Starting phenix.real_space_refine on Sat May 10 23:41:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cr2_16802/05_2025/8cr2_16802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cr2_16802/05_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_16802/05_2025/8cr2_16802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cr2_16802/05_2025/8cr2_16802.map" model { file = "/net/cci-nas-00/data/ceres_data/8cr2_16802/05_2025/8cr2_16802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cr2_16802/05_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-5687/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: 4.58, per 1000 atoms: 0.67 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: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.67 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: 1.91 Time building geometry restraints manager: 2.19 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: 0.700 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.400 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- 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 : 0.723 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: 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: 0.2421 time to fit residues: 65.0181 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 : 0.814 ------------------------------------------------------------------------------- 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 = 0.216748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.155232 restraints weight = 9345.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.159450 restraints weight = 6800.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.162444 restraints weight = 5399.229| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5110 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 : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.5324 (tp-100) cc_final: 0.4902 (tp-100) REVERT: A 332 ASN cc_start: 0.7284 (m-40) cc_final: 0.6988 (p0) REVERT: B 326 ARG cc_start: 0.4481 (tpt90) cc_final: 0.2154 (tpp-160) REVERT: C 1035 MET cc_start: 0.7738 (mmp) cc_final: 0.7443 (ptt) REVERT: D 217 PHE cc_start: 0.7397 (m-80) cc_final: 0.6669 (m-80) REVERT: D 224 TYR cc_start: 0.7218 (t80) cc_final: 0.6915 (t80) REVERT: D 258 ASN cc_start: 0.7665 (t0) cc_final: 0.7303 (m-40) REVERT: D 259 ARG cc_start: 0.3229 (mtt180) cc_final: 0.2891 (ttm170) REVERT: D 261 MET cc_start: 0.4615 (ptt) cc_final: 0.3712 (tmm) REVERT: D 270 VAL cc_start: 0.6379 (m) cc_final: 0.6169 (p) REVERT: D 290 TYR cc_start: 0.2981 (t80) cc_final: 0.1384 (t80) REVERT: D 1022 ASN cc_start: 0.8923 (m110) cc_final: 0.8579 (m-40) REVERT: D 1079 ILE cc_start: 0.8385 (pt) cc_final: 0.8128 (pt) outliers start: 6 outliers final: 0 residues processed: 178 average time/residue: 0.1897 time to fit residues: 44.2371 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 : 0.823 ------------------------------------------------------------------------------- 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: 0.4980 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.0370 chunk 67 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4591 r_free = 0.4591 target = 0.217665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.156748 restraints weight = 9460.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.160281 restraints weight = 7308.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.162094 restraints weight = 5920.051| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5342 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6980 Z= 0.148 Angle : 0.732 14.385 9421 Z= 0.363 Chirality : 0.044 0.159 1081 Planarity : 0.005 0.083 1172 Dihedral : 4.330 17.515 908 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.26 % Allowed : 3.41 % Favored : 96.33 % 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: -0.00 (0.29), residues: 833 helix: 0.75 (0.21), residues: 551 sheet: -2.06 (0.54), residues: 77 loop : -0.96 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D1011 HIS 0.005 0.001 HIS B 323 PHE 0.029 0.002 PHE D1108 TYR 0.025 0.001 TYR D 230 ARG 0.006 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04741 ( 429) hydrogen bonds : angle 4.39289 ( 1278) metal coordination : bond 0.00533 ( 4) metal coordination : angle 9.18191 ( 6) SS BOND : bond 0.00460 ( 1) SS BOND : angle 0.83127 ( 2) covalent geometry : bond 0.00305 ( 6975) covalent geometry : angle 0.69407 ( 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 160 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.777 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 52 THR cc_start: 0.8126 (m) cc_final: 0.7918 (m) REVERT: A 87 PHE cc_start: 0.7149 (m-10) cc_final: 0.6862 (m-10) REVERT: B 326 ARG cc_start: 0.4765 (tpt90) cc_final: 0.2447 (tpp-160) REVERT: B 332 ASN cc_start: 0.7206 (m110) cc_final: 0.6968 (m110) REVERT: C 1035 MET cc_start: 0.7727 (mmp) cc_final: 0.7442 (ptt) REVERT: D 221 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8660 (mm-40) REVERT: D 258 ASN cc_start: 0.7591 (t0) cc_final: 0.7252 (t0) REVERT: D 259 ARG cc_start: 0.3484 (mtt180) cc_final: 0.2153 (mtt180) REVERT: D 261 MET cc_start: 0.4606 (ptt) cc_final: 0.3625 (tmm) REVERT: D 283 PHE cc_start: 0.8427 (m-80) cc_final: 0.8118 (m-80) REVERT: D 1019 PHE cc_start: 0.7588 (m-80) cc_final: 0.7133 (t80) REVERT: D 1022 ASN cc_start: 0.8853 (m110) cc_final: 0.8508 (m-40) REVERT: D 1079 ILE cc_start: 0.8491 (pt) cc_final: 0.7982 (pt) REVERT: D 1082 MET cc_start: 0.7716 (tpt) cc_final: 0.6851 (mmt) outliers start: 2 outliers final: 1 residues processed: 160 average time/residue: 0.1900 time to fit residues: 39.9811 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 : 0.730 ------------------------------------------------------------------------------- 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: 6.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.0370 chunk 63 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 0.0770 overall best weight: 0.9820 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.216655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.177353 restraints weight = 9539.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.175229 restraints weight = 13077.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.176719 restraints weight = 11003.280| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.9629 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= 0.194 Angle : 0.826 12.163 9421 Z= 0.429 Chirality : 0.049 0.184 1081 Planarity : 0.005 0.055 1172 Dihedral : 4.943 21.349 908 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.26 % Allowed : 6.68 % Favored : 93.05 % 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: -0.31 (0.29), residues: 833 helix: 0.69 (0.21), residues: 544 sheet: -2.48 (0.49), residues: 92 loop : -1.28 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP D1011 HIS 0.010 0.002 HIS A 77 PHE 0.031 0.003 PHE A 313 TYR 0.020 0.002 TYR A 148 ARG 0.009 0.001 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.05004 ( 429) hydrogen bonds : angle 4.75724 ( 1278) metal coordination : bond 0.01046 ( 4) metal coordination : angle 5.24852 ( 6) SS BOND : bond 0.00478 ( 1) SS BOND : angle 0.39107 ( 2) covalent geometry : bond 0.00417 ( 6975) covalent geometry : angle 0.81566 ( 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 164 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.798 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 174 LEU cc_start: 0.7201 (tt) cc_final: 0.6654 (tp) REVERT: B 55 CYS cc_start: 0.8246 (m) cc_final: 0.7156 (p) REVERT: B 275 ILE cc_start: 0.8480 (mp) cc_final: 0.8218 (mt) REVERT: B 338 LEU cc_start: 0.3482 (mt) cc_final: 0.2816 (mp) REVERT: D 217 PHE cc_start: 0.5495 (m-80) cc_final: 0.5140 (m-10) REVERT: D 259 ARG cc_start: 0.4338 (mtt180) cc_final: 0.2258 (mtt180) REVERT: D 261 MET cc_start: 0.4544 (ptt) cc_final: 0.3514 (tmm) REVERT: D 1079 ILE cc_start: 0.8435 (pt) cc_final: 0.8102 (pt) outliers start: 2 outliers final: 0 residues processed: 164 average time/residue: 0.2074 time to fit residues: 43.8627 Evaluate side-chains 106 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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: 6.9990 chunk 30 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN 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 B 172 HIS B 323 HIS ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.205566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3990 r_free = 0.3990 target = 0.154810 restraints weight = 9515.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.150851 restraints weight = 9374.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.150755 restraints weight = 8835.732| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 1.0569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6980 Z= 0.166 Angle : 0.753 10.830 9421 Z= 0.382 Chirality : 0.046 0.171 1081 Planarity : 0.005 0.054 1172 Dihedral : 4.461 16.879 908 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.13 % Allowed : 3.28 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.29), residues: 833 helix: 1.04 (0.21), residues: 532 sheet: -2.42 (0.48), residues: 93 loop : -1.10 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.004 TRP D1158 HIS 0.006 0.001 HIS B 323 PHE 0.021 0.002 PHE D1108 TYR 0.020 0.002 TYR D 224 ARG 0.008 0.001 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 429) hydrogen bonds : angle 4.47592 ( 1278) metal coordination : bond 0.00727 ( 4) metal coordination : angle 4.85210 ( 6) SS BOND : bond 0.00201 ( 1) SS BOND : angle 0.35244 ( 2) covalent geometry : bond 0.00357 ( 6975) covalent geometry : angle 0.74340 ( 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: 1 poor density : 155 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: symmetry clash REVERT: A 174 LEU cc_start: 0.7000 (tt) cc_final: 0.6670 (tt) REVERT: A 240 GLU cc_start: 0.5877 (pp20) cc_final: 0.5095 (tm-30) REVERT: A 264 GLU cc_start: 0.6677 (pt0) cc_final: 0.6440 (pt0) REVERT: A 272 THR cc_start: 0.8553 (t) cc_final: 0.8351 (m) REVERT: B 230 ARG cc_start: 0.7843 (tpp80) cc_final: 0.7102 (tpm170) REVERT: B 275 ILE cc_start: 0.8687 (mp) cc_final: 0.8485 (mt) REVERT: C 1065 MET cc_start: 0.8275 (mmp) cc_final: 0.7992 (mmp) REVERT: D 261 MET cc_start: 0.5076 (ptt) cc_final: 0.3961 (tmm) REVERT: D 283 PHE cc_start: 0.8525 (m-80) cc_final: 0.8201 (m-80) REVERT: D 1079 ILE cc_start: 0.8699 (pt) cc_final: 0.8469 (pt) REVERT: D 1082 MET cc_start: 0.7701 (mmm) cc_final: 0.7011 (mmt) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1923 time to fit residues: 39.4519 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 : 0.799 ------------------------------------------------------------------------------- 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: 0.6980 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 0.0050 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.200899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145994 restraints weight = 9637.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141075 restraints weight = 8672.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141579 restraints weight = 8142.520| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 1.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6980 Z= 0.186 Angle : 0.769 9.483 9421 Z= 0.402 Chirality : 0.047 0.159 1081 Planarity : 0.005 0.054 1172 Dihedral : 4.598 19.238 908 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.13 % Allowed : 1.97 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.29), residues: 833 helix: 0.89 (0.21), residues: 538 sheet: -2.18 (0.50), residues: 95 loop : -1.01 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP D1158 HIS 0.012 0.002 HIS A 273 PHE 0.019 0.002 PHE D1031 TYR 0.020 0.002 TYR D 224 ARG 0.007 0.001 ARG D1050 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 429) hydrogen bonds : angle 4.62907 ( 1278) metal coordination : bond 0.00759 ( 4) metal coordination : angle 3.70441 ( 6) SS BOND : bond 0.00618 ( 1) SS BOND : angle 0.28189 ( 2) covalent geometry : bond 0.00423 ( 6975) covalent geometry : angle 0.76402 ( 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 154 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.787 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 174 LEU cc_start: 0.7310 (tt) cc_final: 0.6910 (tt) REVERT: A 240 GLU cc_start: 0.6128 (pp20) cc_final: 0.5558 (tm-30) REVERT: A 260 ARG cc_start: 0.8557 (tmm-80) cc_final: 0.8273 (tmm-80) REVERT: A 264 GLU cc_start: 0.7163 (pt0) cc_final: 0.6897 (pt0) REVERT: B 230 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7278 (tpm170) REVERT: B 291 MET cc_start: 0.8679 (ppp) cc_final: 0.8425 (ppp) REVERT: D 261 MET cc_start: 0.5104 (ptt) cc_final: 0.3946 (tmm) REVERT: D 267 MET cc_start: 0.2093 (mmm) cc_final: 0.1261 (mpp) REVERT: D 1022 ASN cc_start: 0.8962 (m-40) cc_final: 0.8635 (m-40) REVERT: D 1065 MET cc_start: 0.8409 (tpp) cc_final: 0.7958 (mmm) REVERT: D 1079 ILE cc_start: 0.8895 (pt) cc_final: 0.8658 (pt) outliers start: 1 outliers final: 1 residues processed: 153 average time/residue: 0.1812 time to fit residues: 36.8821 Evaluate side-chains 125 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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: 0.4980 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 HIS B 235 GLN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.203051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3865 r_free = 0.3865 target = 0.143440 restraints weight = 9520.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.143104 restraints weight = 8931.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.143104 restraints weight = 8156.546| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 1.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6980 Z= 0.144 Angle : 0.739 10.263 9421 Z= 0.373 Chirality : 0.045 0.152 1081 Planarity : 0.004 0.054 1172 Dihedral : 4.279 17.403 908 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: 0.21 (0.29), residues: 833 helix: 1.04 (0.22), residues: 538 sheet: -1.87 (0.52), residues: 96 loop : -1.07 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.004 TRP D1158 HIS 0.003 0.001 HIS B 314 PHE 0.021 0.001 PHE D 279 TYR 0.026 0.001 TYR D 210 ARG 0.007 0.001 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 429) hydrogen bonds : angle 4.43991 ( 1278) metal coordination : bond 0.00531 ( 4) metal coordination : angle 4.96385 ( 6) SS BOND : bond 0.00549 ( 1) SS BOND : angle 0.20924 ( 2) covalent geometry : bond 0.00302 ( 6975) covalent geometry : angle 0.72812 ( 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 149 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.750 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 70 ILE cc_start: 0.9094 (tt) cc_final: 0.8840 (mt) REVERT: A 240 GLU cc_start: 0.5829 (pp20) cc_final: 0.5422 (tm-30) REVERT: A 260 ARG cc_start: 0.8459 (tmm-80) cc_final: 0.8117 (tmm-80) REVERT: A 304 ASP cc_start: 0.7818 (m-30) cc_final: 0.7587 (m-30) REVERT: B 230 ARG cc_start: 0.7588 (tpp80) cc_final: 0.7151 (tpm170) REVERT: D 221 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8526 (pp30) REVERT: D 261 MET cc_start: 0.5100 (ptt) cc_final: 0.4031 (tmm) REVERT: D 267 MET cc_start: 0.2323 (mmm) cc_final: 0.1542 (mpp) REVERT: D 1022 ASN cc_start: 0.9162 (m-40) cc_final: 0.8881 (m110) REVERT: D 1065 MET cc_start: 0.8254 (tpp) cc_final: 0.7993 (mmm) REVERT: D 1082 MET cc_start: 0.7939 (mmm) cc_final: 0.7319 (mmt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1803 time to fit residues: 35.7742 Evaluate side-chains 125 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 0.0670 chunk 74 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 305 GLN ** B 299 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 = 0.4490 r_free = 0.4490 target = 0.202593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.173645 restraints weight = 9543.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.166585 restraints weight = 12558.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.164286 restraints weight = 13244.001| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 1.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6980 Z= 0.145 Angle : 0.741 11.111 9421 Z= 0.377 Chirality : 0.045 0.156 1081 Planarity : 0.005 0.054 1172 Dihedral : 4.215 18.957 908 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: 1.09 (0.22), residues: 544 sheet: -1.74 (0.54), residues: 96 loop : -0.88 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.004 TRP D1158 HIS 0.003 0.001 HIS B 314 PHE 0.015 0.002 PHE D1108 TYR 0.030 0.002 TYR D 224 ARG 0.009 0.001 ARG D1050 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 429) hydrogen bonds : angle 4.46972 ( 1278) metal coordination : bond 0.00529 ( 4) metal coordination : angle 5.85235 ( 6) SS BOND : bond 0.00365 ( 1) SS BOND : angle 0.24637 ( 2) covalent geometry : bond 0.00304 ( 6975) covalent geometry : angle 0.72611 ( 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 148 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.797 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 61 LEU cc_start: 0.6977 (tp) cc_final: 0.6428 (tp) REVERT: A 70 ILE cc_start: 0.8979 (tt) cc_final: 0.8755 (mt) REVERT: A 174 LEU cc_start: 0.7151 (tp) cc_final: 0.6572 (tp) REVERT: A 230 ARG cc_start: 0.8539 (ptm160) cc_final: 0.8322 (ptm-80) REVERT: B 306 MET cc_start: 0.7838 (mtp) cc_final: 0.7500 (ttp) REVERT: C 1065 MET cc_start: 0.8283 (mmp) cc_final: 0.7818 (mmp) REVERT: D 261 MET cc_start: 0.4687 (ptt) cc_final: 0.3604 (tmm) REVERT: D 267 MET cc_start: 0.2467 (mmm) cc_final: 0.1704 (mpp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1829 time to fit residues: 36.3330 Evaluate side-chains 116 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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: 6.9990 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.0010 chunk 81 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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** B 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.201808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.176409 restraints weight = 9588.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.164696 restraints weight = 10915.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.163607 restraints weight = 11269.119| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 1.3222 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= 0.147 Angle : 0.744 9.509 9421 Z= 0.381 Chirality : 0.045 0.168 1081 Planarity : 0.004 0.054 1172 Dihedral : 4.161 18.205 908 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: 0.49 (0.29), residues: 833 helix: 1.21 (0.22), residues: 539 sheet: -1.61 (0.54), residues: 96 loop : -0.94 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.003 TRP D1158 HIS 0.004 0.001 HIS B 323 PHE 0.017 0.001 PHE D 279 TYR 0.019 0.002 TYR B 148 ARG 0.007 0.001 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 429) hydrogen bonds : angle 4.46209 ( 1278) metal coordination : bond 0.00489 ( 4) metal coordination : angle 4.33560 ( 6) SS BOND : bond 0.00349 ( 1) SS BOND : angle 0.24535 ( 2) covalent geometry : bond 0.00310 ( 6975) covalent geometry : angle 0.73571 ( 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 149 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.722 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 61 LEU cc_start: 0.7292 (tp) cc_final: 0.6812 (tp) REVERT: A 70 ILE cc_start: 0.8975 (tt) cc_final: 0.8725 (mt) REVERT: A 174 LEU cc_start: 0.7071 (tp) cc_final: 0.6577 (tp) REVERT: A 279 GLN cc_start: 0.8073 (mp10) cc_final: 0.7828 (mp10) REVERT: A 304 ASP cc_start: 0.7761 (m-30) cc_final: 0.7545 (m-30) REVERT: B 37 LEU cc_start: 0.8383 (mm) cc_final: 0.8171 (mm) REVERT: B 306 MET cc_start: 0.7876 (mtp) cc_final: 0.7649 (ttm) REVERT: B 332 ASN cc_start: 0.7982 (m110) cc_final: 0.7704 (m110) REVERT: D 261 MET cc_start: 0.4761 (ptt) cc_final: 0.3690 (tmm) REVERT: D 267 MET cc_start: 0.3283 (mmm) cc_final: 0.2542 (mpp) REVERT: D 1060 LEU cc_start: 0.7525 (tt) cc_final: 0.7226 (tt) REVERT: D 1082 MET cc_start: 0.7463 (mmm) cc_final: 0.6941 (mmt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1776 time to fit residues: 35.6281 Evaluate side-chains 124 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 0.0570 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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** A 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.201237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.166792 restraints weight = 9741.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.152730 restraints weight = 11616.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.150983 restraints weight = 13956.711| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 1.3635 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= 0.149 Angle : 0.752 9.624 9421 Z= 0.393 Chirality : 0.045 0.159 1081 Planarity : 0.005 0.054 1172 Dihedral : 4.190 19.127 908 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % 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: 0.51 (0.30), residues: 833 helix: 1.13 (0.22), residues: 544 sheet: -1.51 (0.57), residues: 93 loop : -0.71 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.005 TRP D1158 HIS 0.003 0.001 HIS B 323 PHE 0.021 0.001 PHE D1108 TYR 0.019 0.002 TYR B 148 ARG 0.007 0.001 ARG C1037 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 429) hydrogen bonds : angle 4.50463 ( 1278) metal coordination : bond 0.00435 ( 4) metal coordination : angle 3.41162 ( 6) SS BOND : bond 0.00329 ( 1) SS BOND : angle 0.30649 ( 2) covalent geometry : bond 0.00312 ( 6975) covalent geometry : angle 0.74732 ( 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 143 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.816 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 61 LEU cc_start: 0.7413 (tp) cc_final: 0.6953 (tp) REVERT: A 70 ILE cc_start: 0.8968 (tt) cc_final: 0.8695 (mt) REVERT: A 174 LEU cc_start: 0.7487 (tp) cc_final: 0.7286 (tp) REVERT: A 279 GLN cc_start: 0.8269 (mp10) cc_final: 0.7944 (mp10) REVERT: B 37 LEU cc_start: 0.8329 (mm) cc_final: 0.8119 (mm) REVERT: B 332 ASN cc_start: 0.8257 (m110) cc_final: 0.7873 (m110) REVERT: C 1080 ASN cc_start: 0.8258 (m-40) cc_final: 0.7984 (m110) REVERT: D 261 MET cc_start: 0.5055 (ptt) cc_final: 0.3946 (tmm) REVERT: D 265 SER cc_start: 0.5267 (p) cc_final: 0.4910 (p) REVERT: D 267 MET cc_start: 0.2901 (mmm) cc_final: 0.2253 (mpp) REVERT: D 1060 LEU cc_start: 0.7784 (tt) cc_final: 0.7509 (tt) REVERT: D 1082 MET cc_start: 0.7771 (mmm) cc_final: 0.7569 (mmm) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1773 time to fit residues: 34.4802 Evaluate side-chains 126 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.4477 r_free = 0.4477 target = 0.201010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.163321 restraints weight = 9554.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.155081 restraints weight = 11980.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.149272 restraints weight = 11209.857| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 1.3877 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= 0.148 Angle : 0.757 9.697 9421 Z= 0.395 Chirality : 0.045 0.180 1081 Planarity : 0.004 0.053 1172 Dihedral : 4.138 18.455 908 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: 0.60 (0.30), residues: 833 helix: 1.18 (0.22), residues: 544 sheet: -1.49 (0.57), residues: 93 loop : -0.61 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.004 TRP D1158 HIS 0.004 0.001 HIS A 172 PHE 0.015 0.001 PHE D 279 TYR 0.018 0.001 TYR B 148 ARG 0.006 0.001 ARG D1074 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 429) hydrogen bonds : angle 4.53592 ( 1278) metal coordination : bond 0.00428 ( 4) metal coordination : angle 3.54883 ( 6) SS BOND : bond 0.00331 ( 1) SS BOND : angle 0.23721 ( 2) covalent geometry : bond 0.00311 ( 6975) covalent geometry : angle 0.75176 ( 9413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2582.01 seconds wall clock time: 45 minutes 47.67 seconds (2747.67 seconds total)