0.228 Chirality : 0.035 0.159 1446 Planarity : 0.003 0.034 1543 Dihedral : 3.271 12.620 1221 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.02 % Allowed : 26.06 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.24), residues: 1148 helix: 2.94 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -0.62 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.002 0.000 HIS E 136 PHE 0.012 0.001 PHE A 39 TYR 0.005 0.000 TYR D 237 ARG 0.003 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.894 Fit side-chains REVERT: B 49 GLN cc_start: 0.6779 (mp10) cc_final: 0.6450 (mp10) REVERT: C 36 LEU cc_start: 0.8666 (tp) cc_final: 0.8197 (mp) REVERT: D 36 LEU cc_start: 0.8937 (tp) cc_final: 0.8671 (tt) REVERT: D 56 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.7021 (m-10) REVERT: D 68 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6968 (m-10) REVERT: D 219 MET cc_start: 0.6106 (tmm) cc_final: 0.5563 (tmm) REVERT: E 202 ASP cc_start: 0.7533 (m-30) cc_final: 0.7223 (m-30) REVERT: E 244 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6760 (tt0) REVERT: F 20 MET cc_start: 0.2723 (mmt) cc_final: 0.2297 (mmm) REVERT: G 102 ASN cc_start: 0.6928 (OUTLIER) cc_final: 0.6646 (t0) REVERT: G 148 ASP cc_start: 0.7673 (m-30) cc_final: 0.7388 (m-30) outliers start: 19 outliers final: 6 residues processed: 146 average time/residue: 0.2131 time to fit residues: 42.8750 Evaluate side-chains 139 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 PHE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 192 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 47 optimal weight: 30.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.209679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.147337 restraints weight = 8999.907| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.56 r_work: 0.3111 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9029 Z= 0.183 Angle : 0.450 8.669 12160 Z= 0.237 Chirality : 0.036 0.160 1446 Planarity : 0.003 0.038 1543 Dihedral : 3.259 12.519 1221 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.66 % Allowed : 25.53 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.24), residues: 1148 helix: 2.99 (0.16), residues: 997 sheet: None (None), residues: 0 loop : -0.47 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.003 0.000 HIS E 136 PHE 0.011 0.001 PHE E 56 TYR 0.005 0.001 TYR D 237 ARG 0.004 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: C 36 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8216 (mp) REVERT: D 36 LEU cc_start: 0.8917 (tp) cc_final: 0.8642 (tt) REVERT: D 67 MET cc_start: 0.7813 (tmm) cc_final: 0.7402 (tmm) REVERT: D 68 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6974 (m-10) REVERT: D 219 MET cc_start: 0.6117 (tmm) cc_final: 0.5836 (tmm) REVERT: E 202 ASP cc_start: 0.7759 (m-30) cc_final: 0.7390 (m-30) REVERT: E 244 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6689 (tt0) REVERT: F 20 MET cc_start: 0.2715 (mmt) cc_final: 0.2404 (mmm) REVERT: G 148 ASP cc_start: 0.7696 (m-30) cc_final: 0.7361 (m-30) outliers start: 25 outliers final: 19 residues processed: 150 average time/residue: 0.2142 time to fit residues: 44.8827 Evaluate side-chains 152 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 200 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 0.0070 chunk 36 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN G 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.210291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147796 restraints weight = 8923.098| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.60 r_work: 0.3083 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9029 Z= 0.209 Angle : 0.464 8.763 12160 Z= 0.244 Chirality : 0.036 0.165 1446 Planarity : 0.003 0.039 1543 Dihedral : 3.309 12.650 1221 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.09 % Allowed : 25.85 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.24), residues: 1148 helix: 2.95 (0.16), residues: 997 sheet: None (None), residues: 0 loop : -0.54 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.003 0.001 HIS E 136 PHE 0.012 0.001 PHE D 143 TYR 0.005 0.001 TYR D 237 ARG 0.004 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: B 30 MET cc_start: 0.8191 (tmm) cc_final: 0.7974 (tmm) REVERT: B 49 GLN cc_start: 0.6516 (mp10) cc_final: 0.6241 (mp10) REVERT: D 36 LEU cc_start: 0.8938 (tp) cc_final: 0.8659 (tt) REVERT: D 219 MET cc_start: 0.6172 (tmm) cc_final: 0.5924 (tmm) REVERT: E 202 ASP cc_start: 0.7843 (m-30) cc_final: 0.7469 (m-30) REVERT: E 244 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6813 (tt0) REVERT: F 3 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6550 (tt) REVERT: F 20 MET cc_start: 0.2799 (mmt) cc_final: 0.2497 (mmm) REVERT: G 72 GLU cc_start: 0.7269 (pm20) cc_final: 0.7023 (pm20) REVERT: G 148 ASP cc_start: 0.7777 (m-30) cc_final: 0.7375 (m-30) outliers start: 29 outliers final: 20 residues processed: 151 average time/residue: 0.2116 time to fit residues: 44.2354 Evaluate side-chains 151 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 200 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 24 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 27 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN G 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.211007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149103 restraints weight = 8932.271| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.48 r_work: 0.3078 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9029 Z= 0.189 Angle : 0.453 8.767 12160 Z= 0.238 Chirality : 0.036 0.163 1446 Planarity : 0.003 0.040 1543 Dihedral : 3.284 12.654 1221 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.87 % Allowed : 26.38 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.24), residues: 1148 helix: 2.99 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -0.51 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.002 0.000 HIS E 136 PHE 0.012 0.001 PHE D 143 TYR 0.005 0.001 TYR D 237 ARG 0.004 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 MET cc_start: 0.8120 (tmm) cc_final: 0.7856 (tmm) REVERT: B 49 GLN cc_start: 0.6555 (mp10) cc_final: 0.6269 (mp10) REVERT: D 36 LEU cc_start: 0.8927 (tp) cc_final: 0.8651 (tt) REVERT: D 68 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6986 (m-10) REVERT: D 179 MET cc_start: 0.8458 (mmm) cc_final: 0.8098 (tpt) REVERT: D 219 MET cc_start: 0.6094 (tmm) cc_final: 0.5829 (tmm) REVERT: E 56 PHE cc_start: 0.7546 (m-80) cc_final: 0.7275 (m-80) REVERT: E 202 ASP cc_start: 0.7865 (m-30) cc_final: 0.7508 (m-30) REVERT: E 244 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6242 (tt0) REVERT: F 3 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6597 (tt) REVERT: F 20 MET cc_start: 0.2818 (mmt) cc_final: 0.2513 (mmm) REVERT: G 105 MET cc_start: 0.6235 (ttp) cc_final: 0.5884 (ttp) REVERT: G 148 ASP cc_start: 0.7847 (m-30) cc_final: 0.7424 (m-30) outliers start: 27 outliers final: 19 residues processed: 155 average time/residue: 0.2121 time to fit residues: 45.7724 Evaluate side-chains 157 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 241 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 63 optimal weight: 0.0050 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN D 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.210428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147851 restraints weight = 9029.172| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.55 r_work: 0.3082 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9029 Z= 0.204 Angle : 0.465 8.702 12160 Z= 0.244 Chirality : 0.036 0.165 1446 Planarity : 0.003 0.040 1543 Dihedral : 3.300 12.589 1221 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.19 % Allowed : 25.85 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.25), residues: 1148 helix: 2.89 (0.16), residues: 1011 sheet: None (None), residues: 0 loop : -0.48 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.003 0.000 HIS E 136 PHE 0.012 0.001 PHE D 143 TYR 0.004 0.001 TYR D 237 ARG 0.004 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 MET cc_start: 0.8102 (tmm) cc_final: 0.7828 (tmm) REVERT: B 49 GLN cc_start: 0.6455 (mp10) cc_final: 0.6167 (mp10) REVERT: D 36 LEU cc_start: 0.8932 (tp) cc_final: 0.8662 (tt) REVERT: D 179 MET cc_start: 0.8467 (mmm) cc_final: 0.8129 (tpt) REVERT: D 219 MET cc_start: 0.6055 (tmm) cc_final: 0.5790 (tmm) REVERT: E 52 MET cc_start: 0.7561 (tpp) cc_final: 0.7131 (tpt) REVERT: E 56 PHE cc_start: 0.7650 (m-80) cc_final: 0.7381 (m-80) REVERT: E 202 ASP cc_start: 0.7853 (m-30) cc_final: 0.7489 (m-30) REVERT: E 244 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6212 (tt0) REVERT: F 3 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6676 (tt) REVERT: F 20 MET cc_start: 0.2837 (mmt) cc_final: 0.2530 (mmm) REVERT: F 232 ARG cc_start: 0.4435 (OUTLIER) cc_final: 0.2418 (ttm110) REVERT: G 72 GLU cc_start: 0.7223 (pm20) cc_final: 0.7005 (pm20) REVERT: G 105 MET cc_start: 0.6207 (ttp) cc_final: 0.5901 (tmm) REVERT: G 148 ASP cc_start: 0.7830 (m-30) cc_final: 0.7395 (m-30) REVERT: G 217 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5555 (mp) outliers start: 30 outliers final: 23 residues processed: 159 average time/residue: 0.2333 time to fit residues: 50.7045 Evaluate side-chains 162 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 241 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.194951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133258 restraints weight = 9042.951| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.39 r_work: 0.2995 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9029 Z= 0.372 Angle : 0.560 8.652 12160 Z= 0.294 Chirality : 0.040 0.165 1446 Planarity : 0.004 0.039 1543 Dihedral : 3.581 14.854 1221 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.94 % Allowed : 25.43 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.25), residues: 1148 helix: 2.56 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.82 (0.49), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.004 0.001 HIS E 136 PHE 0.015 0.002 PHE A 39 TYR 0.008 0.001 TYR D 188 ARG 0.005 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 MET cc_start: 0.8213 (tmm) cc_final: 0.7928 (tmm) REVERT: B 49 GLN cc_start: 0.6482 (mp10) cc_final: 0.6169 (mp10) REVERT: C 173 LYS cc_start: 0.8621 (mttt) cc_final: 0.8371 (mtpt) REVERT: D 36 LEU cc_start: 0.8932 (tp) cc_final: 0.8630 (tt) REVERT: D 179 MET cc_start: 0.8679 (mmm) cc_final: 0.8369 (tpt) REVERT: D 195 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8751 (mtm) REVERT: D 219 MET cc_start: 0.6146 (tmm) cc_final: 0.5420 (tmm) REVERT: E 56 PHE cc_start: 0.7966 (m-80) cc_final: 0.7552 (m-80) REVERT: E 202 ASP cc_start: 0.7780 (m-30) cc_final: 0.7216 (m-30) REVERT: E 244 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6323 (tt0) REVERT: F 3 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6700 (tt) REVERT: F 20 MET cc_start: 0.2840 (mmt) cc_final: 0.2536 (mmm) REVERT: F 135 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7748 (mmm-85) REVERT: F 144 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8075 (ttm-80) REVERT: F 232 ARG cc_start: 0.4587 (OUTLIER) cc_final: 0.2907 (mmp-170) REVERT: G 72 GLU cc_start: 0.7261 (pm20) cc_final: 0.6960 (pm20) REVERT: G 105 MET cc_start: 0.6266 (ttp) cc_final: 0.6012 (ttp) REVERT: G 148 ASP cc_start: 0.7918 (m-30) cc_final: 0.7627 (m-30) REVERT: G 217 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5533 (mp) outliers start: 37 outliers final: 23 residues processed: 164 average time/residue: 0.2258 time to fit residues: 50.3470 Evaluate side-chains 163 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 144 ARG Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 241 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 35 optimal weight: 20.0000 chunk 108 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.198200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135811 restraints weight = 8885.829| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.26 r_work: 0.3036 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9029 Z= 0.221 Angle : 0.486 8.692 12160 Z= 0.255 Chirality : 0.037 0.191 1446 Planarity : 0.003 0.040 1543 Dihedral : 3.436 13.991 1221 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.30 % Allowed : 26.17 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.25), residues: 1148 helix: 2.75 (0.16), residues: 1007 sheet: None (None), residues: 0 loop : -0.54 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 18 HIS 0.003 0.000 HIS E 136 PHE 0.013 0.001 PHE D 143 TYR 0.004 0.001 TYR D 237 ARG 0.005 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: B 30 MET cc_start: 0.8192 (tmm) cc_final: 0.7901 (tmm) REVERT: B 49 GLN cc_start: 0.6525 (mp10) cc_final: 0.6212 (mp10) REVERT: C 209 ASP cc_start: 0.6239 (m-30) cc_final: 0.5971 (m-30) REVERT: D 36 LEU cc_start: 0.8981 (tp) cc_final: 0.8690 (tt) REVERT: D 179 MET cc_start: 0.8544 (mmm) cc_final: 0.8144 (tpt) REVERT: D 219 MET cc_start: 0.6301 (tmm) cc_final: 0.5534 (tmm) REVERT: E 52 MET cc_start: 0.7531 (tpp) cc_final: 0.7033 (tpt) REVERT: E 56 PHE cc_start: 0.7580 (m-80) cc_final: 0.7091 (m-80) REVERT: E 202 ASP cc_start: 0.7865 (m-30) cc_final: 0.7468 (m-30) REVERT: E 244 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6253 (tt0) REVERT: F 3 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6456 (tt) REVERT: F 20 MET cc_start: 0.2823 (mmt) cc_final: 0.2530 (mmm) REVERT: F 144 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7913 (ttm-80) REVERT: F 232 ARG cc_start: 0.4514 (OUTLIER) cc_final: 0.2794 (mmp-170) REVERT: G 72 GLU cc_start: 0.7333 (pm20) cc_final: 0.7048 (pm20) REVERT: G 105 MET cc_start: 0.6264 (ttp) cc_final: 0.6009 (ttp) REVERT: G 148 ASP cc_start: 0.7865 (m-30) cc_final: 0.7301 (m-30) REVERT: G 217 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5497 (mp) outliers start: 31 outliers final: 23 residues processed: 155 average time/residue: 0.2313 time to fit residues: 49.0041 Evaluate side-chains 160 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 144 ARG Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.198619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136831 restraints weight = 8901.106| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.28 r_work: 0.3066 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9029 Z= 0.209 Angle : 0.478 8.760 12160 Z= 0.250 Chirality : 0.036 0.165 1446 Planarity : 0.003 0.040 1543 Dihedral : 3.380 13.711 1221 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.19 % Allowed : 26.28 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.25), residues: 1148 helix: 2.83 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -0.58 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 18 HIS 0.003 0.001 HIS E 136 PHE 0.013 0.001 PHE D 143 TYR 0.004 0.001 TYR D 237 ARG 0.005 0.000 ARG D 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: B 30 MET cc_start: 0.8102 (tmm) cc_final: 0.7826 (tmm) REVERT: B 49 GLN cc_start: 0.6523 (mp10) cc_final: 0.6188 (mp10) REVERT: D 36 LEU cc_start: 0.8952 (tp) cc_final: 0.8682 (tt) REVERT: D 179 MET cc_start: 0.8461 (mmm) cc_final: 0.8117 (tpt) REVERT: D 219 MET cc_start: 0.6288 (tmm) cc_final: 0.5952 (tmm) REVERT: E 52 MET cc_start: 0.7452 (tpp) cc_final: 0.6894 (tpt) REVERT: E 56 PHE cc_start: 0.7583 (m-80) cc_final: 0.7066 (m-80) REVERT: E 202 ASP cc_start: 0.7859 (m-30) cc_final: 0.7472 (m-30) REVERT: E 244 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5654 (tt0) REVERT: F 3 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6120 (tt) REVERT: F 20 MET cc_start: 0.2840 (mmt) cc_final: 0.2549 (mmm) REVERT: F 105 MET cc_start: 0.6748 (ttm) cc_final: 0.6393 (ttm) REVERT: F 232 ARG cc_start: 0.4512 (OUTLIER) cc_final: 0.2590 (ttm110) REVERT: G 72 GLU cc_start: 0.7293 (pm20) cc_final: 0.7022 (pm20) REVERT: G 105 MET cc_start: 0.6275 (ttp) cc_final: 0.5977 (tmm) REVERT: G 148 ASP cc_start: 0.7928 (m-30) cc_final: 0.7463 (m-30) REVERT: G 217 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5470 (mp) outliers start: 30 outliers final: 25 residues processed: 154 average time/residue: 0.2192 time to fit residues: 46.1043 Evaluate side-chains 161 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 241 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.209097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146945 restraints weight = 9019.715| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.98 r_work: 0.3103 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9029 Z= 0.170 Angle : 0.463 8.852 12160 Z= 0.241 Chirality : 0.036 0.165 1446 Planarity : 0.003 0.040 1543 Dihedral : 3.317 13.004 1221 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.98 % Allowed : 26.60 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.25), residues: 1148 helix: 2.93 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.51 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 18 HIS 0.002 0.000 HIS E 136 PHE 0.017 0.001 PHE A 39 TYR 0.005 0.001 TYR D 237 ARG 0.005 0.000 ARG D 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4083.49 seconds wall clock time: 73 minutes 8.49 seconds (4388.49 seconds total)