Starting phenix.real_space_refine on Sun Jun 15 21:58:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmb_51447/06_2025/9gmb_51447.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmb_51447/06_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_51447/06_2025/9gmb_51447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmb_51447/06_2025/9gmb_51447.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmb_51447/06_2025/9gmb_51447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmb_51447/06_2025/9gmb_51447.cif" } resolution = 4.2 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= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.88, per 1000 atoms: 0.66 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: 5.11 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.32 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: 5.95 Time building geometry restraints manager: 6.15 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: 26.150 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: 0.390 Extract box with map and model: 0.830 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 44.250 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.370 ------------------------------------------------------------------------------- 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 : 9.18 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (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 TRP 0.088 0.005 TRP C 197 HIS 0.005 0.001 HIS E 44 PHE 0.029 0.001 PHE C 284 TYR 0.032 0.002 TYR C 277 ARG 0.015 0.001 ARG D 198 Details of bonding type rmsd hydrogen bonds : bond 0.14472 ( 638) hydrogen bonds : angle 5.76551 ( 1863) covalent geometry : bond 0.00894 ( 9152) covalent geometry : angle 0.89095 (12363) *********************** 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 : 1.492 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: 0.5533 time to fit residues: 135.7225 Evaluate side-chains 128 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.081444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.056905 restraints weight = 119833.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.059325 restraints weight = 57789.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.060936 restraints weight = 36383.052| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3260 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= 0.187 Angle : 0.548 5.212 12363 Z= 0.311 Chirality : 0.035 0.151 1370 Planarity : 0.005 0.068 1629 Dihedral : 4.087 22.011 1233 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.10 % Allowed : 2.98 % Favored : 96.91 % 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: 1.93 (0.25), residues: 1099 helix: 2.03 (0.18), residues: 793 sheet: 0.39 (0.93), residues: 32 loop : -0.86 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 266 HIS 0.005 0.002 HIS D 282 PHE 0.011 0.001 PHE D 56 TYR 0.025 0.002 TYR F 53 ARG 0.006 0.001 ARG D 102 Details of bonding type rmsd hydrogen bonds : bond 0.05570 ( 638) hydrogen bonds : angle 4.99133 ( 1863) covalent geometry : bond 0.00385 ( 9152) covalent geometry : angle 0.54782 (12363) *********************** 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 142 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.456 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: 0.8835 (t80) cc_final: 0.8467 (t80) REVERT: E 94 MET cc_start: 0.8894 (mmm) cc_final: 0.8552 (mmm) REVERT: E 173 HIS cc_start: 0.7365 (t-90) cc_final: 0.7070 (t-90) REVERT: I 31 LYS cc_start: 0.9587 (mmmm) cc_final: 0.9346 (mmmm) REVERT: J 15 ASP cc_start: 0.8194 (m-30) cc_final: 0.7790 (m-30) REVERT: J 20 ILE cc_start: 0.8963 (mt) cc_final: 0.8728 (mt) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.6332 time to fit residues: 118.0046 Evaluate side-chains 116 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 27 ASN ** 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 = 0.3769 r_free = 0.3769 target = 0.081168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.056586 restraints weight = 118724.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059140 restraints weight = 57377.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.060759 restraints weight = 36062.108| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9152 Z= 0.163 Angle : 0.507 5.959 12363 Z= 0.287 Chirality : 0.033 0.151 1370 Planarity : 0.004 0.051 1629 Dihedral : 3.975 23.378 1233 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.25), residues: 1099 helix: 2.27 (0.18), residues: 786 sheet: 0.43 (0.98), residues: 32 loop : -0.64 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 266 HIS 0.004 0.001 HIS D 282 PHE 0.009 0.001 PHE F 72 TYR 0.017 0.002 TYR E 58 ARG 0.008 0.000 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.05160 ( 638) hydrogen bonds : angle 4.71141 ( 1863) covalent geometry : bond 0.00328 ( 9152) covalent geometry : angle 0.50725 (12363) *********************** 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 138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.626 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: E 23 PHE cc_start: 0.8745 (t80) cc_final: 0.8419 (t80) REVERT: E 42 ASP cc_start: 0.8339 (p0) cc_final: 0.7926 (p0) REVERT: E 74 TYR cc_start: 0.7193 (p90) cc_final: 0.6963 (p90) REVERT: E 94 MET cc_start: 0.8828 (mmm) cc_final: 0.8495 (mmm) REVERT: I 21 ASP cc_start: 0.8179 (t0) cc_final: 0.7966 (t0) REVERT: I 31 LYS cc_start: 0.9637 (mmmm) cc_final: 0.9356 (mmmm) REVERT: J 20 ILE cc_start: 0.8953 (mt) cc_final: 0.8699 (mt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.6901 time to fit residues: 126.8137 Evaluate side-chains 114 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 17 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 ASN C 182 GLN C 306 GLN E 173 HIS ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.079919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.055453 restraints weight = 120324.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057859 restraints weight = 59733.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.059444 restraints weight = 38200.658| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9152 Z= 0.170 Angle : 0.491 5.079 12363 Z= 0.278 Chirality : 0.033 0.137 1370 Planarity : 0.004 0.051 1629 Dihedral : 3.893 20.573 1233 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.25), residues: 1099 helix: 2.28 (0.18), residues: 800 sheet: 0.27 (1.02), residues: 32 loop : -0.76 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 266 HIS 0.007 0.001 HIS E 173 PHE 0.016 0.001 PHE E 57 TYR 0.021 0.002 TYR J 40 ARG 0.005 0.000 ARG D 102 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 638) hydrogen bonds : angle 4.59560 ( 1863) covalent geometry : bond 0.00348 ( 9152) covalent geometry : angle 0.49069 (12363) *********************** 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 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.420 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 188 ASP cc_start: 0.7575 (m-30) cc_final: 0.7359 (m-30) REVERT: E 10 MET cc_start: 0.4164 (mtm) cc_final: 0.3772 (ptp) REVERT: E 23 PHE cc_start: 0.8887 (t80) cc_final: 0.8479 (t80) REVERT: E 42 ASP cc_start: 0.8284 (p0) cc_final: 0.7818 (p0) REVERT: E 94 MET cc_start: 0.8768 (mmm) cc_final: 0.8463 (mmm) REVERT: I 17 GLN cc_start: 0.9150 (tp40) cc_final: 0.8929 (tp40) REVERT: J 15 ASP cc_start: 0.8281 (m-30) cc_final: 0.8065 (m-30) REVERT: J 20 ILE cc_start: 0.8953 (mt) cc_final: 0.8629 (mt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.5999 time to fit residues: 108.7908 Evaluate side-chains 114 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN ** 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 = 0.3735 r_free = 0.3735 target = 0.079322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.054687 restraints weight = 120835.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057170 restraints weight = 58824.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058782 restraints weight = 37013.583| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9152 Z= 0.189 Angle : 0.496 5.007 12363 Z= 0.283 Chirality : 0.033 0.137 1370 Planarity : 0.004 0.048 1629 Dihedral : 3.899 22.973 1233 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.25), residues: 1099 helix: 2.27 (0.18), residues: 794 sheet: -0.02 (1.04), residues: 32 loop : -0.76 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 14 HIS 0.005 0.001 HIS D 282 PHE 0.009 0.001 PHE D 56 TYR 0.020 0.002 TYR J 40 ARG 0.004 0.000 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.04840 ( 638) hydrogen bonds : angle 4.60430 ( 1863) covalent geometry : bond 0.00387 ( 9152) covalent geometry : angle 0.49635 (12363) *********************** 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 130 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.405 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: E 10 MET cc_start: 0.4224 (mtm) cc_final: 0.3522 (ptp) REVERT: E 23 PHE cc_start: 0.8851 (t80) cc_final: 0.8479 (t80) REVERT: E 42 ASP cc_start: 0.8259 (p0) cc_final: 0.7815 (p0) REVERT: E 94 MET cc_start: 0.8828 (mmm) cc_final: 0.8500 (mmm) REVERT: E 173 HIS cc_start: 0.7352 (t-90) cc_final: 0.7034 (t-90) REVERT: I 21 ASP cc_start: 0.7976 (t0) cc_final: 0.7775 (t0) REVERT: I 27 ASN cc_start: 0.9352 (m-40) cc_final: 0.9122 (m-40) REVERT: J 15 ASP cc_start: 0.8305 (m-30) cc_final: 0.8066 (m-30) REVERT: J 20 ILE cc_start: 0.9020 (mt) cc_final: 0.8680 (mt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.6016 time to fit residues: 101.6049 Evaluate side-chains 108 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN E 62 ASN F 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.078006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.053840 restraints weight = 120137.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056192 restraints weight = 59682.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057718 restraints weight = 37942.546| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9152 Z= 0.230 Angle : 0.534 5.029 12363 Z= 0.308 Chirality : 0.034 0.135 1370 Planarity : 0.004 0.043 1629 Dihedral : 3.971 20.503 1233 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1099 helix: 2.02 (0.18), residues: 795 sheet: -0.60 (1.04), residues: 32 loop : -0.99 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 266 HIS 0.005 0.001 HIS D 282 PHE 0.011 0.002 PHE D 56 TYR 0.015 0.002 TYR J 40 ARG 0.005 0.001 ARG C 138 Details of bonding type rmsd hydrogen bonds : bond 0.05152 ( 638) hydrogen bonds : angle 4.78426 ( 1863) covalent geometry : bond 0.00472 ( 9152) covalent geometry : angle 0.53409 (12363) *********************** 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 124 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.465 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: C 254 PHE cc_start: 0.8739 (t80) cc_final: 0.8521 (t80) REVERT: E 10 MET cc_start: 0.4048 (mtm) cc_final: 0.3659 (ptp) REVERT: E 23 PHE cc_start: 0.8804 (t80) cc_final: 0.8377 (t80) REVERT: E 42 ASP cc_start: 0.8279 (p0) cc_final: 0.7709 (p0) REVERT: E 94 MET cc_start: 0.8831 (mmm) cc_final: 0.8528 (mmm) REVERT: E 173 HIS cc_start: 0.7667 (t-90) cc_final: 0.7385 (t-90) REVERT: E 177 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8778 (mmmm) REVERT: F 94 MET cc_start: 0.9056 (mmm) cc_final: 0.8723 (mmm) REVERT: I 21 ASP cc_start: 0.7834 (t0) cc_final: 0.7633 (t0) REVERT: I 27 ASN cc_start: 0.9377 (m-40) cc_final: 0.8906 (m110) REVERT: I 31 LYS cc_start: 0.9643 (mmmm) cc_final: 0.9353 (mmmm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.6195 time to fit residues: 99.9694 Evaluate side-chains 103 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 ASN C 128 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.079538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055442 restraints weight = 121554.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.057794 restraints weight = 60553.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.059324 restraints weight = 38860.239| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9152 Z= 0.146 Angle : 0.472 5.004 12363 Z= 0.268 Chirality : 0.032 0.140 1370 Planarity : 0.004 0.044 1629 Dihedral : 3.835 21.202 1233 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.25), residues: 1099 helix: 2.38 (0.18), residues: 794 sheet: -0.70 (1.04), residues: 32 loop : -0.82 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 266 HIS 0.004 0.001 HIS C 282 PHE 0.011 0.001 PHE E 57 TYR 0.013 0.001 TYR J 40 ARG 0.007 0.000 ARG C 198 Details of bonding type rmsd hydrogen bonds : bond 0.04747 ( 638) hydrogen bonds : angle 4.51123 ( 1863) covalent geometry : bond 0.00300 ( 9152) covalent geometry : angle 0.47166 (12363) *********************** 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 125 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.434 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: C 118 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7755 (tpt90) REVERT: E 10 MET cc_start: 0.3958 (mtm) cc_final: 0.3660 (ptp) REVERT: E 23 PHE cc_start: 0.8766 (t80) cc_final: 0.8442 (t80) REVERT: E 42 ASP cc_start: 0.8227 (p0) cc_final: 0.7632 (p0) REVERT: E 173 HIS cc_start: 0.7738 (t-90) cc_final: 0.7480 (t-170) REVERT: E 177 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8802 (mmmm) REVERT: I 31 LYS cc_start: 0.9658 (mmmm) cc_final: 0.9400 (mmmm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.5696 time to fit residues: 94.7915 Evaluate side-chains 101 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** 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 = 0.3746 r_free = 0.3746 target = 0.079606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055571 restraints weight = 121042.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.057939 restraints weight = 60514.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059468 restraints weight = 38859.590| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9152 Z= 0.133 Angle : 0.457 4.921 12363 Z= 0.256 Chirality : 0.032 0.140 1370 Planarity : 0.004 0.045 1629 Dihedral : 3.717 18.839 1233 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.25), residues: 1099 helix: 2.56 (0.18), residues: 796 sheet: -0.75 (1.05), residues: 32 loop : -0.71 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 266 HIS 0.003 0.001 HIS D 151 PHE 0.010 0.001 PHE E 57 TYR 0.015 0.001 TYR J 40 ARG 0.007 0.000 ARG C 198 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 638) hydrogen bonds : angle 4.33568 ( 1863) covalent geometry : bond 0.00274 ( 9152) covalent geometry : angle 0.45707 (12363) *********************** 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 : 1.452 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 118 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7779 (tpt90) REVERT: E 10 MET cc_start: 0.3886 (mtm) cc_final: 0.3651 (ptp) REVERT: E 23 PHE cc_start: 0.8775 (t80) cc_final: 0.8545 (t80) REVERT: E 42 ASP cc_start: 0.8194 (p0) cc_final: 0.7618 (p0) REVERT: E 58 TYR cc_start: 0.8318 (m-80) cc_final: 0.7793 (m-10) REVERT: E 177 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8779 (mmmm) REVERT: I 21 ASP cc_start: 0.8268 (t70) cc_final: 0.8018 (t0) REVERT: I 31 LYS cc_start: 0.9625 (mmmm) cc_final: 0.9345 (mmmm) REVERT: J 20 ILE cc_start: 0.9029 (mt) cc_final: 0.8817 (mt) REVERT: J 26 GLU cc_start: 0.8438 (mp0) cc_final: 0.8230 (mp0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.5480 time to fit residues: 92.6655 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 : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 0.0980 chunk 85 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 E 173 HIS ** E 201 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 = 0.3764 r_free = 0.3764 target = 0.080255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056311 restraints weight = 120552.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.058692 restraints weight = 58383.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.060328 restraints weight = 37030.754| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5371 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= 0.107 Angle : 0.439 4.904 12363 Z= 0.243 Chirality : 0.032 0.147 1370 Planarity : 0.004 0.045 1629 Dihedral : 3.603 19.475 1233 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.26), residues: 1099 helix: 2.86 (0.18), residues: 801 sheet: -0.71 (1.05), residues: 32 loop : -0.61 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP I 13 HIS 0.005 0.001 HIS E 173 PHE 0.009 0.001 PHE E 57 TYR 0.013 0.001 TYR J 40 ARG 0.006 0.000 ARG J 25 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 638) hydrogen bonds : angle 4.11139 ( 1863) covalent geometry : bond 0.00225 ( 9152) covalent geometry : angle 0.43872 (12363) *********************** 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 126 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.551 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: C 118 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7792 (tpt90) REVERT: E 10 MET cc_start: 0.3923 (mtm) cc_final: 0.3698 (ptp) REVERT: E 23 PHE cc_start: 0.8789 (t80) cc_final: 0.8550 (t80) REVERT: E 42 ASP cc_start: 0.8106 (p0) cc_final: 0.7492 (p0) REVERT: E 58 TYR cc_start: 0.8376 (m-80) cc_final: 0.7789 (m-10) REVERT: I 21 ASP cc_start: 0.8324 (t70) cc_final: 0.8010 (t0) REVERT: I 31 LYS cc_start: 0.9621 (mmmm) cc_final: 0.9355 (mmmm) REVERT: J 20 ILE cc_start: 0.9005 (mt) cc_final: 0.8714 (mt) outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 0.5377 time to fit residues: 90.4936 Evaluate side-chains 103 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 0.0670 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- 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 306 GLN ** E 201 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 = 0.3744 r_free = 0.3744 target = 0.079346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055258 restraints weight = 121959.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.057670 restraints weight = 59891.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059233 restraints weight = 38107.653| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9152 Z= 0.147 Angle : 0.462 5.803 12363 Z= 0.260 Chirality : 0.032 0.141 1370 Planarity : 0.004 0.045 1629 Dihedral : 3.633 18.764 1233 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.26), residues: 1099 helix: 2.75 (0.18), residues: 802 sheet: -0.90 (1.03), residues: 32 loop : -0.66 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP I 13 HIS 0.003 0.001 HIS D 280 PHE 0.008 0.001 PHE E 57 TYR 0.020 0.001 TYR I 19 ARG 0.006 0.000 ARG J 25 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 638) hydrogen bonds : angle 4.25916 ( 1863) covalent geometry : bond 0.00302 ( 9152) covalent geometry : angle 0.46237 (12363) ********************** 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 119 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.507 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: C 118 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7787 (tpt90) REVERT: C 254 PHE cc_start: 0.8628 (t80) cc_final: 0.8427 (t80) REVERT: E 23 PHE cc_start: 0.8805 (t80) cc_final: 0.8471 (t80) REVERT: E 42 ASP cc_start: 0.8213 (p0) cc_final: 0.7647 (p0) REVERT: E 58 TYR cc_start: 0.8265 (m-80) cc_final: 0.7670 (m-10) REVERT: I 21 ASP cc_start: 0.8290 (t70) cc_final: 0.7992 (t0) REVERT: I 31 LYS cc_start: 0.9616 (mmmm) cc_final: 0.9321 (mmmm) REVERT: J 20 ILE cc_start: 0.9031 (mt) cc_final: 0.8797 (mt) REVERT: J 24 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8584 (mm-30) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.5433 time to fit residues: 86.4636 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 : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.0370 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.1064 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.079871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.055830 restraints weight = 120979.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.058275 restraints weight = 59387.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.059859 restraints weight = 37781.215| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9152 Z= 0.118 Angle : 0.449 7.852 12363 Z= 0.247 Chirality : 0.032 0.140 1370 Planarity : 0.004 0.045 1629 Dihedral : 3.560 19.078 1233 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 3.04 (0.26), residues: 1099 helix: 2.92 (0.18), residues: 802 sheet: -0.86 (1.03), residues: 32 loop : -0.60 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 13 HIS 0.003 0.001 HIS E 173 PHE 0.009 0.001 PHE E 57 TYR 0.014 0.001 TYR J 40 ARG 0.009 0.000 ARG E 163 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 638) hydrogen bonds : angle 4.10699 ( 1863) covalent geometry : bond 0.00246 ( 9152) covalent geometry : angle 0.44895 (12363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5951.21 seconds wall clock time: 103 minutes 2.88 seconds (6182.88 seconds total)