Starting phenix.real_space_refine on Thu Sep 18 15:15:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmb_51447/09_2025/9gmb_51447.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmb_51447/09_2025/9gmb_51447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gmb_51447/09_2025/9gmb_51447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmb_51447/09_2025/9gmb_51447.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmb_51447/09_2025/9gmb_51447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmb_51447/09_2025/9gmb_51447.cif" } resolution = 4.2 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 5648 2.51 5 N 1591 2.21 5 O 1731 1.98 5 H 8865 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17867 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 5168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 5168 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 5, 'TRANS': 317} Chain: "E" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3333 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain: "F" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3305 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "I" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 738 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "J" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 762 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "D" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4561 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 4, 'TRANS': 282} Time building chain proxies: 3.57, per 1000 atoms: 0.20 Number of scatterers: 17867 At special positions: 0 Unit cell: (83.9529, 146.562, 113.834, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 1731 8.00 N 1591 7.00 C 5648 6.00 H 8865 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.54 Conformation dependent library (CDL) restraints added in 587.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 11 sheets defined 75.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'C' and resid 9 through 19 Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 49 through 64 Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 69 through 84 Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.647A pdb=" N TYR C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 146 removed outlier: 3.815A pdb=" N LEU C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 156 Processing helix chain 'C' and resid 156 through 163 Processing helix chain 'C' and resid 163 through 196 removed outlier: 3.725A pdb=" N ASP C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 241 removed outlier: 3.565A pdb=" N SER C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 289 removed outlier: 3.610A pdb=" N ASP C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY C 267 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN C 268 " --> pdb=" O ILE C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 307 removed outlier: 3.669A pdb=" N GLN C 299 " --> pdb=" O ARG C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 311 Processing helix chain 'E' and resid 11 through 19 Processing helix chain 'E' and resid 22 through 31 removed outlier: 3.825A pdb=" N LEU E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG E 31 " --> pdb=" O ASP E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 50 Processing helix chain 'E' and resid 50 through 59 Processing helix chain 'E' and resid 89 through 105 removed outlier: 3.740A pdb=" N LEU E 104 " --> pdb=" O CYS E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 112 removed outlier: 3.648A pdb=" N LEU E 109 " --> pdb=" O PRO E 106 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA E 110 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 125 Processing helix chain 'E' and resid 129 through 138 removed outlier: 4.170A pdb=" N LEU E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 165 removed outlier: 3.598A pdb=" N ARG E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 187 Processing helix chain 'E' and resid 188 through 193 removed outlier: 4.620A pdb=" N ALA E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 208 Processing helix chain 'F' and resid 11 through 19 Processing helix chain 'F' and resid 22 through 32 removed outlier: 3.677A pdb=" N LEU F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 50 through 59 removed outlier: 3.597A pdb=" N LEU F 54 " --> pdb=" O PHE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 104 removed outlier: 3.819A pdb=" N LEU F 104 " --> pdb=" O CYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 112 removed outlier: 4.267A pdb=" N ALA F 110 " --> pdb=" O PRO F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.586A pdb=" N LEU F 120 " --> pdb=" O THR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 138 Processing helix chain 'F' and resid 144 through 166 removed outlier: 3.576A pdb=" N ARG F 148 " --> pdb=" O SER F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 192 removed outlier: 3.580A pdb=" N PHE F 185 " --> pdb=" O GLU F 182 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA F 189 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASP F 190 " --> pdb=" O PHE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 208 Processing helix chain 'I' and resid 10 through 49 removed outlier: 3.537A pdb=" N ASN I 32 " --> pdb=" O ASP I 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 49 removed outlier: 4.284A pdb=" N ASP J 15 " --> pdb=" O ASP J 11 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN J 17 " --> pdb=" O TRP J 13 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP J 21 " --> pdb=" O GLN J 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 25 through 40 Processing helix chain 'D' and resid 49 through 63 Processing helix chain 'D' and resid 69 through 85 Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.998A pdb=" N TYR D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 146 removed outlier: 3.745A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 156 Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 163 through 196 removed outlier: 3.564A pdb=" N LYS D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 241 removed outlier: 4.506A pdb=" N SER D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 289 removed outlier: 3.663A pdb=" N LEU D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY D 267 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN D 268 " --> pdb=" O ILE D 264 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 22 through 24 Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 48 removed outlier: 4.155A pdb=" N MET C 47 " --> pdb=" O TYR C 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 313 through 315 removed outlier: 3.748A pdb=" N ALA C 314 " --> pdb=" O MET E 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 317 through 318 Processing sheet with id=AA5, first strand: chain 'C' and resid 323 through 325 removed outlier: 5.828A pdb=" N LEU C 323 " --> pdb=" O SER F 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 63 through 66 Processing sheet with id=AA7, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.743A pdb=" N PHE E 178 " --> pdb=" O PHE E 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 63 through 67 Processing sheet with id=AA9, first strand: chain 'F' and resid 114 through 115 Processing sheet with id=AB1, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 48 removed outlier: 3.890A pdb=" N MET D 47 " --> pdb=" O TYR D 101 " (cutoff:3.500A) 638 hydrogen bonds defined for protein. 1863 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: 3.98 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8637 1.03 - 1.23: 236 1.23 - 1.42: 3912 1.42 - 1.62: 5172 1.62 - 1.81: 60 Bond restraints: 18017 Sorted by residual: bond pdb=" ND1 HIS C 280 " pdb=" CE1 HIS C 280 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.74e+01 bond pdb=" ND1 HIS C 282 " pdb=" CE1 HIS C 282 " ideal model delta sigma weight residual 1.321 1.234 0.087 1.00e-02 1.00e+04 7.59e+01 bond pdb=" N ASP C 187 " pdb=" H ASP C 187 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE1 HIS C 282 " pdb=" HE1 HIS C 282 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 HIS C 282 " pdb=" HD2 HIS C 282 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 18012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 32019 3.13 - 6.25: 345 6.25 - 9.38: 84 9.38 - 12.51: 6 12.51 - 15.63: 2 Bond angle restraints: 32456 Sorted by residual: angle pdb=" C ILE C 289 " pdb=" N ASP C 290 " pdb=" CA ASP C 290 " ideal model delta sigma weight residual 120.68 134.53 -13.85 1.70e+00 3.46e-01 6.64e+01 angle pdb=" O ILE C 289 " pdb=" C ILE C 289 " pdb=" N ASP C 290 " ideal model delta sigma weight residual 122.12 111.66 10.46 1.38e+00 5.25e-01 5.75e+01 angle pdb=" CA HIS C 282 " pdb=" CB HIS C 282 " pdb=" CG HIS C 282 " ideal model delta sigma weight residual 113.80 120.66 -6.86 1.00e+00 1.00e+00 4.70e+01 angle pdb=" CA ILE C 289 " pdb=" C ILE C 289 " pdb=" N ASP C 290 " ideal model delta sigma weight residual 118.25 127.35 -9.10 1.33e+00 5.65e-01 4.68e+01 angle pdb=" CA ASP C 188 " pdb=" CB ASP C 188 " pdb=" CG ASP C 188 " ideal model delta sigma weight residual 112.60 119.43 -6.83 1.00e+00 1.00e+00 4.67e+01 ... (remaining 32451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 7326 16.89 - 33.79: 736 33.79 - 50.68: 215 50.68 - 67.57: 85 67.57 - 84.46: 20 Dihedral angle restraints: 8382 sinusoidal: 4619 harmonic: 3763 Sorted by residual: dihedral pdb=" CA VAL D 8 " pdb=" C VAL D 8 " pdb=" N PRO D 9 " pdb=" CA PRO D 9 " ideal model delta harmonic sigma weight residual -180.00 -154.58 -25.42 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" C GLN C 191 " pdb=" N GLN C 191 " pdb=" CA GLN C 191 " pdb=" CB GLN C 191 " ideal model delta harmonic sigma weight residual -122.60 -134.07 11.47 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" N GLN C 191 " pdb=" C GLN C 191 " pdb=" CA GLN C 191 " pdb=" CB GLN C 191 " ideal model delta harmonic sigma weight residual 122.80 133.84 -11.04 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 8379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 1334 0.142 - 0.284: 5 0.284 - 0.427: 3 0.427 - 0.569: 20 0.569 - 0.711: 8 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CG LEU C 208 " pdb=" CB LEU C 208 " pdb=" CD1 LEU C 208 " pdb=" CD2 LEU C 208 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CG LEU C 192 " pdb=" CB LEU C 192 " pdb=" CD1 LEU C 192 " pdb=" CD2 LEU C 192 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CG LEU C 207 " pdb=" CB LEU C 207 " pdb=" CD1 LEU C 207 " pdb=" CD2 LEU C 207 " both_signs ideal model delta sigma weight residual False -2.59 -1.90 -0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 1367 not shown) Planarity restraints: 2706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 197 " -0.140 2.00e-02 2.50e+03 4.79e-02 9.18e+01 pdb=" CG TRP C 197 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP C 197 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP C 197 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP C 197 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TRP C 197 " 0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP C 197 " 0.050 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 197 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 197 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 197 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 TRP C 197 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP C 197 " 0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP C 197 " 0.077 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 197 " -0.031 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 197 " -0.012 2.00e-02 2.50e+03 pdb=" HH2 TRP C 197 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 287 " -0.023 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C THR C 287 " 0.080 2.00e-02 2.50e+03 pdb=" O THR C 287 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA C 288 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 196 " -0.078 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO E 197 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO E 197 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 197 " -0.060 5.00e-02 4.00e+02 ... (remaining 2703 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 219 2.04 - 2.68: 26708 2.68 - 3.32: 51396 3.32 - 3.96: 60462 3.96 - 4.60: 95913 Nonbonded interactions: 234698 Sorted by model distance: nonbonded pdb=" HZ1 LYS E 177 " pdb=" HB2 ASN D 98 " model vdw 1.401 2.270 nonbonded pdb="HH21 ARG C 89 " pdb=" OH TYR C 101 " model vdw 1.521 2.450 nonbonded pdb=" OE1 GLU F 119 " pdb=" H GLU F 119 " model vdw 1.542 2.450 nonbonded pdb="HH12 ARG C 300 " pdb=" O ALA E 193 " model vdw 1.544 2.450 nonbonded pdb=" OE1 GLU D 93 " pdb=" H GLU D 93 " model vdw 1.549 2.450 ... (remaining 234693 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 'C' and resid 6 through 292) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 9 through 209) selection = (chain 'F' and resid 9 through 209) } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 4 through 49) } 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.120 Find NCS groups from input model: 0.200 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 : 0.009 0.136 9152 Z= 0.495 Angle : 0.891 13.851 12363 Z= 0.564 Chirality : 0.090 0.711 1370 Planarity : 0.007 0.159 1629 Dihedral : 16.350 84.464 3461 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.51 % Allowed : 19.24 % Favored : 80.25 % Cbeta Deviations : 1.32 % 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: 1.82 (0.25), residues: 1099 helix: 2.00 (0.18), residues: 776 sheet: 0.40 (0.86), residues: 32 loop : -0.90 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 198 TYR 0.032 0.002 TYR C 277 PHE 0.029 0.001 PHE C 284 TRP 0.088 0.005 TRP C 197 HIS 0.005 0.001 HIS E 44 Details of bonding type rmsd covalent geometry : bond 0.00894 ( 9152) covalent geometry : angle 0.89095 (12363) hydrogen bonds : bond 0.14472 ( 638) hydrogen bonds : angle 5.76551 ( 1863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 GLU cc_start: 0.8439 (tp30) cc_final: 0.8202 (tp30) outliers start: 5 outliers final: 3 residues processed: 187 average time/residue: 0.2793 time to fit residues: 68.6096 Evaluate side-chains 127 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 17 GLN D 175 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.083248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.058653 restraints weight = 118595.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.061170 restraints weight = 57799.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.062788 restraints weight = 36480.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.063802 restraints weight = 27192.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.064438 restraints weight = 22682.324| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9152 Z= 0.138 Angle : 0.517 5.382 12363 Z= 0.288 Chirality : 0.034 0.154 1370 Planarity : 0.005 0.066 1629 Dihedral : 3.952 21.047 1233 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.25), residues: 1099 helix: 2.36 (0.18), residues: 791 sheet: 0.66 (0.92), residues: 32 loop : -0.77 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 198 TYR 0.024 0.002 TYR F 53 PHE 0.008 0.001 PHE C 284 TRP 0.023 0.001 TRP D 266 HIS 0.004 0.001 HIS E 44 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9152) covalent geometry : angle 0.51720 (12363) hydrogen bonds : bond 0.05346 ( 638) hydrogen bonds : angle 4.70868 ( 1863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 GLU cc_start: 0.8851 (tp30) cc_final: 0.8588 (tp30) REVERT: E 23 PHE cc_start: 0.8800 (t80) cc_final: 0.8435 (t80) REVERT: E 94 MET cc_start: 0.8870 (mmm) cc_final: 0.8478 (mmp) REVERT: E 95 VAL cc_start: 0.9266 (t) cc_final: 0.8818 (p) REVERT: I 24 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8474 (tm-30) REVERT: I 31 LYS cc_start: 0.9578 (mmmm) cc_final: 0.9327 (mmmm) REVERT: J 15 ASP cc_start: 0.8195 (m-30) cc_final: 0.7784 (m-30) REVERT: J 19 TYR cc_start: 0.9080 (m-10) cc_final: 0.8865 (m-10) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3014 time to fit residues: 60.2090 Evaluate side-chains 118 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 GLN ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.082073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057494 restraints weight = 119974.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.060004 restraints weight = 58957.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.061672 restraints weight = 37185.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.062736 restraints weight = 27585.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.063388 restraints weight = 22770.629| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9152 Z= 0.146 Angle : 0.493 5.152 12363 Z= 0.277 Chirality : 0.033 0.146 1370 Planarity : 0.004 0.053 1629 Dihedral : 3.976 23.129 1233 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 2.67 (0.25), residues: 1099 helix: 2.60 (0.18), residues: 783 sheet: 0.63 (0.97), residues: 32 loop : -0.53 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 116 TYR 0.014 0.001 TYR E 58 PHE 0.009 0.001 PHE F 72 TRP 0.007 0.001 TRP D 274 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9152) covalent geometry : angle 0.49296 (12363) hydrogen bonds : bond 0.04960 ( 638) hydrogen bonds : angle 4.53417 ( 1863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 23 PHE cc_start: 0.8815 (t80) cc_final: 0.8478 (t80) REVERT: E 94 MET cc_start: 0.8892 (mmm) cc_final: 0.8550 (mmp) REVERT: E 173 HIS cc_start: 0.7423 (t-90) cc_final: 0.7060 (t-90) REVERT: I 21 ASP cc_start: 0.8843 (t70) cc_final: 0.8418 (t0) REVERT: I 24 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8624 (tm-30) REVERT: I 27 ASN cc_start: 0.9236 (m110) cc_final: 0.8766 (m110) REVERT: I 31 LYS cc_start: 0.9625 (mmmm) cc_final: 0.9353 (mmmm) REVERT: J 15 ASP cc_start: 0.8233 (m-30) cc_final: 0.7953 (m-30) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3067 time to fit residues: 56.6858 Evaluate side-chains 111 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN I 27 ASN ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.081770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.057385 restraints weight = 119895.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.059882 restraints weight = 58792.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.061499 restraints weight = 37093.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.062521 restraints weight = 27620.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.063068 restraints weight = 22919.924| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9152 Z= 0.124 Angle : 0.463 5.204 12363 Z= 0.256 Chirality : 0.032 0.148 1370 Planarity : 0.004 0.054 1629 Dihedral : 3.802 19.810 1233 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: 3.06 (0.26), residues: 1099 helix: 2.85 (0.18), residues: 786 sheet: 0.88 (0.87), residues: 42 loop : -0.35 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 302 TYR 0.018 0.001 TYR J 40 PHE 0.012 0.001 PHE E 57 TRP 0.007 0.001 TRP D 266 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9152) covalent geometry : angle 0.46285 (12363) hydrogen bonds : bond 0.04478 ( 638) hydrogen bonds : angle 4.27719 ( 1863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 MET cc_start: 0.3823 (mtm) cc_final: 0.3277 (ptp) REVERT: E 23 PHE cc_start: 0.8753 (t80) cc_final: 0.8345 (t80) REVERT: E 42 ASP cc_start: 0.8287 (p0) cc_final: 0.7617 (p0) REVERT: I 21 ASP cc_start: 0.8847 (t70) cc_final: 0.8404 (t0) REVERT: I 24 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8440 (tm-30) REVERT: I 31 LYS cc_start: 0.9635 (mmmm) cc_final: 0.9355 (mmmm) REVERT: J 15 ASP cc_start: 0.8492 (m-30) cc_final: 0.7885 (m-30) REVERT: J 20 ILE cc_start: 0.8881 (mt) cc_final: 0.8632 (mt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2948 time to fit residues: 54.4130 Evaluate side-chains 111 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.0010 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** 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 = 0.3776 r_free = 0.3776 target = 0.081241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056653 restraints weight = 120739.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059164 restraints weight = 59590.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060777 restraints weight = 37708.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.061671 restraints weight = 28172.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.062411 restraints weight = 23734.868| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9152 Z= 0.122 Angle : 0.456 5.019 12363 Z= 0.253 Chirality : 0.032 0.148 1370 Planarity : 0.004 0.051 1629 Dihedral : 3.712 22.038 1233 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 3.07 (0.26), residues: 1099 helix: 2.93 (0.18), residues: 792 sheet: 0.51 (1.03), residues: 32 loop : -0.57 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 302 TYR 0.014 0.001 TYR J 40 PHE 0.010 0.001 PHE E 57 TRP 0.007 0.001 TRP I 13 HIS 0.010 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9152) covalent geometry : angle 0.45582 (12363) hydrogen bonds : bond 0.04299 ( 638) hydrogen bonds : angle 4.18432 ( 1863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 188 ASP cc_start: 0.7586 (m-30) cc_final: 0.7384 (m-30) REVERT: E 10 MET cc_start: 0.3457 (mtm) cc_final: 0.2420 (ptp) REVERT: E 23 PHE cc_start: 0.8775 (t80) cc_final: 0.8422 (t80) REVERT: E 42 ASP cc_start: 0.8325 (p0) cc_final: 0.7676 (p0) REVERT: I 21 ASP cc_start: 0.8817 (t70) cc_final: 0.8358 (t0) REVERT: I 24 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8378 (tm-30) REVERT: I 31 LYS cc_start: 0.9629 (mmmm) cc_final: 0.9322 (mmmm) REVERT: J 15 ASP cc_start: 0.8192 (m-30) cc_final: 0.7977 (m-30) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2920 time to fit residues: 52.6310 Evaluate side-chains 115 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 44 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 182 GLN C 306 GLN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.079366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.054839 restraints weight = 120007.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057263 restraints weight = 60118.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.058791 restraints weight = 38498.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059790 restraints weight = 29038.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060282 restraints weight = 24291.047| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9152 Z= 0.182 Angle : 0.493 4.893 12363 Z= 0.279 Chirality : 0.032 0.137 1370 Planarity : 0.004 0.046 1629 Dihedral : 3.739 20.071 1233 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 2.83 (0.25), residues: 1099 helix: 2.72 (0.18), residues: 785 sheet: 0.14 (1.04), residues: 32 loop : -0.44 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 102 TYR 0.012 0.001 TYR J 40 PHE 0.009 0.001 PHE E 115 TRP 0.009 0.001 TRP D 266 HIS 0.004 0.001 HIS D 282 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9152) covalent geometry : angle 0.49289 (12363) hydrogen bonds : bond 0.04582 ( 638) hydrogen bonds : angle 4.42053 ( 1863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 PHE cc_start: 0.8799 (t80) cc_final: 0.8551 (t80) REVERT: E 10 MET cc_start: 0.3961 (mtm) cc_final: 0.3360 (ptp) REVERT: E 23 PHE cc_start: 0.8883 (t80) cc_final: 0.8492 (t80) REVERT: E 42 ASP cc_start: 0.8174 (p0) cc_final: 0.7474 (p0) REVERT: I 21 ASP cc_start: 0.8751 (t70) cc_final: 0.8357 (t0) REVERT: I 31 LYS cc_start: 0.9625 (mmmm) cc_final: 0.9400 (mmmm) REVERT: J 15 ASP cc_start: 0.8266 (m-30) cc_final: 0.8052 (m-30) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.3025 time to fit residues: 51.8476 Evaluate side-chains 111 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 0.0050 chunk 17 optimal weight: 2.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** 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 = 0.3768 r_free = 0.3768 target = 0.080727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056128 restraints weight = 120963.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.058645 restraints weight = 59563.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060159 restraints weight = 37855.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.061239 restraints weight = 28558.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.061770 restraints weight = 23788.118| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9152 Z= 0.109 Angle : 0.444 5.058 12363 Z= 0.246 Chirality : 0.032 0.148 1370 Planarity : 0.004 0.046 1629 Dihedral : 3.614 20.501 1233 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 3.23 (0.26), residues: 1099 helix: 3.04 (0.18), residues: 787 sheet: 0.40 (0.89), residues: 42 loop : -0.42 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 279 TYR 0.011 0.001 TYR J 40 PHE 0.011 0.001 PHE E 57 TRP 0.006 0.001 TRP C 266 HIS 0.002 0.001 HIS D 282 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9152) covalent geometry : angle 0.44419 (12363) hydrogen bonds : bond 0.04173 ( 638) hydrogen bonds : angle 4.10288 ( 1863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 PHE cc_start: 0.8702 (t80) cc_final: 0.8478 (t80) REVERT: E 10 MET cc_start: 0.3971 (mtm) cc_final: 0.3499 (ptp) REVERT: E 23 PHE cc_start: 0.8856 (t80) cc_final: 0.8519 (t80) REVERT: E 42 ASP cc_start: 0.8110 (p0) cc_final: 0.7444 (p0) REVERT: E 58 TYR cc_start: 0.8345 (m-80) cc_final: 0.7783 (m-10) REVERT: F 94 MET cc_start: 0.9079 (mmm) cc_final: 0.8754 (mmm) REVERT: I 21 ASP cc_start: 0.8262 (t70) cc_final: 0.8036 (t0) REVERT: J 15 ASP cc_start: 0.8242 (m-30) cc_final: 0.8029 (m-30) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3174 time to fit residues: 54.9045 Evaluate side-chains 112 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** 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 = 0.3761 r_free = 0.3761 target = 0.080489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055961 restraints weight = 120656.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.058379 restraints weight = 60093.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059944 restraints weight = 38486.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060947 restraints weight = 28919.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.061575 restraints weight = 24202.911| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9152 Z= 0.125 Angle : 0.463 6.833 12363 Z= 0.255 Chirality : 0.032 0.147 1370 Planarity : 0.004 0.048 1629 Dihedral : 3.615 19.276 1233 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 3.19 (0.26), residues: 1099 helix: 3.03 (0.18), residues: 787 sheet: 0.24 (0.89), residues: 42 loop : -0.49 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 154 TYR 0.008 0.001 TYR J 40 PHE 0.017 0.001 PHE F 185 TRP 0.006 0.001 TRP D 274 HIS 0.003 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9152) covalent geometry : angle 0.46324 (12363) hydrogen bonds : bond 0.04089 ( 638) hydrogen bonds : angle 4.08950 ( 1863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 PHE cc_start: 0.8635 (t80) cc_final: 0.8409 (t80) REVERT: E 10 MET cc_start: 0.3832 (mtm) cc_final: 0.3454 (ptp) REVERT: E 23 PHE cc_start: 0.8836 (t80) cc_final: 0.8436 (t80) REVERT: E 42 ASP cc_start: 0.8099 (p0) cc_final: 0.7425 (p0) REVERT: E 74 TYR cc_start: 0.7667 (p90) cc_final: 0.7226 (p90) REVERT: F 94 MET cc_start: 0.9040 (mmm) cc_final: 0.8658 (mmm) REVERT: I 21 ASP cc_start: 0.8227 (t70) cc_final: 0.8010 (t0) REVERT: I 31 LYS cc_start: 0.9633 (mmmm) cc_final: 0.9356 (mmmm) REVERT: J 20 ILE cc_start: 0.8942 (mt) cc_final: 0.8601 (mt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3006 time to fit residues: 50.2872 Evaluate side-chains 104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** 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 = 0.3736 r_free = 0.3736 target = 0.079362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.054902 restraints weight = 121235.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.057329 restraints weight = 60356.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058897 restraints weight = 38539.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059916 restraints weight = 28985.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060541 restraints weight = 24295.664| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9152 Z= 0.175 Angle : 0.490 5.255 12363 Z= 0.278 Chirality : 0.033 0.136 1370 Planarity : 0.004 0.046 1629 Dihedral : 3.708 21.442 1233 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 2.84 (0.25), residues: 1099 helix: 2.78 (0.18), residues: 791 sheet: -0.24 (1.06), residues: 32 loop : -0.62 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 154 TYR 0.009 0.001 TYR D 101 PHE 0.010 0.001 PHE E 57 TRP 0.012 0.001 TRP D 274 HIS 0.004 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9152) covalent geometry : angle 0.49049 (12363) hydrogen bonds : bond 0.04389 ( 638) hydrogen bonds : angle 4.33286 ( 1863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 PHE cc_start: 0.8751 (t80) cc_final: 0.8497 (t80) REVERT: E 10 MET cc_start: 0.3819 (mtm) cc_final: 0.3523 (ptp) REVERT: E 23 PHE cc_start: 0.8871 (t80) cc_final: 0.8507 (t80) REVERT: E 40 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8815 (pm20) REVERT: E 42 ASP cc_start: 0.8179 (p0) cc_final: 0.7593 (p0) REVERT: I 21 ASP cc_start: 0.8287 (t70) cc_final: 0.8047 (t0) REVERT: I 31 LYS cc_start: 0.9633 (mmmm) cc_final: 0.9338 (mmmm) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2915 time to fit residues: 49.6762 Evaluate side-chains 106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.078329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.053901 restraints weight = 120875.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.056246 restraints weight = 60381.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.057767 restraints weight = 38739.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.058755 restraints weight = 29219.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059223 restraints weight = 24511.104| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9152 Z= 0.219 Angle : 0.536 5.906 12363 Z= 0.305 Chirality : 0.034 0.138 1370 Planarity : 0.004 0.045 1629 Dihedral : 3.904 20.046 1233 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.22 (0.25), residues: 1099 helix: 2.31 (0.18), residues: 803 sheet: -0.54 (1.06), residues: 32 loop : -0.94 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 154 TYR 0.011 0.002 TYR F 101 PHE 0.016 0.002 PHE F 185 TRP 0.010 0.001 TRP D 274 HIS 0.004 0.001 HIS D 280 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9152) covalent geometry : angle 0.53614 (12363) hydrogen bonds : bond 0.04797 ( 638) hydrogen bonds : angle 4.58088 ( 1863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 PHE cc_start: 0.8828 (t80) cc_final: 0.8595 (t80) REVERT: E 10 MET cc_start: 0.3875 (mtm) cc_final: 0.3540 (ptp) REVERT: E 23 PHE cc_start: 0.8810 (t80) cc_final: 0.8361 (t80) REVERT: E 42 ASP cc_start: 0.8230 (p0) cc_final: 0.7654 (p0) REVERT: I 21 ASP cc_start: 0.8215 (t70) cc_final: 0.7954 (t0) REVERT: I 31 LYS cc_start: 0.9634 (mmmm) cc_final: 0.9340 (mmmm) REVERT: J 20 ILE cc_start: 0.8950 (mt) cc_final: 0.8580 (mt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2866 time to fit residues: 46.1854 Evaluate side-chains 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.079185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054408 restraints weight = 121826.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056854 restraints weight = 59939.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.058434 restraints weight = 38174.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.059451 restraints weight = 28708.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.059999 restraints weight = 24035.579| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9152 Z= 0.148 Angle : 0.490 5.219 12363 Z= 0.275 Chirality : 0.033 0.141 1370 Planarity : 0.004 0.050 1629 Dihedral : 3.744 19.295 1233 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 2.60 (0.25), residues: 1099 helix: 2.62 (0.18), residues: 792 sheet: -0.61 (1.07), residues: 32 loop : -0.75 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 279 TYR 0.015 0.001 TYR F 58 PHE 0.011 0.001 PHE E 57 TRP 0.008 0.001 TRP C 266 HIS 0.008 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9152) covalent geometry : angle 0.49025 (12363) hydrogen bonds : bond 0.04500 ( 638) hydrogen bonds : angle 4.39813 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3402.08 seconds wall clock time: 58 minutes 36.80 seconds (3516.80 seconds total)