Starting phenix.real_space_refine on Mon Apr 28 06:15:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cr2_16802/04_2025/8cr2_16802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cr2_16802/04_2025/8cr2_16802.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/8cr2_16802/04_2025/8cr2_16802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cr2_16802/04_2025/8cr2_16802.map" model { file = "/net/cci-nas-00/data/ceres_data/8cr2_16802/04_2025/8cr2_16802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cr2_16802/04_2025/8cr2_16802.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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 306 atoms to isotropic. 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 Zn 1 6.06 5 S 51 5.16 5 C 4419 2.51 5 N 1133 2.21 5 O 1234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6838 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2113 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 16, 'TRANS': 251} Chain breaks: 2 Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2066 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 16, 'TRANS': 245} Chain breaks: 2 Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1856 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 4, 'TRANS': 223} Chain breaks: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1658 SG CYS A 289 37.717 41.793 15.466 1.00 88.42 S ATOM 1681 SG CYS A 292 36.187 44.539 16.689 1.00 83.88 S ATOM 3724 SG CYS B 289 39.158 45.820 14.919 1.00 94.34 S ATOM 3747 SG CYS B 292 40.200 43.439 17.412 1.00 83.96 S Time building chain proxies: 4.38, per 1000 atoms: 0.64 Number of scatterers: 6838 At special positions: 0 Unit cell: (74.37, 96.57, 135.42, 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) Zn 1 29.99 S 51 16.00 O 1234 8.00 N 1133 7.00 C 4419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 208 " - pdb=" SG CYS D 284 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 926.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 292 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 292 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 289 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 289 " Number of angles added : 6 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 4 sheets defined 69.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 49 through 65 removed outlier: 3.949A pdb=" N LYS A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 removed outlier: 3.922A pdb=" N ASP A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 158 removed outlier: 4.132A pdb=" N MET A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 217 through 238 Proline residue: A 227 - end of helix removed outlier: 3.532A pdb=" N GLU A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'A' and resid 290 through 310 removed outlier: 3.562A pdb=" N HIS A 296 " --> pdb=" O CYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 49 through 65 removed outlier: 3.868A pdb=" N LYS B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.775A pdb=" N ASP B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 removed outlier: 4.105A pdb=" N ALA B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 removed outlier: 4.092A pdb=" N LEU B 176 " --> pdb=" O HIS B 172 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 178' Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.974A pdb=" N ILE B 182 " --> pdb=" O ASN B 178 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 Proline residue: B 227 - end of helix removed outlier: 4.137A pdb=" N VAL B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 290 through 310 Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.681A pdb=" N LEU B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1039 Processing helix chain 'C' and resid 1039 through 1062 removed outlier: 3.820A pdb=" N SER C1047 " --> pdb=" O ALA C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1124 Processing helix chain 'D' and resid 190 through 207 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 214 through 234 removed outlier: 3.520A pdb=" N GLY D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 255 through 284 removed outlier: 3.925A pdb=" N PHE D 281 " --> pdb=" O TYR D 277 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 282 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 1006 through 1035 removed outlier: 3.969A pdb=" N VAL D1014 " --> pdb=" O ALA D1010 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU D1015 " --> pdb=" O TRP D1011 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D1016 " --> pdb=" O LEU D1012 " (cutoff:3.500A) Proline residue: D1029 - end of helix Processing helix chain 'D' and resid 1035 through 1062 removed outlier: 4.559A pdb=" N LYS D1041 " --> pdb=" O ARG D1037 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN D1045 " --> pdb=" O LYS D1041 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR D1062 " --> pdb=" O GLN D1058 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1123 removed outlier: 4.752A pdb=" N LYS D1099 " --> pdb=" O ALA D1095 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1161 Processing helix chain 'D' and resid 1162 through 1171 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.565A pdb=" N LEU A 69 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 164 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 10.597A pdb=" N THR A 242 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N ASN A 274 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE A 244 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE A 276 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS A 246 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS A 273 " --> pdb=" O HIS A 314 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL A 316 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 275 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 removed outlier: 6.963A pdb=" N ILE B 40 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP B 39 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE B 245 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE B 41 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 247 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY B 43 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ILE B 249 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR B 272 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE B 244 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 274 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N HIS B 273 " --> pdb=" O HIS B 314 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL B 316 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE B 275 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 69 removed outlier: 6.008A pdb=" N VAL B 68 " --> pdb=" O PHE B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 429 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1313 1.33 - 1.45: 1584 1.45 - 1.57: 3997 1.57 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 6975 Sorted by residual: bond pdb=" CA HIS A 323 " pdb=" C HIS A 323 " ideal model delta sigma weight residual 1.522 1.562 -0.041 1.72e-02 3.38e+03 5.62e+00 bond pdb=" CG GLN A 235 " pdb=" CD GLN A 235 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.90e+00 bond pdb=" CG GLN D1112 " pdb=" CD GLN D1112 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.88e+00 bond pdb=" CG GLU C1076 " pdb=" CD GLU C1076 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.23e+00 bond pdb=" CG1 ILE B 249 " pdb=" CD1 ILE B 249 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.12e+00 ... (remaining 6970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 9190 3.09 - 6.18: 194 6.18 - 9.28: 20 9.28 - 12.37: 8 12.37 - 15.46: 1 Bond angle restraints: 9413 Sorted by residual: angle pdb=" CA HIS A 323 " pdb=" C HIS A 323 " pdb=" N GLU A 324 " ideal model delta sigma weight residual 118.59 129.17 -10.58 1.63e+00 3.76e-01 4.21e+01 angle pdb=" N GLU C1076 " pdb=" CA GLU C1076 " pdb=" CB GLU C1076 " ideal model delta sigma weight residual 110.12 118.20 -8.08 1.47e+00 4.63e-01 3.02e+01 angle pdb=" N GLN D1112 " pdb=" CA GLN D1112 " pdb=" CB GLN D1112 " ideal model delta sigma weight residual 110.30 118.33 -8.03 1.54e+00 4.22e-01 2.72e+01 angle pdb=" CB MET D1116 " pdb=" CG MET D1116 " pdb=" SD MET D1116 " ideal model delta sigma weight residual 112.70 128.16 -15.46 3.00e+00 1.11e-01 2.66e+01 angle pdb=" CA GLU C1076 " pdb=" CB GLU C1076 " pdb=" CG GLU C1076 " ideal model delta sigma weight residual 114.10 123.54 -9.44 2.00e+00 2.50e-01 2.23e+01 ... (remaining 9408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3863 17.96 - 35.93: 337 35.93 - 53.89: 48 53.89 - 71.85: 4 71.85 - 89.82: 6 Dihedral angle restraints: 4258 sinusoidal: 1745 harmonic: 2513 Sorted by residual: dihedral pdb=" CB CYS D 208 " pdb=" SG CYS D 208 " pdb=" SG CYS D 284 " pdb=" CB CYS D 284 " ideal model delta sinusoidal sigma weight residual -86.00 -175.82 89.82 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" N GLU C1076 " pdb=" C GLU C1076 " pdb=" CA GLU C1076 " pdb=" CB GLU C1076 " ideal model delta harmonic sigma weight residual 122.80 132.72 -9.92 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" CA HIS A 273 " pdb=" C HIS A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta harmonic sigma weight residual -180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 788 0.056 - 0.111: 220 0.111 - 0.167: 60 0.167 - 0.222: 10 0.222 - 0.278: 3 Chirality restraints: 1081 Sorted by residual: chirality pdb=" CA PRO B 169 " pdb=" N PRO B 169 " pdb=" C PRO B 169 " pdb=" CB PRO B 169 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA GLU C1076 " pdb=" N GLU C1076 " pdb=" C GLU C1076 " pdb=" CB GLU C1076 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLN A 235 " pdb=" N GLN A 235 " pdb=" C GLN A 235 " pdb=" CB GLN A 235 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1078 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D1158 " -0.030 2.00e-02 2.50e+03 3.06e-02 2.34e+01 pdb=" CG TRP D1158 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP D1158 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP D1158 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D1158 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D1158 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D1158 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP D1158 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D1158 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D1158 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D1011 " -0.027 2.00e-02 2.50e+03 2.84e-02 2.01e+01 pdb=" CG TRP D1011 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP D1011 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP D1011 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D1011 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D1011 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D1011 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D1011 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D1011 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D1011 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 220 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C LEU D 220 " 0.077 2.00e-02 2.50e+03 pdb=" O LEU D 220 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN D 221 " -0.026 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 43 2.51 - 3.11: 5613 3.11 - 3.71: 10443 3.71 - 4.30: 14029 4.30 - 4.90: 21621 Nonbonded interactions: 51749 Sorted by model distance: nonbonded pdb=" O PHE B 83 " pdb=" OD1 ASP B 84 " model vdw 1.914 3.040 nonbonded pdb=" O LYS D1101 " pdb=" OG SER D1105 " model vdw 2.198 3.040 nonbonded pdb=" O GLN A 235 " pdb=" OG1 THR A 242 " model vdw 2.223 3.040 nonbonded pdb=" O TYR D 277 " pdb=" OG1 THR D 280 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLN A 263 " pdb=" NH2 ARG D1077 " model vdw 2.241 3.120 ... (remaining 51744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 190 or resid 220 through 344)) selection = (chain 'B' and resid 23 through 344) } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.470 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3059 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 : 0.004 0.057 6980 Z= 0.216 Angle : 1.141 24.972 9421 Z= 0.598 Chirality : 0.057 0.278 1081 Planarity : 0.007 0.058 1172 Dihedral : 13.243 87.522 2613 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.12 % 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: -3.18 (0.27), residues: 833 helix: -1.65 (0.19), residues: 535 sheet: -3.24 (0.52), residues: 81 loop : -2.24 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.005 TRP D1158 HIS 0.020 0.002 HIS B 172 PHE 0.036 0.002 PHE D1019 TYR 0.052 0.002 TYR D 224 ARG 0.013 0.001 ARG D1093 Details of bonding type rmsd hydrogen bonds : bond 0.13592 ( 429) hydrogen bonds : angle 6.04226 ( 1278) metal coordination : bond 0.00651 ( 4) metal coordination : angle 15.98554 ( 6) SS BOND : bond 0.00187 ( 1) SS BOND : angle 1.45608 ( 2) covalent geometry : bond 0.00433 ( 6975) covalent geometry : angle 1.06773 ( 9413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.685 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: A 103 MET cc_start: -0.2862 (mmm) cc_final: -0.4250 (ptm) REVERT: A 291 MET cc_start: 0.6140 (ptp) cc_final: 0.5606 (ptp) REVERT: B 158 MET cc_start: 0.6750 (mpp) cc_final: 0.6458 (mpp) REVERT: B 326 ARG cc_start: 0.3648 (tpt90) cc_final: 0.1145 (mmp80) REVERT: C 1116 MET cc_start: 0.4065 (ttt) cc_final: 0.3604 (ttt) REVERT: D 222 LEU cc_start: 0.7355 (pp) cc_final: 0.7115 (tp) REVERT: D 259 ARG cc_start: 0.3986 (mtt180) cc_final: 0.2349 (mpt-90) REVERT: D 261 MET cc_start: 0.2969 (ptt) cc_final: 0.1806 (tmm) REVERT: D 270 VAL cc_start: 0.6126 (m) cc_final: 0.4950 (p) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2467 time to fit residues: 66.3063 Evaluate side-chains 122 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 0.0870 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 241 GLN B 159 ASN B 274 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1045 GLN D1054 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.216761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155398 restraints weight = 9345.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.159534 restraints weight = 6802.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161990 restraints weight = 5450.947| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5118 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6980 Z= 0.202 Angle : 0.876 15.743 9421 Z= 0.437 Chirality : 0.051 0.191 1081 Planarity : 0.006 0.055 1172 Dihedral : 4.817 19.889 908 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.79 % Allowed : 7.99 % Favored : 91.22 % 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: -0.71 (0.28), residues: 833 helix: 0.35 (0.21), residues: 534 sheet: -2.53 (0.50), residues: 85 loop : -1.39 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP D1158 HIS 0.006 0.002 HIS A 172 PHE 0.028 0.003 PHE D1108 TYR 0.026 0.002 TYR D 230 ARG 0.006 0.001 ARG C1037 Details of bonding type rmsd hydrogen bonds : bond 0.05357 ( 429) hydrogen bonds : angle 4.81898 ( 1278) metal coordination : bond 0.00267 ( 4) metal coordination : angle 10.42021 ( 6) SS BOND : bond 0.00549 ( 1) SS BOND : angle 0.98825 ( 2) covalent geometry : bond 0.00427 ( 6975) covalent geometry : angle 0.83604 ( 9413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.5322 (tp-100) cc_final: 0.4898 (tp-100) REVERT: A 332 ASN cc_start: 0.7307 (m-40) cc_final: 0.6999 (p0) REVERT: B 326 ARG cc_start: 0.4488 (tpt90) cc_final: 0.2154 (tpp-160) REVERT: C 1035 MET cc_start: 0.7757 (mmp) cc_final: 0.7448 (ptt) REVERT: D 217 PHE cc_start: 0.7394 (m-80) cc_final: 0.6665 (m-80) REVERT: D 224 TYR cc_start: 0.7196 (t80) cc_final: 0.6888 (t80) REVERT: D 258 ASN cc_start: 0.7668 (t0) cc_final: 0.7307 (m-40) REVERT: D 259 ARG cc_start: 0.3236 (mtt180) cc_final: 0.2899 (ttm170) REVERT: D 261 MET cc_start: 0.4622 (ptt) cc_final: 0.3716 (tmm) REVERT: D 270 VAL cc_start: 0.6374 (m) cc_final: 0.6163 (p) REVERT: D 290 TYR cc_start: 0.2978 (t80) cc_final: 0.1380 (t80) REVERT: D 1022 ASN cc_start: 0.8915 (m110) cc_final: 0.8572 (m-40) REVERT: D 1079 ILE cc_start: 0.8386 (pt) cc_final: 0.8130 (pt) outliers start: 6 outliers final: 0 residues processed: 178 average time/residue: 0.1940 time to fit residues: 45.3402 Evaluate side-chains 119 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.0470 chunk 67 optimal weight: 7.9990 chunk 28 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.0670 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 241 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS B 274 ASN B 305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.217149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.164199 restraints weight = 9441.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.164908 restraints weight = 7295.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.164051 restraints weight = 5700.558| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5338 moved from start: 0.6548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6980 Z= 0.159 Angle : 0.734 14.305 9421 Z= 0.367 Chirality : 0.045 0.159 1081 Planarity : 0.006 0.100 1172 Dihedral : 4.346 17.829 908 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % 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: 0.01 (0.29), residues: 833 helix: 0.77 (0.21), residues: 551 sheet: -2.07 (0.55), residues: 77 loop : -0.98 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP D1011 HIS 0.005 0.001 HIS B 323 PHE 0.030 0.002 PHE D1108 TYR 0.023 0.002 TYR D 228 ARG 0.006 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 429) hydrogen bonds : angle 4.40423 ( 1278) metal coordination : bond 0.00433 ( 4) metal coordination : angle 9.05339 ( 6) SS BOND : bond 0.00463 ( 1) SS BOND : angle 0.85421 ( 2) covalent geometry : bond 0.00308 ( 6975) covalent geometry : angle 0.69773 ( 9413) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.723 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: A 87 PHE cc_start: 0.7202 (m-10) cc_final: 0.6923 (m-10) REVERT: B 326 ARG cc_start: 0.4679 (tpt90) cc_final: 0.2414 (tpp-160) REVERT: B 332 ASN cc_start: 0.7280 (m110) cc_final: 0.7011 (m110) REVERT: D 221 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8645 (mm-40) REVERT: D 258 ASN cc_start: 0.7724 (t0) cc_final: 0.7426 (t0) REVERT: D 261 MET cc_start: 0.4706 (ptt) cc_final: 0.3660 (tmm) REVERT: D 283 PHE cc_start: 0.8307 (m-80) cc_final: 0.8092 (m-80) REVERT: D 1019 PHE cc_start: 0.7303 (m-80) cc_final: 0.7091 (t80) REVERT: D 1022 ASN cc_start: 0.8695 (m110) cc_final: 0.8365 (m-40) REVERT: D 1079 ILE cc_start: 0.8458 (pt) cc_final: 0.7921 (pt) outliers start: 1 outliers final: 1 residues processed: 162 average time/residue: 0.1943 time to fit residues: 41.4308 Evaluate side-chains 116 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 21 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.214863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.4030 r_free = 0.4030 target = 0.159069 restraints weight = 9532.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.159367 restraints weight = 8686.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.160197 restraints weight = 7785.642| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.8858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6980 Z= 0.183 Angle : 0.784 11.075 9421 Z= 0.402 Chirality : 0.047 0.191 1081 Planarity : 0.005 0.054 1172 Dihedral : 4.589 18.704 908 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.39 % Allowed : 4.85 % Favored : 94.76 % 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: -0.11 (0.29), residues: 833 helix: 0.82 (0.21), residues: 545 sheet: -2.33 (0.49), residues: 92 loop : -1.20 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D1011 HIS 0.010 0.002 HIS A 77 PHE 0.021 0.002 PHE D1108 TYR 0.014 0.001 TYR A 148 ARG 0.007 0.001 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 429) hydrogen bonds : angle 4.62761 ( 1278) metal coordination : bond 0.00774 ( 4) metal coordination : angle 5.51496 ( 6) SS BOND : bond 0.00502 ( 1) SS BOND : angle 0.48327 ( 2) covalent geometry : bond 0.00388 ( 6975) covalent geometry : angle 0.77175 ( 9413) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.833 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: A 174 LEU cc_start: 0.7047 (tt) cc_final: 0.6608 (tp) REVERT: B 158 MET cc_start: 0.7087 (mtm) cc_final: 0.6703 (mtm) REVERT: B 338 LEU cc_start: 0.3238 (mt) cc_final: 0.2836 (mt) REVERT: D 261 MET cc_start: 0.4695 (ptt) cc_final: 0.3634 (tmm) REVERT: D 283 PHE cc_start: 0.8629 (m-80) cc_final: 0.8305 (m-80) REVERT: D 1022 ASN cc_start: 0.8881 (m110) cc_final: 0.8601 (m110) REVERT: D 1048 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6070 (pp30) REVERT: D 1049 MET cc_start: 0.7782 (ptp) cc_final: 0.7296 (ptp) REVERT: D 1052 GLU cc_start: 0.8683 (pm20) cc_final: 0.8364 (pm20) REVERT: D 1079 ILE cc_start: 0.8593 (pt) cc_final: 0.8374 (pt) REVERT: D 1082 MET cc_start: 0.7430 (mmm) cc_final: 0.6942 (mmt) REVERT: D 1116 MET cc_start: 0.9147 (mtp) cc_final: 0.8924 (mtm) outliers start: 3 outliers final: 0 residues processed: 161 average time/residue: 0.1965 time to fit residues: 41.4478 Evaluate side-chains 117 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 62 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 80 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS B 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.213299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.184309 restraints weight = 9415.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.180790 restraints weight = 11806.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.177446 restraints weight = 10122.887| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.9820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6980 Z= 0.155 Angle : 0.712 8.979 9421 Z= 0.364 Chirality : 0.045 0.156 1081 Planarity : 0.005 0.054 1172 Dihedral : 4.326 17.372 908 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.26 % Allowed : 3.54 % Favored : 96.20 % 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: 0.22 (0.29), residues: 833 helix: 1.04 (0.22), residues: 534 sheet: -2.02 (0.53), residues: 91 loop : -0.97 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP D1011 HIS 0.006 0.001 HIS B 323 PHE 0.020 0.002 PHE D1108 TYR 0.034 0.002 TYR D 210 ARG 0.007 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 429) hydrogen bonds : angle 4.38879 ( 1278) metal coordination : bond 0.00601 ( 4) metal coordination : angle 4.82140 ( 6) SS BOND : bond 0.00603 ( 1) SS BOND : angle 0.44143 ( 2) covalent geometry : bond 0.00329 ( 6975) covalent geometry : angle 0.70200 ( 9413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.765 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: A 87 PHE cc_start: 0.7430 (m-10) cc_final: 0.7209 (m-10) REVERT: A 103 MET cc_start: 0.7240 (tpt) cc_final: 0.6569 (tpp) REVERT: A 174 LEU cc_start: 0.6928 (tt) cc_final: 0.6342 (tt) REVERT: A 240 GLU cc_start: 0.5821 (pp20) cc_final: 0.4916 (tm-30) REVERT: A 264 GLU cc_start: 0.6599 (pt0) cc_final: 0.6231 (pt0) REVERT: A 272 THR cc_start: 0.8280 (t) cc_final: 0.8053 (m) REVERT: B 55 CYS cc_start: 0.8168 (m) cc_final: 0.6976 (p) REVERT: B 158 MET cc_start: 0.7057 (mtm) cc_final: 0.6762 (mtm) REVERT: B 230 ARG cc_start: 0.7746 (tpp80) cc_final: 0.7330 (tpm170) REVERT: C 1035 MET cc_start: 0.6574 (ptt) cc_final: 0.6322 (ptt) REVERT: D 261 MET cc_start: 0.4329 (ptt) cc_final: 0.3429 (tmm) REVERT: D 1079 ILE cc_start: 0.8724 (pt) cc_final: 0.8436 (pt) REVERT: D 1096 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6156 (tp-100) outliers start: 2 outliers final: 1 residues processed: 155 average time/residue: 0.1817 time to fit residues: 37.5065 Evaluate side-chains 122 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 39 optimal weight: 0.0970 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 75 optimal weight: 0.0970 chunk 80 optimal weight: 6.9990 overall best weight: 1.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS B 241 GLN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS B 323 HIS D1008 HIS D1022 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.196949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.157980 restraints weight = 9766.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.157104 restraints weight = 14070.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143103 restraints weight = 14582.776| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 1.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 6980 Z= 0.251 Angle : 0.918 10.408 9421 Z= 0.484 Chirality : 0.052 0.246 1081 Planarity : 0.006 0.052 1172 Dihedral : 5.325 21.437 908 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.67 % 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: -0.71 (0.28), residues: 833 helix: 0.26 (0.21), residues: 537 sheet: -2.30 (0.51), residues: 93 loop : -1.15 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.005 TRP D1158 HIS 0.006 0.002 HIS A 314 PHE 0.033 0.003 PHE A 313 TYR 0.026 0.003 TYR D 230 ARG 0.012 0.001 ARG D1050 Details of bonding type rmsd hydrogen bonds : bond 0.05979 ( 429) hydrogen bonds : angle 4.99476 ( 1278) metal coordination : bond 0.01065 ( 4) metal coordination : angle 3.60684 ( 6) SS BOND : bond 0.00389 ( 1) SS BOND : angle 0.49052 ( 2) covalent geometry : bond 0.00572 ( 6975) covalent geometry : angle 0.91344 ( 9413) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.774 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: A 103 MET cc_start: 0.8260 (tpt) cc_final: 0.7909 (tpp) REVERT: A 240 GLU cc_start: 0.6161 (pp20) cc_final: 0.5584 (tm-30) REVERT: B 230 ARG cc_start: 0.7679 (tpp80) cc_final: 0.7294 (tpm170) REVERT: B 275 ILE cc_start: 0.9082 (mp) cc_final: 0.8846 (mt) REVERT: B 291 MET cc_start: 0.8614 (ppp) cc_final: 0.8253 (ppp) REVERT: C 1059 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7156 (mt-10) REVERT: C 1065 MET cc_start: 0.8900 (mmp) cc_final: 0.8290 (mmp) REVERT: D 218 LEU cc_start: 0.8555 (pp) cc_final: 0.8296 (pp) REVERT: D 261 MET cc_start: 0.4829 (ptt) cc_final: 0.3776 (tmm) REVERT: D 267 MET cc_start: 0.2047 (mmm) cc_final: 0.1331 (mpp) REVERT: D 1082 MET cc_start: 0.7690 (mmm) cc_final: 0.7057 (mmt) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1880 time to fit residues: 39.7028 Evaluate side-chains 118 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS B 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.200616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.175845 restraints weight = 9608.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.164475 restraints weight = 11244.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.162672 restraints weight = 10895.645| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 1.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6980 Z= 0.168 Angle : 0.770 10.648 9421 Z= 0.399 Chirality : 0.047 0.174 1081 Planarity : 0.005 0.053 1172 Dihedral : 4.656 21.995 908 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.15 (0.29), residues: 833 helix: 0.76 (0.22), residues: 535 sheet: -2.05 (0.52), residues: 96 loop : -1.16 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D1158 HIS 0.007 0.001 HIS A 273 PHE 0.024 0.002 PHE D 279 TYR 0.012 0.001 TYR B 310 ARG 0.008 0.001 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 429) hydrogen bonds : angle 4.60378 ( 1278) metal coordination : bond 0.00729 ( 4) metal coordination : angle 5.78432 ( 6) SS BOND : bond 0.00464 ( 1) SS BOND : angle 0.19007 ( 2) covalent geometry : bond 0.00364 ( 6975) covalent geometry : angle 0.75617 ( 9413) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.6942 (tp) cc_final: 0.6340 (tp) REVERT: A 153 ARG cc_start: 0.7195 (ttp80) cc_final: 0.6893 (ptp-170) REVERT: A 156 LYS cc_start: 0.8023 (ptmm) cc_final: 0.7668 (tttp) REVERT: A 240 GLU cc_start: 0.6196 (pp20) cc_final: 0.5562 (tm-30) REVERT: B 37 LEU cc_start: 0.8273 (mm) cc_final: 0.7955 (mm) REVERT: B 332 ASN cc_start: 0.7897 (m110) cc_final: 0.7608 (m110) REVERT: C 1065 MET cc_start: 0.8626 (mmp) cc_final: 0.8159 (mmp) REVERT: D 261 MET cc_start: 0.4629 (ptt) cc_final: 0.3592 (tmm) REVERT: D 265 SER cc_start: 0.4852 (p) cc_final: 0.4496 (p) REVERT: D 267 MET cc_start: 0.2271 (mmm) cc_final: 0.1629 (mpp) REVERT: D 1068 GLU cc_start: 0.6066 (tp30) cc_final: 0.5753 (mm-30) REVERT: D 1079 ILE cc_start: 0.8828 (pt) cc_final: 0.8559 (pt) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1843 time to fit residues: 34.9665 Evaluate side-chains 114 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 0.0050 chunk 74 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 273 HIS ** A 305 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 = 0.4481 r_free = 0.4481 target = 0.202170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.178036 restraints weight = 9552.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.167874 restraints weight = 10537.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.164239 restraints weight = 12649.418| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 1.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6980 Z= 0.146 Angle : 0.775 9.975 9421 Z= 0.396 Chirality : 0.046 0.163 1081 Planarity : 0.005 0.054 1172 Dihedral : 4.400 21.707 908 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 0.12 (0.29), residues: 833 helix: 0.94 (0.22), residues: 537 sheet: -1.84 (0.54), residues: 96 loop : -1.03 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP D1158 HIS 0.004 0.001 HIS D1008 PHE 0.018 0.001 PHE D 279 TYR 0.023 0.002 TYR D 228 ARG 0.012 0.001 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 429) hydrogen bonds : angle 4.52874 ( 1278) metal coordination : bond 0.00458 ( 4) metal coordination : angle 5.52186 ( 6) SS BOND : bond 0.00408 ( 1) SS BOND : angle 0.21178 ( 2) covalent geometry : bond 0.00302 ( 6975) covalent geometry : angle 0.76218 ( 9413) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9089 (tt) cc_final: 0.8764 (mt) REVERT: A 156 LYS cc_start: 0.8140 (ptmm) cc_final: 0.7796 (tttp) REVERT: A 240 GLU cc_start: 0.6052 (pp20) cc_final: 0.5569 (tm-30) REVERT: B 37 LEU cc_start: 0.8341 (mm) cc_final: 0.8032 (mm) REVERT: B 306 MET cc_start: 0.8146 (mtp) cc_final: 0.7932 (mtm) REVERT: B 332 ASN cc_start: 0.8015 (m110) cc_final: 0.7679 (m110) REVERT: C 1116 MET cc_start: 0.4688 (ttt) cc_final: 0.4342 (ttt) REVERT: D 261 MET cc_start: 0.4701 (ptt) cc_final: 0.3649 (tmm) REVERT: D 267 MET cc_start: 0.2387 (mmm) cc_final: 0.1764 (mpp) REVERT: D 1068 GLU cc_start: 0.6084 (tp30) cc_final: 0.5568 (mm-30) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1903 time to fit residues: 36.4706 Evaluate side-chains 117 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 50 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 81 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 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 = 0.4480 r_free = 0.4480 target = 0.202205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.178126 restraints weight = 9519.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.169941 restraints weight = 11118.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.167886 restraints weight = 12808.559| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 1.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6980 Z= 0.143 Angle : 0.750 8.673 9421 Z= 0.389 Chirality : 0.046 0.166 1081 Planarity : 0.004 0.053 1172 Dihedral : 4.290 22.470 908 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.29), residues: 833 helix: 1.09 (0.22), residues: 537 sheet: -1.74 (0.55), residues: 96 loop : -1.03 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP D1158 HIS 0.005 0.001 HIS B 323 PHE 0.015 0.001 PHE D1108 TYR 0.026 0.002 TYR D 230 ARG 0.008 0.001 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 429) hydrogen bonds : angle 4.52961 ( 1278) metal coordination : bond 0.00555 ( 4) metal coordination : angle 4.26609 ( 6) SS BOND : bond 0.00334 ( 1) SS BOND : angle 0.25821 ( 2) covalent geometry : bond 0.00297 ( 6975) covalent geometry : angle 0.74258 ( 9413) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.781 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: A 61 LEU cc_start: 0.7282 (tp) cc_final: 0.6687 (tp) REVERT: A 70 ILE cc_start: 0.9093 (tt) cc_final: 0.8779 (mt) REVERT: A 156 LYS cc_start: 0.8313 (ptmm) cc_final: 0.7906 (tttp) REVERT: A 240 GLU cc_start: 0.5823 (pp20) cc_final: 0.5399 (tm-30) REVERT: B 37 LEU cc_start: 0.8287 (mm) cc_final: 0.7997 (mm) REVERT: B 306 MET cc_start: 0.8122 (mtp) cc_final: 0.7891 (mtm) REVERT: C 1116 MET cc_start: 0.4729 (ttt) cc_final: 0.4419 (ttt) REVERT: D 261 MET cc_start: 0.4574 (ptt) cc_final: 0.3448 (tmm) REVERT: D 265 SER cc_start: 0.5989 (p) cc_final: 0.4867 (p) REVERT: D 267 MET cc_start: 0.3345 (mmm) cc_final: 0.2731 (mpp) REVERT: D 1082 MET cc_start: 0.7432 (mmm) cc_final: 0.6892 (mmt) REVERT: D 1118 SER cc_start: 0.8834 (p) cc_final: 0.8620 (p) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1825 time to fit residues: 34.7962 Evaluate side-chains 117 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 38 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.201519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.177476 restraints weight = 9630.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.168857 restraints weight = 11640.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.167078 restraints weight = 12871.236| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 1.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6980 Z= 0.148 Angle : 0.748 8.751 9421 Z= 0.393 Chirality : 0.046 0.175 1081 Planarity : 0.005 0.055 1172 Dihedral : 4.306 22.392 908 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.13 % Allowed : 0.39 % Favored : 99.48 % 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: 0.36 (0.29), residues: 833 helix: 1.07 (0.22), residues: 539 sheet: -1.60 (0.57), residues: 93 loop : -0.90 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP D1158 HIS 0.003 0.001 HIS A 172 PHE 0.016 0.001 PHE D1017 TYR 0.016 0.001 TYR D 228 ARG 0.009 0.001 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 429) hydrogen bonds : angle 4.53766 ( 1278) metal coordination : bond 0.00424 ( 4) metal coordination : angle 3.47027 ( 6) SS BOND : bond 0.00332 ( 1) SS BOND : angle 0.26604 ( 2) covalent geometry : bond 0.00310 ( 6975) covalent geometry : angle 0.74340 ( 9413) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.842 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: A 61 LEU cc_start: 0.7550 (tp) cc_final: 0.6823 (tp) REVERT: A 70 ILE cc_start: 0.8934 (tt) cc_final: 0.8611 (mt) REVERT: A 156 LYS cc_start: 0.8367 (ptmm) cc_final: 0.7892 (tttp) REVERT: A 323 HIS cc_start: 0.6415 (OUTLIER) cc_final: 0.6078 (p90) REVERT: B 37 LEU cc_start: 0.8402 (mm) cc_final: 0.8087 (mm) REVERT: B 95 LYS cc_start: 0.7832 (tptm) cc_final: 0.7629 (tppt) REVERT: B 158 MET cc_start: 0.7244 (mpp) cc_final: 0.6849 (mtm) REVERT: C 1072 TYR cc_start: 0.7887 (t80) cc_final: 0.7663 (t80) REVERT: C 1116 MET cc_start: 0.4752 (ttt) cc_final: 0.4465 (ttt) REVERT: D 261 MET cc_start: 0.4625 (ptt) cc_final: 0.3597 (tmm) REVERT: D 265 SER cc_start: 0.5468 (p) cc_final: 0.4977 (p) REVERT: D 267 MET cc_start: 0.3233 (mmm) cc_final: 0.2662 (mpp) REVERT: D 1068 GLU cc_start: 0.5991 (mm-30) cc_final: 0.5358 (tp30) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.1908 time to fit residues: 35.8862 Evaluate side-chains 117 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 4 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 75 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS ** A 305 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 = 0.4466 r_free = 0.4466 target = 0.200568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.177113 restraints weight = 9576.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.168563 restraints weight = 11825.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.167052 restraints weight = 12376.096| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 1.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6980 Z= 0.158 Angle : 0.762 8.647 9421 Z= 0.404 Chirality : 0.047 0.194 1081 Planarity : 0.004 0.054 1172 Dihedral : 4.406 22.236 908 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.37 (0.29), residues: 833 helix: 1.06 (0.22), residues: 545 sheet: -1.70 (0.56), residues: 94 loop : -0.82 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP D1158 HIS 0.003 0.001 HIS A 172 PHE 0.014 0.001 PHE D 279 TYR 0.017 0.001 TYR D 210 ARG 0.009 0.001 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 429) hydrogen bonds : angle 4.55685 ( 1278) metal coordination : bond 0.00521 ( 4) metal coordination : angle 3.72493 ( 6) SS BOND : bond 0.00374 ( 1) SS BOND : angle 0.30050 ( 2) covalent geometry : bond 0.00336 ( 6975) covalent geometry : angle 0.75611 ( 9413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2490.77 seconds wall clock time: 44 minutes 5.23 seconds (2645.23 seconds total)