Starting phenix.real_space_refine on Mon May 19 02:01:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gmb_51447/05_2025/9gmb_51447.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gmb_51447/05_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_51447/05_2025/9gmb_51447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gmb_51447/05_2025/9gmb_51447.map" model { file = "/net/cci-nas-00/data/ceres_data/9gmb_51447/05_2025/9gmb_51447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gmb_51447/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.31, per 1000 atoms: 0.47 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: 5.19 Conformation dependent library (CDL) restraints added in 1.5 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: 1.29 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: 6.04 Time building geometry restraints manager: 6.13 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.300 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.370 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.220 ------------------------------------------------------------------------------- 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 : 1.386 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: 0.5375 time to fit residues: 131.7450 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 : 1.374 ------------------------------------------------------------------------------- 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 = 0.081434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.056857 restraints weight = 119860.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.059341 restraints weight = 57845.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060961 restraints weight = 36316.429| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- 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 : 1.495 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: 0.8837 (t80) cc_final: 0.8468 (t80) REVERT: E 94 MET cc_start: 0.8893 (mmm) cc_final: 0.8550 (mmm) REVERT: E 173 HIS cc_start: 0.7365 (t-90) cc_final: 0.7070 (t-90) REVERT: I 31 LYS cc_start: 0.9588 (mmmm) cc_final: 0.9347 (mmmm) REVERT: J 15 ASP cc_start: 0.8193 (m-30) cc_final: 0.7789 (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: 0.5530 time to fit residues: 102.1392 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 : 1.385 ------------------------------------------------------------------------------- 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: 9.9990 chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.081863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.057451 restraints weight = 118952.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.059950 restraints weight = 58078.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.061595 restraints weight = 36755.047| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3747 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= 0.134 Angle : 0.491 5.796 12363 Z= 0.275 Chirality : 0.033 0.149 1370 Planarity : 0.004 0.052 1629 Dihedral : 3.911 23.013 1233 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 2.49 (0.25), residues: 1099 helix: 2.44 (0.18), residues: 787 sheet: 0.49 (0.97), residues: 32 loop : -0.54 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 266 HIS 0.003 0.001 HIS D 282 PHE 0.009 0.001 PHE F 72 TYR 0.017 0.001 TYR E 58 ARG 0.006 0.000 ARG C 302 Details of bonding type rmsd hydrogen bonds : bond 0.04986 ( 638) hydrogen bonds : angle 4.55880 ( 1863) covalent geometry : bond 0.00274 ( 9152) covalent geometry : angle 0.49098 (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 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.502 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 135 GLU cc_start: 0.8869 (tp30) cc_final: 0.8631 (tp30) REVERT: E 23 PHE cc_start: 0.8721 (t80) cc_final: 0.8349 (t80) REVERT: E 42 ASP cc_start: 0.8321 (p0) cc_final: 0.7896 (p0) REVERT: E 94 MET cc_start: 0.8804 (mmm) cc_final: 0.8490 (mmm) REVERT: I 21 ASP cc_start: 0.8189 (t0) cc_final: 0.7979 (t0) REVERT: I 31 LYS cc_start: 0.9635 (mmmm) cc_final: 0.9368 (mmmm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.5861 time to fit residues: 107.7568 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 : 1.412 ------------------------------------------------------------------------------- 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: 0.9990 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: 4.9990 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 ASN C 155 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.079646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.055166 restraints weight = 120164.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.057585 restraints weight = 60120.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059127 restraints weight = 38415.334| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9152 Z= 0.189 Angle : 0.514 5.075 12363 Z= 0.293 Chirality : 0.033 0.135 1370 Planarity : 0.004 0.061 1629 Dihedral : 3.916 20.602 1233 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 2.16 (0.25), residues: 1099 helix: 2.22 (0.18), residues: 800 sheet: 0.20 (1.03), residues: 32 loop : -0.89 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.009 0.001 HIS E 173 PHE 0.010 0.001 PHE E 57 TYR 0.013 0.002 TYR E 58 ARG 0.006 0.000 ARG D 102 Details of bonding type rmsd hydrogen bonds : bond 0.04986 ( 638) hydrogen bonds : angle 4.65072 ( 1863) covalent geometry : bond 0.00388 ( 9152) covalent geometry : angle 0.51412 (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 : 1.543 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: 0.7566 (m-30) cc_final: 0.7363 (m-30) REVERT: E 23 PHE cc_start: 0.8881 (t80) cc_final: 0.8517 (t80) REVERT: E 42 ASP cc_start: 0.8299 (p0) cc_final: 0.7823 (p0) REVERT: E 58 TYR cc_start: 0.8093 (m-80) cc_final: 0.7425 (m-10) REVERT: E 94 MET cc_start: 0.8842 (mmm) cc_final: 0.8500 (mmm) REVERT: I 17 GLN cc_start: 0.9175 (tp40) cc_final: 0.8928 (tp40) REVERT: J 15 ASP cc_start: 0.8274 (m-30) cc_final: 0.8066 (m-30) REVERT: J 20 ILE cc_start: 0.8989 (mt) cc_final: 0.8688 (mt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.6072 time to fit residues: 108.9924 Evaluate side-chains 117 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 52 optimal weight: 8.9990 chunk 91 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 152 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 = 0.3773 r_free = 0.3773 target = 0.081021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.056739 restraints weight = 118909.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.059187 restraints weight = 58624.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060798 restraints weight = 37128.209| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9152 Z= 0.115 Angle : 0.449 5.211 12363 Z= 0.249 Chirality : 0.032 0.152 1370 Planarity : 0.004 0.049 1629 Dihedral : 3.710 21.332 1233 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % 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 (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: 2.87 (0.26), residues: 1099 helix: 2.72 (0.18), residues: 796 sheet: 0.56 (0.90), residues: 42 loop : -0.54 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 313 HIS 0.003 0.001 HIS D 282 PHE 0.011 0.001 PHE E 57 TYR 0.026 0.001 TYR J 40 ARG 0.011 0.000 ARG D 116 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 638) hydrogen bonds : angle 4.23903 ( 1863) covalent geometry : bond 0.00235 ( 9152) covalent geometry : angle 0.44911 (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 139 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.473 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: E 23 PHE cc_start: 0.8832 (t80) cc_final: 0.8422 (t80) REVERT: E 42 ASP cc_start: 0.8104 (p0) cc_final: 0.7633 (p0) REVERT: E 94 MET cc_start: 0.8801 (mmm) cc_final: 0.8454 (mmm) REVERT: E 173 HIS cc_start: 0.7461 (t-90) cc_final: 0.7143 (t-90) REVERT: I 27 ASN cc_start: 0.9300 (m-40) cc_final: 0.9084 (m-40) REVERT: J 15 ASP cc_start: 0.8314 (m-30) cc_final: 0.8074 (m-30) REVERT: J 20 ILE cc_start: 0.8982 (mt) cc_final: 0.8714 (mt) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.5925 time to fit residues: 106.8101 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 : 1.518 ------------------------------------------------------------------------------- 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: 3.9990 chunk 56 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN E 152 GLN ** 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 = 0.3731 r_free = 0.3731 target = 0.079033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054696 restraints weight = 120314.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.057150 restraints weight = 58686.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.058742 restraints weight = 37095.400| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4757 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= 0.192 Angle : 0.495 4.915 12363 Z= 0.283 Chirality : 0.032 0.143 1370 Planarity : 0.004 0.043 1629 Dihedral : 3.792 20.434 1233 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.10 % Allowed : 1.34 % 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 (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: 2.42 (0.25), residues: 1099 helix: 2.41 (0.18), residues: 796 sheet: -0.21 (1.03), residues: 32 loop : -0.69 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 14 HIS 0.004 0.001 HIS D 282 PHE 0.013 0.001 PHE E 115 TYR 0.013 0.002 TYR J 40 ARG 0.005 0.001 ARG C 138 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 638) hydrogen bonds : angle 4.50236 ( 1863) covalent geometry : bond 0.00394 ( 9152) covalent geometry : angle 0.49500 (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 131 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.437 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 118 ARG cc_start: 0.8010 (mmm160) cc_final: 0.7789 (tpt90) REVERT: C 254 PHE cc_start: 0.8790 (t80) cc_final: 0.8582 (t80) REVERT: E 23 PHE cc_start: 0.8840 (t80) cc_final: 0.8399 (t80) REVERT: E 42 ASP cc_start: 0.8242 (p0) cc_final: 0.7593 (p0) REVERT: E 94 MET cc_start: 0.8810 (mmm) cc_final: 0.8475 (mmm) REVERT: E 173 HIS cc_start: 0.7500 (t-90) cc_final: 0.7232 (t-90) REVERT: I 27 ASN cc_start: 0.9340 (m-40) cc_final: 0.8967 (m-40) REVERT: I 31 LYS cc_start: 0.9638 (mmmm) cc_final: 0.9370 (mmmm) REVERT: J 15 ASP cc_start: 0.8226 (m-30) cc_final: 0.7951 (m-30) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.6115 time to fit residues: 102.5616 Evaluate side-chains 109 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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: 9.9990 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 ASN C 303 GLN C 306 GLN E 62 ASN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS I 33 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.077204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.053194 restraints weight = 120868.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.055539 restraints weight = 60115.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057076 restraints weight = 38297.729| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9152 Z= 0.265 Angle : 0.575 4.694 12363 Z= 0.333 Chirality : 0.035 0.152 1370 Planarity : 0.005 0.052 1629 Dihedral : 4.128 23.834 1233 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.25), residues: 1099 helix: 1.71 (0.18), residues: 800 sheet: -0.83 (1.05), residues: 32 loop : -1.05 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 14 HIS 0.006 0.002 HIS C 282 PHE 0.014 0.002 PHE F 185 TYR 0.021 0.002 TYR J 40 ARG 0.007 0.001 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.05357 ( 638) hydrogen bonds : angle 4.96004 ( 1863) covalent geometry : bond 0.00540 ( 9152) covalent geometry : angle 0.57455 (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 126 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.498 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 254 PHE cc_start: 0.8891 (t80) cc_final: 0.8676 (t80) REVERT: E 23 PHE cc_start: 0.8759 (t80) cc_final: 0.8339 (t80) REVERT: E 42 ASP cc_start: 0.8316 (p0) cc_final: 0.7770 (p0) REVERT: E 94 MET cc_start: 0.8844 (mmm) cc_final: 0.8498 (mmm) REVERT: E 173 HIS cc_start: 0.7687 (t-90) cc_final: 0.7427 (t-90) REVERT: E 177 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8734 (mmmm) REVERT: I 21 ASP cc_start: 0.7905 (t0) cc_final: 0.7698 (t0) REVERT: I 27 ASN cc_start: 0.9357 (m-40) cc_final: 0.8954 (m-40) REVERT: I 31 LYS cc_start: 0.9650 (mmmm) cc_final: 0.9354 (mmmm) REVERT: J 20 ILE cc_start: 0.9043 (mt) cc_final: 0.8717 (mt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.6117 time to fit residues: 100.5442 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 : 1.524 ------------------------------------------------------------------------------- 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: 1.9990 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN E 152 GLN ** 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 = 0.3731 r_free = 0.3731 target = 0.079065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055142 restraints weight = 120314.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057435 restraints weight = 60379.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.058994 restraints weight = 39071.844| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9152 Z= 0.138 Angle : 0.463 5.135 12363 Z= 0.260 Chirality : 0.032 0.141 1370 Planarity : 0.004 0.049 1629 Dihedral : 3.818 19.343 1233 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % 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 (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: 2.25 (0.26), residues: 1099 helix: 2.31 (0.18), residues: 799 sheet: -0.85 (1.05), residues: 32 loop : -0.77 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 266 HIS 0.002 0.001 HIS D 151 PHE 0.010 0.001 PHE E 57 TYR 0.019 0.001 TYR J 40 ARG 0.006 0.000 ARG C 279 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 638) hydrogen bonds : angle 4.45061 ( 1863) covalent geometry : bond 0.00285 ( 9152) covalent geometry : angle 0.46306 (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 125 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.399 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 254 PHE cc_start: 0.8752 (t80) cc_final: 0.8542 (t80) REVERT: E 23 PHE cc_start: 0.8773 (t80) cc_final: 0.8468 (t80) REVERT: E 42 ASP cc_start: 0.8220 (p0) cc_final: 0.7632 (p0) REVERT: E 173 HIS cc_start: 0.7770 (t-90) cc_final: 0.7464 (t-90) REVERT: E 177 LYS cc_start: 0.9135 (mmmm) cc_final: 0.8784 (mmmm) REVERT: I 27 ASN cc_start: 0.9290 (m-40) cc_final: 0.8830 (m-40) REVERT: I 31 LYS cc_start: 0.9650 (mmmm) cc_final: 0.9377 (mmmm) REVERT: J 20 ILE cc_start: 0.9066 (mt) cc_final: 0.8839 (mt) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.5829 time to fit residues: 94.3682 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 : 1.395 ------------------------------------------------------------------------------- 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: 0.8980 chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3732 r_free = 0.3732 target = 0.078990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.055126 restraints weight = 120734.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.057448 restraints weight = 60305.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.058976 restraints weight = 38706.315| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9152 Z= 0.148 Angle : 0.473 5.740 12363 Z= 0.265 Chirality : 0.033 0.137 1370 Planarity : 0.004 0.050 1629 Dihedral : 3.820 20.431 1233 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 (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: 2.39 (0.25), residues: 1099 helix: 2.42 (0.18), residues: 801 sheet: -0.94 (1.04), residues: 32 loop : -0.76 (0.38), residues: 266 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 0.017 0.001 PHE F 185 TYR 0.018 0.001 TYR J 40 ARG 0.007 0.000 ARG C 279 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 638) hydrogen bonds : angle 4.39161 ( 1863) covalent geometry : bond 0.00307 ( 9152) covalent geometry : angle 0.47267 (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 121 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.393 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: C 254 PHE cc_start: 0.8716 (t80) cc_final: 0.8501 (t80) REVERT: E 23 PHE cc_start: 0.8712 (t80) cc_final: 0.8386 (t80) REVERT: E 42 ASP cc_start: 0.8248 (p0) cc_final: 0.7682 (p0) REVERT: E 173 HIS cc_start: 0.7853 (t-90) cc_final: 0.7437 (t-90) REVERT: E 177 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8784 (mmmm) REVERT: I 21 ASP cc_start: 0.8323 (t70) cc_final: 0.8034 (t0) REVERT: I 27 ASN cc_start: 0.9278 (m-40) cc_final: 0.8794 (m110) REVERT: I 31 LYS cc_start: 0.9628 (mmmm) cc_final: 0.9356 (mmmm) REVERT: J 20 ILE cc_start: 0.9053 (mt) cc_final: 0.8843 (mt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.5856 time to fit residues: 93.1196 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 : 1.412 ------------------------------------------------------------------------------- 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: 0.0870 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 36 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: ** 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 = 0.3730 r_free = 0.3730 target = 0.078846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.054844 restraints weight = 121545.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.057255 restraints weight = 59660.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.058842 restraints weight = 37885.023| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9152 Z= 0.144 Angle : 0.464 5.017 12363 Z= 0.260 Chirality : 0.032 0.136 1370 Planarity : 0.004 0.051 1629 Dihedral : 3.746 18.814 1233 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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 (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: 2.49 (0.25), residues: 1099 helix: 2.52 (0.18), residues: 801 sheet: -1.06 (1.02), residues: 32 loop : -0.79 (0.37), residues: 266 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 0.008 0.001 PHE E 57 TYR 0.017 0.001 TYR J 40 ARG 0.007 0.000 ARG C 279 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 638) hydrogen bonds : angle 4.34731 ( 1863) covalent geometry : bond 0.00298 ( 9152) covalent geometry : angle 0.46387 (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 : 1.540 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: C 254 PHE cc_start: 0.8731 (t80) cc_final: 0.8508 (t80) REVERT: E 23 PHE cc_start: 0.8749 (t80) cc_final: 0.8400 (t80) REVERT: E 42 ASP cc_start: 0.8184 (p0) cc_final: 0.7548 (p0) REVERT: E 58 TYR cc_start: 0.8183 (m-80) cc_final: 0.7653 (m-10) REVERT: E 173 HIS cc_start: 0.7888 (t-90) cc_final: 0.7489 (t-90) REVERT: I 21 ASP cc_start: 0.8280 (t70) cc_final: 0.8007 (t0) REVERT: I 31 LYS cc_start: 0.9622 (mmmm) cc_final: 0.9339 (mmmm) REVERT: J 20 ILE cc_start: 0.9066 (mt) cc_final: 0.8756 (mt) REVERT: J 24 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8701 (mm-30) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.5840 time to fit residues: 90.5175 Evaluate side-chains 99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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: 9.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3755 r_free = 0.3755 target = 0.079940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.055934 restraints weight = 119506.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.058380 restraints weight = 58584.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.059993 restraints weight = 37109.797| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5621 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= 0.107 Angle : 0.432 4.961 12363 Z= 0.237 Chirality : 0.032 0.146 1370 Planarity : 0.004 0.053 1629 Dihedral : 3.576 18.851 1233 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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 (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: 2.94 (0.26), residues: 1099 helix: 2.86 (0.18), residues: 801 sheet: -0.94 (1.02), residues: 32 loop : -0.65 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 266 HIS 0.002 0.001 HIS D 151 PHE 0.010 0.001 PHE E 57 TYR 0.016 0.001 TYR J 40 ARG 0.007 0.000 ARG C 279 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 638) hydrogen bonds : angle 4.06913 ( 1863) covalent geometry : bond 0.00224 ( 9152) covalent geometry : angle 0.43152 (12363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5419.91 seconds wall clock time: 94 minutes 1.56 seconds (5641.56 seconds total)